travis_fold:start:worker_info Worker information hostname: a1e5dcd5-bc3d-427d-a900-bdc79c748eaf@1.production-4-worker-org-a-2-gce version: v3.1.0 https://github.com/travis-ci/worker/tree/5b106cb773802277034d07b0a865af58d67bb1d2 instance: testing-gce-b7ab7604-4dc9-4336-9de8-7ffde676c60e:travis-ci-amethyst-trusty-1503972832 (via amqp) startup: 21.22182751s travis_fold:end:worker_info travis_fold:start:system_info Build system information Build language: r Build group: stable Build dist: trusty Build id: 291012809 Job id: 291012811 Runtime kernel version: 4.4.0-93-generic travis-build version: 3fd6c3fda Build image provisioning date and time Tue Aug 29 02:44:32 UTC 2017 Operating System Details Distributor ID: Ubuntu Description: Ubuntu 14.04.5 LTS Release: 14.04 Codename: trusty Cookbooks Version 4642454 https://github.com/travis-ci/travis-cookbooks/tree/4642454 git version git version 2.14.1 bash version GNU bash, version 4.3.11(1)-release (x86_64-pc-linux-gnu) gcc version gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. docker version Client: Version: 17.03.1-ce API version: 1.27 Go version: go1.7.5 Git commit: c6d412e Built: Mon Mar 27 17:10:36 2017 OS/Arch: linux/amd64 Server: Version: 17.03.1-ce API version: 1.27 (minimum version 1.12) Go version: go1.7.5 Git commit: c6d412e Built: Mon Mar 27 17:10:36 2017 OS/Arch: linux/amd64 Experimental: false clang version clang version 3.9.0 (tags/RELEASE_390/final) Target: x86_64-unknown-linux-gnu Thread model: posix InstalledDir: /usr/local/clang-3.9.0/bin jq version jq-1.5 bats version Bats 0.4.0 shellcheck version 0.4.6 shfmt version v1.3.1 ccache version ccache version 3.1.9 Copyright (C) 2002-2007 Andrew Tridgell Copyright (C) 2009-2011 Joel Rosdahl This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. cmake version cmake version 3.2.2 CMake suite maintained and supported by Kitware (kitware.com/cmake). heroku version heroku-cli/6.13.19-6cd27b3 (linux-x64) node-v8.3.0 imagemagick version Version: ImageMagick 6.7.7-10 2017-07-31 Q16 http://www.imagemagick.org md5deep version 4.2 mercurial version Mercurial Distributed SCM (version 4.2.2) (see https://mercurial-scm.org for more information) Copyright (C) 2005-2017 Matt Mackall and others This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. mysql version mysql Ver 14.14 Distrib 5.6.33, for debian-linux-gnu (x86_64) using EditLine wrapper openssl version OpenSSL 1.0.1f 6 Jan 2014 packer version Packer v1.0.2 Your version of Packer is out of date! The latest version is 1.0.4. You can update by downloading from www.packer.io postgresql client version psql (PostgreSQL) 9.6.4 ragel version Ragel State Machine Compiler version 6.8 Feb 2013 Copyright (c) 2001-2009 by Adrian Thurston subversion version svn, version 1.8.8 (r1568071) compiled Aug 10 2017, 17:20:39 on x86_64-pc-linux-gnu Copyright (C) 2013 The Apache Software Foundation. This software consists of contributions made by many people; see the NOTICE file for more information. Subversion is open source software, see http://subversion.apache.org/ The following repository access (RA) modules are available: * ra_svn : Module for accessing a repository using the svn network protocol. - with Cyrus SASL authentication - handles 'svn' scheme * ra_local : Module for accessing a repository on local disk. - handles 'file' scheme * ra_serf : Module for accessing a repository via WebDAV protocol using serf. - using serf 1.3.3 - handles 'http' scheme - handles 'https' scheme sudo version Sudo version 1.8.9p5 Configure options: --prefix=/usr -v --with-all-insults --with-pam --with-fqdn --with-logging=syslog --with-logfac=authpriv --with-env-editor --with-editor=/usr/bin/editor --with-timeout=15 --with-password-timeout=0 --with-passprompt=[sudo] password for %p: --without-lecture --with-tty-tickets --disable-root-mailer --enable-admin-flag --with-sendmail=/usr/sbin/sendmail --with-timedir=/var/lib/sudo --mandir=/usr/share/man --libexecdir=/usr/lib/sudo --with-sssd --with-sssd-lib=/usr/lib/x86_64-linux-gnu --with-selinux Sudoers policy plugin version 1.8.9p5 Sudoers file grammar version 43 Sudoers path: /etc/sudoers Authentication methods: 'pam' Syslog facility if syslog is being used for logging: authpriv Syslog priority to use when user authenticates successfully: notice Syslog priority to use when user authenticates unsuccessfully: alert Send mail if the user is not in sudoers Use a separate timestamp for each user/tty combo Lecture user the first time they run sudo Root may run sudo Allow some information gathering to give useful error messages Require fully-qualified hostnames in the sudoers file Visudo will honor the EDITOR environment variable Set the LOGNAME and USER environment variables Length at which to wrap log file lines (0 for no wrap): 80 Authentication timestamp timeout: 15.0 minutes Password prompt timeout: 0.0 minutes Number of tries to enter a password: 3 Umask to use or 0777 to use user's: 022 Path to mail program: /usr/sbin/sendmail Flags for mail program: -t Address to send mail to: root Subject line for mail messages: *** SECURITY information for %h *** Incorrect password message: Sorry, try again. Path to authentication timestamp dir: /var/lib/sudo Default password prompt: [sudo] password for %p: Default user to run commands as: root Value to override user's $PATH with: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin Path to the editor for use by visudo: /usr/bin/editor When to require a password for 'list' pseudocommand: any When to require a password for 'verify' pseudocommand: all File descriptors >= 3 will be closed before executing a command Environment variables to check for sanity: TZ TERM LINGUAS LC_* LANGUAGE LANG COLORTERM Environment variables to remove: RUBYOPT RUBYLIB PYTHONUSERBASE PYTHONINSPECT PYTHONPATH PYTHONHOME TMPPREFIX ZDOTDIR READNULLCMD NULLCMD FPATH PERL5DB PERL5OPT PERL5LIB PERLLIB PERLIO_DEBUG JAVA_TOOL_OPTIONS SHELLOPTS GLOBIGNORE PS4 BASH_ENV ENV TERMCAP TERMPATH TERMINFO_DIRS TERMINFO _RLD* LD_* PATH_LOCALE NLSPATH HOSTALIASES RES_OPTIONS LOCALDOMAIN CDPATH IFS Environment variables to preserve: JAVA_HOME TRAVIS CI DEBIAN_FRONTEND XAUTHORIZATION XAUTHORITY PS2 PS1 PATH LS_COLORS KRB5CCNAME HOSTNAME HOME DISPLAY COLORS Locale to use while parsing sudoers: C Directory in which to store input/output logs: /var/log/sudo-io File in which to store the input/output log: %{seq} Add an entry to the utmp/utmpx file when allocating a pty PAM service name to use PAM service name to use for login shells Create a new PAM session for the command to run in Maximum I/O log sequence number: 0 Local IP address and netmask pairs: 10.240.0.11/255.255.255.255 172.17.0.1/255.255.0.0 Sudoers I/O plugin version 1.8.9p5 gzip version gzip 1.6 Copyright (C) 2007, 2010, 2011 Free Software Foundation, Inc. Copyright (C) 1993 Jean-loup Gailly. This is free software. You may redistribute copies of it under the terms of the GNU General Public License . There is NO WARRANTY, to the extent permitted by law. Written by Jean-loup Gailly. zip version Copyright (c) 1990-2008 Info-ZIP - Type 'zip "-L"' for software license. This is Zip 3.0 (July 5th 2008), by Info-ZIP. Currently maintained by E. Gordon. Please send bug reports to the authors using the web page at www.info-zip.org; see README for details. Latest sources and executables are at ftp://ftp.info-zip.org/pub/infozip, as of above date; see http://www.info-zip.org/ for other sites. Compiled with gcc 4.8.2 for Unix (Linux ELF) on Oct 21 2013. Zip special compilation options: USE_EF_UT_TIME (store Universal Time) BZIP2_SUPPORT (bzip2 library version 1.0.6, 6-Sept-2010) bzip2 code and library copyright (c) Julian R Seward (See the bzip2 license for terms of use) SYMLINK_SUPPORT (symbolic links supported) LARGE_FILE_SUPPORT (can read and write large files on file system) ZIP64_SUPPORT (use Zip64 to store large files in archives) UNICODE_SUPPORT (store and read UTF-8 Unicode paths) STORE_UNIX_UIDs_GIDs (store UID/GID sizes/values using new extra field) UIDGID_NOT_16BIT (old Unix 16-bit UID/GID extra field not used) [encryption, version 2.91 of 05 Jan 2007] (modified for Zip 3) Encryption notice: The encryption code of this program is not copyrighted and is put in the public domain. It was originally written in Europe and, to the best of our knowledge, can be freely distributed in both source and object forms from any country, including the USA under License Exception TSU of the U.S. Export Administration Regulations (section 740.13(e)) of 6 June 2002. Zip environment options: ZIP: [none] ZIPOPT: [none] vim version VIM - Vi IMproved 7.4 (2013 Aug 10, compiled Nov 24 2016 16:43:18) Included patches: 1-52 Extra patches: 8.0.0056 Modified by pkg-vim-maintainers@lists.alioth.debian.org Compiled by buildd@ Huge version without GUI. Features included (+) or not (-): +acl +farsi +mouse_netterm +syntax +arabic +file_in_path +mouse_sgr +tag_binary +autocmd +find_in_path -mouse_sysmouse +tag_old_static -balloon_eval +float +mouse_urxvt -tag_any_white -browse +folding +mouse_xterm -tcl ++builtin_terms -footer +multi_byte +terminfo +byte_offset +fork() +multi_lang +termresponse +cindent +gettext -mzscheme +textobjects -clientserver -hangul_input +netbeans_intg +title -clipboard +iconv +path_extra -toolbar +cmdline_compl +insert_expand -perl +user_commands +cmdline_hist +jumplist +persistent_undo +vertsplit +cmdline_info +keymap +postscript +virtualedit +comments +langmap +printer +visual +conceal +libcall +profile +visualextra +cryptv +linebreak +python +viminfo +cscope +lispindent -python3 +vreplace +cursorbind +listcmds +quickfix +wildignore +cursorshape +localmap +reltime +wildmenu +dialog_con -lua +rightleft +windows +diff +menu -ruby +writebackup +digraphs +mksession +scrollbind -X11 -dnd +modify_fname +signs -xfontset -ebcdic +mouse +smartindent -xim +emacs_tags -mouseshape -sniff -xsmp +eval +mouse_dec +startuptime -xterm_clipboard +ex_extra +mouse_gpm +statusline -xterm_save +extra_search -mouse_jsbterm -sun_workshop -xpm system vimrc file: "$VIM/vimrc" user vimrc file: "$HOME/.vimrc" 2nd user vimrc file: "~/.vim/vimrc" user exrc file: "$HOME/.exrc" fall-back for $VIM: "/usr/share/vim" Compilation: gcc -c -I. -Iproto -DHAVE_CONFIG_H -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 Linking: gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,--as-needed -o vim -lm -ltinfo -lnsl -lselinux -lacl -lattr -lgpm -ldl -L/usr/lib/python2.7/config-x86_64-linux-gnu -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions iptables version iptables v1.4.21 curl version curl 7.35.0 (x86_64-pc-linux-gnu) libcurl/7.35.0 OpenSSL/1.0.1f zlib/1.2.8 libidn/1.28 librtmp/2.3 wget version GNU Wget 1.15 built on linux-gnu. rsync version rsync version 3.1.0 protocol version 31 gimme version v1.2.0 nvm version 0.33.2 perlbrew version /home/travis/perl5/perlbrew/bin/perlbrew - App::perlbrew/0.78 phpenv version rbenv 1.1.1-4-g4ebd1bd rvm version rvm 1.29.2 (latest) by Michal Papis, Piotr Kuczynski, Wayne E. Seguin [https://rvm.io/] default ruby version ruby 2.4.1p111 (2017-03-22 revision 58053) [x86_64-linux] CouchDB version couchdb 1.6.1 ElasticSearch version 5.5.0 Installed Firefox version firefox 55.0.2 MongoDB version MongoDB 3.2.16 Pre-installed PostgreSQL versions 9.2.22 9.3.18 9.4.13 9.5.8 9.6.4 RabbitMQ Version 3.6.11 Redis version redis-server 4.0.1 riak version 2.2.3 kerl list installations 19.0 18.3 kiex list kiex elixirs elixir-1.2.6 =* elixir-1.3.2 # => - current # =* - current && default # * - default rebar --version rebar 2.6.4 17 20160831_145136 git 2.6.4-dirty perlbrew list 5.22 (5.22.0) 5.22-extras (5.22.0) 5.22-shrplib (5.22.0) 5.22.0 5.24-extras (5.24.0) 5.24-shrplib (5.24.0) 5.24 (5.24.2) 5.24.2 travis_fold:end:system_info  removed ‘/etc/apt/sources.list.d/basho_riak.list’ W: GPG error: http://repo.mongodb.org/apt/ubuntu trusty/mongodb-org/3.2 Release: The following signatures were invalid: KEYEXPIRED 1507497109 W: The repository 'http://repo.mongodb.org/apt/ubuntu trusty/mongodb-org/3.2 Release' is not signed. W: http://dl.hhvm.com/ubuntu/dists/trusty/InRelease: Signature by key 36AEF64D0207E7EEE352D4875A16E7281BE7A449 uses weak digest algorithm (SHA1) W: http://ppa.launchpad.net/couchdb/stable/ubuntu/dists/trusty/Release.gpg: Signature by key 15866BAFD9BCC4F3C1E0DFC7D69548E1C17EAB57 uses weak digest algorithm (SHA1) Executing: /tmp/tmp.eqPxrFLkkF/gpg.1.sh --keyserver hkp://keyserver.ubuntu.com:80 --recv EA312927 gpg: requesting key EA312927 from hkp server keyserver.ubuntu.com gpg: key EA312927: "MongoDB 3.2 Release Signing Key " 1 new signature gpg: Total number processed: 1 gpg: new signatures: 1 R for Travis-CI is not officially supported, but is community maintained. Please file any issues at https://github.com/travis-ci/travis-ci/issues and mention @craigcitro and @jimhester in the issue travis_fold:start:R-install Installing R travis_time:start:1471735c $ sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)/" travis_time:end:1471735c:start=1508642377220048782,finish=1508642377798938743,duration=578889961 travis_time:start:27b84d60 $ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 Executing: /tmp/tmp.4Z18Eh2rZp/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com gpg: key E084DAB9: public key "Michael Rutter " imported gpg: Total number processed: 1 gpg: imported: 1 (RSA: 1) travis_time:end:27b84d60:start=1508642377804653218,finish=1508642378345829643,duration=541176425 travis_time:start:041a5ded $ sudo add-apt-repository -y "ppa:marutter/rrutter" gpg: keyring `/tmp/tmphy_7rc22/secring.gpg' created gpg: keyring `/tmp/tmphy_7rc22/pubring.gpg' created gpg: requesting key B04C661B from hkp server keyserver.ubuntu.com gpg: /tmp/tmphy_7rc22/trustdb.gpg: trustdb created gpg: key B04C661B: public key "Launchpad PPA for marutter" imported gpg: Total number processed: 1 gpg: imported: 1 (RSA: 1) OK travis_time:end:041a5ded:start=1508642378350212992,finish=1508642379948807882,duration=1598594890 travis_time:start:2948c50e $ sudo add-apt-repository -y "ppa:marutter/c2d4u" gpg: keyring `/tmp/tmppjm1v52t/secring.gpg' created gpg: keyring `/tmp/tmppjm1v52t/pubring.gpg' created gpg: requesting key B04C661B from hkp server keyserver.ubuntu.com gpg: /tmp/tmppjm1v52t/trustdb.gpg: trustdb created gpg: key B04C661B: public key "Launchpad PPA for marutter" imported gpg: Total number processed: 1 gpg: imported: 1 (RSA: 1) OK travis_time:end:2948c50e:start=1508642379953523261,finish=1508642381528767771,duration=1575244510 travis_time:start:0023778d $ sudo apt-get update -qq W: http://dl.hhvm.com/ubuntu/dists/trusty/InRelease: Signature by key 36AEF64D0207E7EEE352D4875A16E7281BE7A449 uses weak digest algorithm (SHA1) W: http://ppa.launchpad.net/couchdb/stable/ubuntu/dists/trusty/Release.gpg: Signature by key 15866BAFD9BCC4F3C1E0DFC7D69548E1C17EAB57 uses weak digest algorithm (SHA1) travis_time:end:0023778d:start=1508642381533380149,finish=1508642389006866014,duration=7473485865 travis_time:start:1f0418e5 $ sudo apt-get install -y --no-install-recommends build-essential gcc g++ libblas-dev liblapack-dev libncurses5-dev libreadline-dev libjpeg-dev libpng-dev zlib1g-dev libbz2-dev liblzma-dev cdbs qpdf texinfo libmagick++-dev libssh2-1-dev gfortran Reading package lists... 0% Reading package lists... 100% Reading package lists... Done Building dependency tree... 0% Building dependency tree... 0% Building dependency tree... 50% Building dependency tree... 50% Building dependency tree Reading state information... 0% Reading state information... 0% Reading state information... Done Note, selecting 'libpng12-dev' instead of 'libpng-dev' build-essential is already the newest version (11.6ubuntu6). g++ is already the newest version (4:4.8.2-1ubuntu6). g++ set to manually installed. gcc is already the newest version (4:4.8.2-1ubuntu6). gcc set to manually installed. libbz2-dev is already the newest version (1.0.6-5). libjpeg-dev is already the newest version (8c-2ubuntu8). liblzma-dev is already the newest version (5.1.1alpha+20120614-2ubuntu2). liblzma-dev set to manually installed. libncurses5-dev is already the newest version (5.9+20140118-1ubuntu1). libreadline-dev is already the newest version (6.3-4ubuntu2). zlib1g-dev is already the newest version (1:1.2.8.dfsg-1ubuntu1). zlib1g-dev set to manually installed. libpng12-dev is already the newest version (1.2.50-1ubuntu2.14.04.2). libpng12-dev set to manually installed. The following additional packages will be installed: debhelper dh-apparmor dh-translations gfortran-4.8 intltool intltool-debian libblas3 libencode-locale-perl libfile-listing-perl libgfortran-4.8-dev libgfortran3 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libintl-perl libio-html-perl libio-socket-ssl-perl liblapack3 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagick++5 libnet-http-perl libnet-ssleay-perl libqpdf13 libssh2-1 libtext-unidecode-perl liburi-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-perl po-debconf python-scour Suggested packages: devscripts dh-make apparmor-easyprof gfortran-multilib gfortran-doc gfortran-4.8-multilib gfortran-4.8-doc libgfortran3-dbg libdata-dump-perl libintl-xs-perl libcrypt-ssleay-perl libauthen-ntlm-perl libmail-box-perl python-rsvg python-cairo texlive-base texlive-latex-base texlive-generic-recommended texinfo-doc-nonfree Recommended packages: libhtml-format-perl libio-socket-inet6-perl | libio-socket-ip-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl libmail-sendmail-perl The following NEW packages will be installed: cdbs debhelper dh-apparmor dh-translations gfortran gfortran-4.8 intltool intltool-debian libblas-dev libblas3 libencode-locale-perl libfile-listing-perl libgfortran-4.8-dev libgfortran3 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libintl-perl libio-html-perl libio-socket-ssl-perl liblapack-dev liblapack3 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagick++-dev libmagick++5 libnet-http-perl libnet-ssleay-perl libqpdf13 libssh2-1 libssh2-1-dev libtext-unidecode-perl liburi-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-perl po-debconf python-scour qpdf texinfo 0 upgraded, 48 newly installed, 0 to remove and 96 not upgraded. Need to get 15.1 MB of archives. After this operation, 57.9 MB of additional disk space will be used. 0% [Working] Get:1 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 libgfortran3 amd64 4.8.4-2ubuntu1~14.04.3 [248 kB] 0% [1 libgfortran3 13.5 kB/248 kB 5%] 2% [Working] Get:2 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 libmagick++5 amd64 8:6.7.7.10-6ubuntu3.9 [102 kB] 2% [2 libmagick++5 4,096 B/102 kB 4%] 3% [Working] Get:3 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libqpdf13 amd64 5.1.1-1 [295 kB] 3% [3 libqpdf13 16.4 kB/295 kB 6%] 5% [Working] Get:4 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/universe amd64 libssh2-1 amd64 1.4.3-2ubuntu0.1 [66.4 kB] 5% [4 libssh2-1 7,618 B/66.4 kB 11%] 5% [Working] Get:5 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 intltool-debian all 0.35.0+20060710.1 [31.6 kB] 5% [5 intltool-debian 6,274 B/31.6 kB 20%] 6% [Working] Get:6 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] 6% [6 po-debconf 8,192 B/210 kB 4%] 8% [Working] Get:7 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 dh-apparmor all 2.10.95-0ubuntu2.6~14.04.1 [13.0 kB] 8% [7 dh-apparmor 13.0 kB/13.0 kB 100%] 8% [Waiting for headers] Get:8 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 debhelper all 9.20131227ubuntu1 [604 kB] 8% [8 debhelper 11.0 kB/604 kB 2%] 12% [Working] Get:9 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 liburi-perl all 1.60-1 [89.6 kB] 12% [9 liburi-perl 8,192 B/89.6 kB 9%] 13% [Working] Get:10 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libencode-locale-perl all 1.03-1 [12.4 kB] 13% [10 libencode-locale-perl 12.4 kB/12.4 kB 100%] 13% [Waiting for headers] Get:11 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libhttp-date-perl all 6.02-1 [10.4 kB] 13% [11 libhttp-date-perl 10.4 kB/10.4 kB 100%] 14% [Working] Get:12 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libfile-listing-perl all 6.04-1 [9,774 B] 14% [12 libfile-listing-perl 9,774 B/9,774 B 100%] 14% [Working] Get:13 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libhtml-tagset-perl all 3.20-2 [13.5 kB] 14% [13 libhtml-tagset-perl 4,730 B/13.5 kB 35%] 14% [Working] Get:14 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libhtml-parser-perl amd64 3.71-1build1 [98.2 kB] 15% [14 libhtml-parser-perl 15.9 kB/98.2 kB 16%] 15% [Working] Get:15 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libhtml-tree-perl all 5.03-1 [215 kB] 15% [15 libhtml-tree-perl 12.4 kB/215 kB 6%] 17% [Working] Get:16 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libio-html-perl all 1.00-1 [15.7 kB] 17% [16 libio-html-perl 15.7 kB/15.7 kB 100%] 17% [Waiting for headers] Get:17 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 liblwp-mediatypes-perl all 6.02-1 [21.7 kB] 18% [17 liblwp-mediatypes-perl 21.7 kB/21.7 kB 100%] 18% [Waiting for headers] Get:18 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libhttp-message-perl all 6.06-1 [78.7 kB] 18% [18 libhttp-message-perl 24.6 kB/78.7 kB 31%] 19% [Working] Get:19 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libhttp-cookies-perl all 6.00-2 [23.3 kB] 19% [Waiting for headers] Get:20 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libhttp-negotiate-perl all 6.00-2 [13.4 kB] 19% [20 libhttp-negotiate-perl 13.4 kB/13.4 kB 100%] 20% [Waiting for headers] Get:21 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libnet-ssleay-perl amd64 1.58-1 [243 kB] 20% [21 libnet-ssleay-perl 20.5 kB/243 kB 8%] 22% [Working] Get:22 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libio-socket-ssl-perl all 1.965-1ubuntu1 [73.7 kB] 22% [22 libio-socket-ssl-perl 32.8 kB/73.7 kB 44%] 22% [Working] Get:23 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libnet-http-perl all 6.06-1 [24.2 kB] 22% [23 libnet-http-perl 24.2 kB/24.2 kB 100%] 23% [Working] Get:24 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 liblwp-protocol-https-perl all 6.04-2ubuntu0.1 [7,644 B] 23% [24 liblwp-protocol-https-perl 7,644 B/7,644 B 100%] 23% [Working] Get:25 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libwww-robotrules-perl all 6.01-1 [14.1 kB] 23% [25 libwww-robotrules-perl 14.1 kB/14.1 kB 100%] 24% [Working] Get:26 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libwww-perl all 6.05-2 [146 kB] 24% [26 libwww-perl 8,192 B/146 kB 6%] 25% [Working] Get:27 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libxml-parser-perl amd64 2.41-1build3 [294 kB] 25% [27 libxml-parser-perl 26.0 kB/294 kB 9%] 27% [Working] Get:28 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 intltool all 0.50.2-2 [52.0 kB] 27% [28 intltool 8,192 B/52.0 kB 16%] 28% [Working] Get:29 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 dh-translations all 121 [21.6 kB] 28% [29 dh-translations 21.6 kB/21.6 kB 100%] 28% [Working] Get:30 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 python-scour all 0.26-3build1 [40.5 kB] 28% [30 python-scour 8,192 B/40.5 kB 20%] 29% [Working] Get:31 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 cdbs all 0.4.122ubuntu2 [42.1 kB] 29% [31 cdbs 16.4 kB/42.1 kB 39%] 30% [Working] Get:32 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 libgfortran-4.8-dev amd64 4.8.4-2ubuntu1~14.04.3 [269 kB] 30% [32 libgfortran-4.8-dev 49.2 kB/269 kB 18%] 31% [Working] Get:33 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 gfortran-4.8 amd64 4.8.4-2ubuntu1~14.04.3 [4,883 kB] 32% [33 gfortran-4.8 123 kB/4,883 kB 3%] 58% [Working] Get:34 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 gfortran amd64 4:4.8.2-1ubuntu6 [1,252 B] 58% [34 gfortran 1,252 B/1,252 B 100%] 58% [Waiting for headers] Get:35 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libblas3 amd64 1.2.20110419-7 [215 kB] 58% [35 libblas3 36.6 kB/215 kB 17%] 60% [Working] Get:36 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libblas-dev amd64 1.2.20110419-7 [240 kB] 60% [36 libblas-dev 16.4 kB/240 kB 7%] 61% [Working] Get:37 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libintl-perl all 1.23-1build1 [1,204 kB] 61% [37 libintl-perl 16.4 kB/1,204 kB 1%] 68% [Working] Get:38 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 liblapack3 amd64 3.5.0-2ubuntu1 [1,730 kB] 68% [38 liblapack3 8,192 B/1,730 kB 0%] 78% [Working] Get:39 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 liblapack-dev amd64 3.5.0-2ubuntu1 [1,740 kB] 78% [39 liblapack-dev 9,600 B/1,740 kB 1%] 87% [Working] Get:40 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 libmagick++-dev amd64 8:6.7.7.10-6ubuntu3.9 [130 kB] 88% [40 libmagick++-dev 65.5 kB/130 kB 50%] 88% [Working] Get:41 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/universe amd64 libssh2-1-dev amd64 1.4.3-2ubuntu0.1 [229 kB] 89% [41 libssh2-1-dev 28.7 kB/229 kB 13%] 90% [Working] Get:42 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libtext-unidecode-perl all 0.04-2 [115 kB] 90% [42 libtext-unidecode-perl 16.4 kB/115 kB 14%] 91% [Working] Get:43 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libxml-namespacesupport-perl all 1.11-1 [13.2 kB] 91% [43 libxml-namespacesupport-perl 13.2 kB/13.2 kB 100%] 92% [Waiting for headers] Get:44 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libxml-sax-base-perl all 1.07-1 [21.5 kB] 92% [44 libxml-sax-base-perl 21.5 kB/21.5 kB 100%] 92% [Working] Get:45 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB] 92% [45 libxml-sax-perl 8,192 B/64.6 kB 13%] 93% [Working] Get:46 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 libxml-libxml-perl amd64 2.0108+dfsg-1ubuntu0.1 [337 kB] 93% [46 libxml-libxml-perl 16.4 kB/337 kB 5%] 95% [Working] Get:47 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 qpdf amd64 5.1.1-1 [207 kB] 95% [47 qpdf 31.6 kB/207 kB 15%] 97% [Working] Get:48 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 texinfo amd64 5.2.0.dfsg.1-2 [561 kB] 97% [48 texinfo 8,192 B/561 kB 1%] 100% [Working] Fetched 15.1 MB in 0s (39.7 MB/s) Extracting templates from packages: 62% Extracting templates from packages: 100% Selecting previously unselected package libgfortran3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 96857 files and directories currently installed.) Preparing to unpack .../libgfortran3_4.8.4-2ubuntu1~14.04.3_amd64.deb ... Unpacking libgfortran3:amd64 (4.8.4-2ubuntu1~14.04.3) ... Selecting previously unselected package libmagick++5:amd64. Preparing to unpack .../libmagick++5_8%3a6.7.7.10-6ubuntu3.9_amd64.deb ... Unpacking libmagick++5:amd64 (8:6.7.7.10-6ubuntu3.9) ... Selecting previously unselected package libqpdf13:amd64. Preparing to unpack .../libqpdf13_5.1.1-1_amd64.deb ... Unpacking libqpdf13:amd64 (5.1.1-1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../libssh2-1_1.4.3-2ubuntu0.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.4.3-2ubuntu0.1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu2ubuntu1_all.deb ... Unpacking po-debconf (1.0.16+nmu2ubuntu1) ... Selecting previously unselected package dh-apparmor. Preparing to unpack .../dh-apparmor_2.10.95-0ubuntu2.6~14.04.1_all.deb ... Unpacking dh-apparmor (2.10.95-0ubuntu2.6~14.04.1) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20131227ubuntu1_all.deb ... Unpacking debhelper (9.20131227ubuntu1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../liburi-perl_1.60-1_all.deb ... Unpacking liburi-perl (1.60-1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../libencode-locale-perl_1.03-1_all.deb ... Unpacking libencode-locale-perl (1.03-1) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../libhttp-date-perl_6.02-1_all.deb ... Unpacking libhttp-date-perl (6.02-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../libfile-listing-perl_6.04-1_all.deb ... Unpacking libfile-listing-perl (6.04-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../libhtml-tagset-perl_3.20-2_all.deb ... Unpacking libhtml-tagset-perl (3.20-2) ... Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../libhtml-parser-perl_3.71-1build1_amd64.deb ... Unpacking libhtml-parser-perl (3.71-1build1) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../libhtml-tree-perl_5.03-1_all.deb ... Unpacking libhtml-tree-perl (5.03-1) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../libio-html-perl_1.00-1_all.deb ... Unpacking libio-html-perl (1.00-1) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../liblwp-mediatypes-perl_6.02-1_all.deb ... Unpacking liblwp-mediatypes-perl (6.02-1) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../libhttp-message-perl_6.06-1_all.deb ... Unpacking libhttp-message-perl (6.06-1) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../libhttp-cookies-perl_6.00-2_all.deb ... Unpacking libhttp-cookies-perl (6.00-2) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../libhttp-negotiate-perl_6.00-2_all.deb ... Unpacking libhttp-negotiate-perl (6.00-2) ... Selecting previously unselected package libnet-ssleay-perl. Preparing to unpack .../libnet-ssleay-perl_1.58-1_amd64.deb ... Unpacking libnet-ssleay-perl (1.58-1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../libio-socket-ssl-perl_1.965-1ubuntu1_all.deb ... Unpacking libio-socket-ssl-perl (1.965-1ubuntu1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../libnet-http-perl_6.06-1_all.deb ... Unpacking libnet-http-perl (6.06-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../liblwp-protocol-https-perl_6.04-2ubuntu0.1_all.deb ... Unpacking liblwp-protocol-https-perl (6.04-2ubuntu0.1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../libwww-robotrules-perl_6.01-1_all.deb ... Unpacking libwww-robotrules-perl (6.01-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../libwww-perl_6.05-2_all.deb ... Unpacking libwww-perl (6.05-2) ... Selecting previously unselected package libxml-parser-perl. Preparing to unpack .../libxml-parser-perl_2.41-1build3_amd64.deb ... Unpacking libxml-parser-perl (2.41-1build3) ... Selecting previously unselected package intltool. Preparing to unpack .../intltool_0.50.2-2_all.deb ... Unpacking intltool (0.50.2-2) ... Selecting previously unselected package dh-translations. Preparing to unpack .../dh-translations_121_all.deb ... Unpacking dh-translations (121) ... Selecting previously unselected package python-scour. Preparing to unpack .../python-scour_0.26-3build1_all.deb ... Unpacking python-scour (0.26-3build1) ... Selecting previously unselected package cdbs. Preparing to unpack .../cdbs_0.4.122ubuntu2_all.deb ... Unpacking cdbs (0.4.122ubuntu2) ... Selecting previously unselected package libgfortran-4.8-dev:amd64. Preparing to unpack .../libgfortran-4.8-dev_4.8.4-2ubuntu1~14.04.3_amd64.deb ... Unpacking libgfortran-4.8-dev:amd64 (4.8.4-2ubuntu1~14.04.3) ... Selecting previously unselected package gfortran-4.8. Preparing to unpack .../gfortran-4.8_4.8.4-2ubuntu1~14.04.3_amd64.deb ... Unpacking gfortran-4.8 (4.8.4-2ubuntu1~14.04.3) ... Selecting previously unselected package gfortran. Preparing to unpack .../gfortran_4%3a4.8.2-1ubuntu6_amd64.deb ... Unpacking gfortran (4:4.8.2-1ubuntu6) ... Selecting previously unselected package libblas3. Preparing to unpack .../libblas3_1.2.20110419-7_amd64.deb ... Unpacking libblas3 (1.2.20110419-7) ... Selecting previously unselected package libblas-dev. Preparing to unpack .../libblas-dev_1.2.20110419-7_amd64.deb ... Unpacking libblas-dev (1.2.20110419-7) ... Selecting previously unselected package libintl-perl. Preparing to unpack .../libintl-perl_1.23-1build1_all.deb ... Unpacking libintl-perl (1.23-1build1) ... Selecting previously unselected package liblapack3. Preparing to unpack .../liblapack3_3.5.0-2ubuntu1_amd64.deb ... Unpacking liblapack3 (3.5.0-2ubuntu1) ... Selecting previously unselected package liblapack-dev. Preparing to unpack .../liblapack-dev_3.5.0-2ubuntu1_amd64.deb ... Unpacking liblapack-dev (3.5.0-2ubuntu1) ... Selecting previously unselected package libmagick++-dev. Preparing to unpack .../libmagick++-dev_8%3a6.7.7.10-6ubuntu3.9_amd64.deb ... Unpacking libmagick++-dev (8:6.7.7.10-6ubuntu3.9) ... Selecting previously unselected package libssh2-1-dev:amd64. Preparing to unpack .../libssh2-1-dev_1.4.3-2ubuntu0.1_amd64.deb ... Unpacking libssh2-1-dev:amd64 (1.4.3-2ubuntu0.1) ... Selecting previously unselected package libtext-unidecode-perl. Preparing to unpack .../libtext-unidecode-perl_0.04-2_all.deb ... Unpacking libtext-unidecode-perl (0.04-2) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../libxml-namespacesupport-perl_1.11-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.11-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../libxml-sax-base-perl_1.07-1_all.deb ... Unpacking libxml-sax-base-perl (1.07-1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../libxml-sax-perl_0.99+dfsg-2ubuntu1_all.deb ... Unpacking libxml-sax-perl (0.99+dfsg-2ubuntu1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../libxml-libxml-perl_2.0108+dfsg-1ubuntu0.1_amd64.deb ... Unpacking libxml-libxml-perl (2.0108+dfsg-1ubuntu0.1) ... Selecting previously unselected package qpdf. Preparing to unpack .../qpdf_5.1.1-1_amd64.deb ... Unpacking qpdf (5.1.1-1) ... Selecting previously unselected package texinfo. Preparing to unpack .../texinfo_5.2.0.dfsg.1-2_amd64.deb ... Unpacking texinfo (5.2.0.dfsg.1-2) ... Processing triggers for man-db (2.6.7.1-1ubuntu1) ... Processing triggers for ccache (3.1.9-1) ... Updating symlinks in /usr/lib/ccache ... Setting up libgfortran3:amd64 (4.8.4-2ubuntu1~14.04.3) ... Setting up libmagick++5:amd64 (8:6.7.7.10-6ubuntu3.9) ... Setting up libqpdf13:amd64 (5.1.1-1) ... Setting up libssh2-1:amd64 (1.4.3-2ubuntu0.1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.10.95-0ubuntu2.6~14.04.1) ... Setting up debhelper (9.20131227ubuntu1) ... Setting up liburi-perl (1.60-1) ... Setting up libencode-locale-perl (1.03-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libhtml-tagset-perl (3.20-2) ... Setting up libhtml-parser-perl (3.71-1build1) ... Setting up libhtml-tree-perl (5.03-1) ... Setting up libio-html-perl (1.00-1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libhttp-message-perl (6.06-1) ... Setting up libhttp-cookies-perl (6.00-2) ... Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libnet-ssleay-perl (1.58-1) ... Setting up libio-socket-ssl-perl (1.965-1ubuntu1) ... Setting up libnet-http-perl (6.06-1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up python-scour (0.26-3build1) ... Setting up libgfortran-4.8-dev:amd64 (4.8.4-2ubuntu1~14.04.3) ... Setting up gfortran-4.8 (4.8.4-2ubuntu1~14.04.3) ... Setting up gfortran (4:4.8.2-1ubuntu6) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode Setting up libblas3 (1.2.20110419-7) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libblas-dev (1.2.20110419-7) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up libintl-perl (1.23-1build1) ... Setting up liblapack3 (3.5.0-2ubuntu1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up liblapack-dev (3.5.0-2ubuntu1) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libmagick++-dev (8:6.7.7.10-6ubuntu3.9) ... Setting up libssh2-1-dev:amd64 (1.4.3-2ubuntu0.1) ... Setting up libtext-unidecode-perl (0.04-2) ... Setting up libxml-namespacesupport-perl (1.11-1) ... Setting up libxml-sax-base-perl (1.07-1) ... Setting up libxml-sax-perl (0.99+dfsg-2ubuntu1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0108+dfsg-1ubuntu0.1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up qpdf (5.1.1-1) ... Setting up texinfo (5.2.0.dfsg.1-2) ... Setting up liblwp-protocol-https-perl (6.04-2ubuntu0.1) ... Setting up libwww-perl (6.05-2) ... Setting up libxml-parser-perl (2.41-1build3) ... Setting up intltool (0.50.2-2) ... Setting up dh-translations (121) ... Setting up cdbs (0.4.122ubuntu2) ... Processing triggers for libc-bin (2.19-0ubuntu6.13) ... travis_time:end:1f0418e5:start=1508642389011441076,finish=1508642400461211264,duration=11449770188 travis_time:start:12ae3d20 $ curl -fLo /tmp/R-3.4.2-$(lsb_release -cs).xz https://s3.amazonaws.com/rstudio-travis/R-3.4.2-$(lsb_release -cs).xz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 44.4M 1 542k 0 0 917k 0 0:00:49 --:--:-- 0:00:49 916k 13 44.4M 13 5982k 0 0 3774k 0 0:00:12 0:00:01 0:00:11 3774k 52 44.4M 52 23.3M 0 0 9238k 0 0:00:04 0:00:02 0:00:02 9235k 100 44.4M 100 44.4M 0 0 14.4M 0 0:00:03 0:00:03 --:--:-- 14.4M travis_time:end:12ae3d20:start=1508642400466428294,finish=1508642403641264690,duration=3174836396 travis_time:start:02a59b42 $ tar xJf /tmp/R-3.4.2-$(lsb_release -cs).xz -C ~ travis_time:end:02a59b42:start=1508642403645725942,finish=1508642407337681273,duration=3691955331 $ rm /tmp/R-3.4.2-$(lsb_release -cs).xz travis_time:start:107108d2 $ sudo mkdir -p /usr/local/lib/R/site-library $R_LIBS_USER travis_time:end:107108d2:start=1508642407390840102,finish=1508642407399836192,duration=8996090 travis_time:start:01360920 $ sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library $R_LIBS_USER travis_time:end:01360920:start=1508642407404255721,finish=1508642407412897315,duration=8641594 travis_time:start:03d25bc8 $ echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' > ~/.Rprofile.site travis_time:end:03d25bc8:start=1508642407417271772,finish=1508642407420933321,duration=3661549 travis_time:start:1b150608 $ curl -fLo /tmp/pandoc-1.15.2-1-amd64.deb https://github.com/jgm/pandoc/releases/download/1.15.2/pandoc-1.15.2-1-amd64.deb % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 613 0 613 0 0 3630 0 --:--:-- --:--:-- --:--:-- 3670 2 18.8M 2 525k 0 0 707k 0 0:00:27 --:--:-- 0:00:27 707k 40 18.8M 40 7920k 0 0 4610k 0 0:00:04 0:00:01 0:00:03 7576k 100 18.8M 100 18.8M 0 0 8930k 0 0:00:02 0:00:02 --:--:-- 12.9M travis_time:end:1b150608:start=1508642407425443509,finish=1508642409605768686,duration=2180325177 travis_time:start:051b1e26 $ sudo dpkg -i /tmp/pandoc-1.15.2-1-amd64.deb Selecting previously unselected package pandoc. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 99061 files and directories currently installed.) Preparing to unpack /tmp/pandoc-1.15.2-1-amd64.deb ... Unpacking pandoc (1.15.2-1) ... Setting up pandoc (1.15.2-1) ... Processing triggers for man-db (2.6.7.1-1ubuntu1) ... travis_time:end:051b1e26:start=1508642409611130733,finish=1508642411220558878,duration=1609428145 travis_time:start:0ab47f68 $ sudo apt-get install -f Reading package lists... 0% Reading package lists... 0% Reading package lists... 8% Reading package lists... Done Building dependency tree... 0% Building dependency tree... 0% Building dependency tree... 50% Building dependency tree... 50% Building dependency tree Reading state information... 0% Reading state information... 0% Reading state information... Done 0 upgraded, 0 newly installed, 0 to remove and 96 not upgraded. travis_time:end:0ab47f68:start=1508642411224875949,finish=1508642412052141654,duration=827265705 $ rm /tmp/pandoc-1.15.2-1-amd64.deb travis_fold:end:R-install travis_fold:start:git.checkout travis_time:start:02623eae $ git clone --depth=50 --branch=master https://github.com/dorianps/LESYMAP.git dorianps/LESYMAP Cloning into 'dorianps/LESYMAP'... remote: Counting objects: 430, done. remote: Compressing objects: 0% (1/206)  remote: Compressing objects: 1% (3/206)  remote: Compressing objects: 2% (5/206)  remote: Compressing objects: 3% (7/206)  remote: Compressing objects: 4% (9/206)  remote: Compressing objects: 5% (11/206)  remote: Compressing objects: 6% (13/206)  remote: Compressing objects: 7% (15/206)  remote: Compressing objects: 8% (17/206)  remote: Compressing objects: 9% (19/206)  remote: Compressing objects: 10% (21/206)  remote: Compressing objects: 11% (23/206)  remote: Compressing objects: 12% (25/206)  remote: Compressing objects: 13% (27/206)  remote: Compressing objects: 14% (29/206)  remote: Compressing objects: 15% (31/206)  remote: Compressing objects: 16% (33/206) remote: Compressing objects: 17% (36/206)  remote: Compressing objects: 18% (38/206)  remote: Compressing objects: 19% (40/206)  remote: Compressing objects: 20% (42/206)  remote: Compressing objects: 21% (44/206)  remote: Compressing objects: 22% (46/206)  remote: Compressing objects: 23% (48/206)  remote: Compressing objects: 24% (50/206)  remote: Compressing objects: 25% (52/206)  remote: Compressing objects: 26% (54/206)  remote: Compressing objects: 27% (56/206)  remote: Compressing objects: 28% (58/206)  remote: Compressing objects: 29% (60/206)  remote: Compressing objects: 30% (62/206)  remote: Compressing objects: 31% (64/206)  remote: Compressing objects: 32% (66/206)  remote: Compressing objects: 33% (68/206)  remote: Compressing objects: 34% (71/206)  remote: Compressing objects: 35% (73/206)  remote: Compressing objects: 36% (75/206)  remote: Compressing objects: 37% (77/206)  remote: Compressing objects: 38% (79/206)  remote: Compressing objects: 39% (81/206)  remote: Compressing objects: 40% (83/206)  remote: Compressing objects: 41% (85/206)  remote: Compressing objects: 42% (87/206)  remote: Compressing objects: 43% (89/206)  remote: Compressing objects: 44% (91/206)  remote: Compressing objects: 45% (93/206)  remote: Compressing objects: 46% (95/206)  remote: Compressing objects: 47% (97/206)  remote: Compressing objects: 48% (99/206)  remote: Compressing objects: 49% (101/206)  remote: Compressing objects: 50% (103/206)  remote: Compressing objects: 51% (106/206)  remote: Compressing objects: 52% (108/206)  remote: Compressing objects: 53% (110/206)  remote: Compressing objects: 54% (112/206)  remote: Compressing objects: 55% (114/206)  remote: Compressing objects: 56% (116/206)  remote: Compressing objects: 57% (118/206)  remote: Compressing objects: 58% (120/206)  remote: Compressing objects: 59% (122/206)  remote: Compressing objects: 60% (124/206)  remote: Compressing objects: 61% (126/206)  remote: Compressing objects: 62% (128/206)  remote: Compressing objects: 63% (130/206)  remote: Compressing objects: 64% (132/206)  remote: Compressing objects: 65% (134/206)  remote: Compressing objects: 66% (136/206)  remote: Compressing objects: 67% (139/206)  remote: Compressing objects: 68% (141/206)  remote: Compressing objects: 69% (143/206)  remote: Compressing objects: 70% (145/206)  remote: Compressing objects: 71% (147/206)  remote: Compressing objects: 72% (149/206)  remote: Compressing objects: 73% (151/206)  remote: Compressing objects: 74% (153/206)  remote: Compressing objects: 75% (155/206)  remote: Compressing objects: 76% (157/206)  remote: Compressing objects: 77% (159/206)  remote: Compressing objects: 78% (161/206)  remote: Compressing objects: 79% (163/206)  remote: Compressing objects: 80% (165/206)  remote: Compressing objects: 81% (167/206)  remote: Compressing objects: 82% (169/206)  remote: Compressing objects: 83% (171/206)  remote: Compressing objects: 84% (174/206)  remote: Compressing objects: 85% (176/206)  remote: Compressing objects: 86% (178/206)  remote: Compressing objects: 87% (180/206)  remote: Compressing objects: 88% (182/206)  remote: Compressing objects: 89% (184/206)  remote: Compressing objects: 90% (186/206)  remote: Compressing objects: 91% (188/206)  remote: Compressing objects: 92% (190/206)  remote: Compressing objects: 93% (192/206)  remote: Compressing objects: 94% (194/206)  remote: Compressing objects: 95% (196/206)  remote: Compressing objects: 96% (198/206)  remote: Compressing objects: 97% (200/206)  remote: Compressing objects: 98% (202/206)  remote: Compressing objects: 99% (204/206)  remote: Compressing objects: 100% (206/206)  remote: Compressing objects: 100% (206/206), done. Receiving objects: 0% (1/430) Receiving objects: 1% (5/430) Receiving objects: 2% (9/430) Receiving objects: 3% (13/430) Receiving objects: 4% (18/430) Receiving objects: 5% (22/430) Receiving objects: 6% (26/430) Receiving objects: 7% (31/430) Receiving objects: 8% (35/430) Receiving objects: 9% (39/430) Receiving objects: 10% (43/430) Receiving objects: 11% (48/430) Receiving objects: 12% (52/430) Receiving objects: 13% (56/430) Receiving objects: 14% (61/430) Receiving objects: 15% (65/430) Receiving objects: 16% (69/430) Receiving objects: 17% (74/430) Receiving objects: 18% (78/430) Receiving objects: 19% (82/430) Receiving objects: 20% (86/430) Receiving objects: 21% (91/430) Receiving objects: 22% (95/430) Receiving objects: 23% (99/430) Receiving objects: 24% (104/430) Receiving objects: 25% (108/430) Receiving objects: 26% (112/430) Receiving objects: 27% (117/430) Receiving objects: 28% (121/430) Receiving objects: 29% (125/430) Receiving objects: 30% (129/430) Receiving objects: 31% (134/430) Receiving objects: 32% (138/430) Receiving objects: 33% (142/430) Receiving objects: 34% (147/430) Receiving objects: 35% (151/430) Receiving objects: 36% (155/430) Receiving objects: 37% (160/430) Receiving objects: 38% (164/430) Receiving objects: 39% (168/430) Receiving objects: 40% (172/430) Receiving objects: 41% (177/430) Receiving objects: 42% (181/430) Receiving objects: 43% (185/430) Receiving objects: 44% (190/430) Receiving objects: 45% (194/430) Receiving objects: 46% (198/430) Receiving objects: 47% (203/430) Receiving objects: 48% (207/430) Receiving objects: 49% (211/430) Receiving objects: 50% (215/430) Receiving objects: 51% (220/430) Receiving objects: 52% (224/430) Receiving objects: 53% (228/430) Receiving objects: 54% (233/430) Receiving objects: 55% (237/430) Receiving objects: 56% (241/430) Receiving objects: 57% (246/430) Receiving objects: 58% (250/430) Receiving objects: 59% (254/430) Receiving objects: 60% (258/430) Receiving objects: 61% (263/430) Receiving objects: 62% (267/430) Receiving objects: 63% (271/430) Receiving objects: 64% (276/430) Receiving objects: 65% (280/430) Receiving objects: 66% (284/430) Receiving objects: 67% (289/430) Receiving objects: 68% (293/430) Receiving objects: 69% (297/430) Receiving objects: 70% (301/430) Receiving objects: 71% (306/430) Receiving objects: 72% (310/430) Receiving objects: 73% (314/430) Receiving objects: 74% (319/430) Receiving objects: 75% (323/430) Receiving objects: 76% (327/430) Receiving objects: 77% (332/430) Receiving objects: 78% (336/430) Receiving objects: 79% (340/430) Receiving objects: 80% (344/430) Receiving objects: 81% (349/430) Receiving objects: 82% (353/430) Receiving objects: 83% (357/430) Receiving objects: 84% (362/430) Receiving objects: 85% (366/430) Receiving objects: 86% (370/430) Receiving objects: 87% (375/430) Receiving objects: 88% (379/430) Receiving objects: 89% (383/430) Receiving objects: 90% (387/430) Receiving objects: 91% (392/430) Receiving objects: 92% (396/430) Receiving objects: 93% (400/430) Receiving objects: 94% (405/430) Receiving objects: 95% (409/430) Receiving objects: 96% (413/430) Receiving objects: 97% (418/430) Receiving objects: 98% (422/430) Receiving objects: 99% (426/430) remote: Total 430 (delta 246), reused 367 (delta 219), pack-reused 0 Receiving objects: 100% (430/430) Receiving objects: 100% (430/430), 5.55 MiB | 16.48 MiB/s, done. Resolving deltas: 0% (0/246) Resolving deltas: 6% (16/246) Resolving deltas: 10% (27/246) Resolving deltas: 18% (45/246) Resolving deltas: 23% (59/246) Resolving deltas: 26% (66/246) Resolving deltas: 28% (71/246) Resolving deltas: 29% (72/246) Resolving deltas: 30% (76/246) Resolving deltas: 31% (77/246) Resolving deltas: 32% (80/246) Resolving deltas: 34% (86/246) Resolving deltas: 36% (89/246) Resolving deltas: 37% (93/246) Resolving deltas: 38% (94/246) Resolving deltas: 39% (96/246) Resolving deltas: 40% (99/246) Resolving deltas: 41% (102/246) Resolving deltas: 42% (105/246) Resolving deltas: 43% (106/246) Resolving deltas: 50% (125/246) Resolving deltas: 55% (136/246) Resolving deltas: 60% (149/246) Resolving deltas: 68% (168/246) Resolving deltas: 72% (179/246) Resolving deltas: 73% (180/246) Resolving deltas: 74% (183/246) Resolving deltas: 76% (188/246) Resolving deltas: 79% (195/246) Resolving deltas: 83% (205/246) Resolving deltas: 84% (208/246) Resolving deltas: 85% (210/246) Resolving deltas: 87% (216/246) Resolving deltas: 89% (219/246) Resolving deltas: 90% (222/246) Resolving deltas: 91% (224/246) Resolving deltas: 93% (229/246) Resolving deltas: 95% (234/246) Resolving deltas: 96% (237/246) Resolving deltas: 97% (240/246) Resolving deltas: 98% (242/246) Resolving deltas: 99% (245/246) Resolving deltas: 100% (246/246) Resolving deltas: 100% (246/246), done. travis_time:end:02623eae:start=1508642412061659332,finish=1508642413041161567,duration=979502235 $ cd dorianps/LESYMAP $ git checkout -qf b7c9e12959598a1ad5a779de1918ac63b04dc6e9 travis_fold:end:git.checkout travis_fold:start:R-session-info R session information $ Rscript -e 'sessionInfo()' R version 3.4.2 (2017-01-27) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /home/travis/R-bin/lib/R/lib/libRblas.so LAPACK: /home/travis/R-bin/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets base loaded via a namespace (and not attached): [1] compiler_3.4.2 travis_fold:end:R-session-info travis_fold:start:before_install.1 travis_time:start:036a09e4 $ export itkrrel=0.4.12 travis_time:end:036a09e4:start=1508642413227293480,finish=1508642413231073592,duration=3780112 travis_fold:end:before_install.1 travis_fold:start:before_install.2 travis_time:start:1db17d20 $ export gh_user=stnava travis_time:end:1db17d20:start=1508642413235844722,finish=1508642413239738862,duration=3894140 travis_fold:end:before_install.2 travis_fold:start:before_install.3 travis_time:start:10871b40 $ export ANTsRCorerel=0.4.2.1 travis_time:end:10871b40:start=1508642413244909382,finish=1508642413248810654,duration=3901272 travis_fold:end:before_install.3 travis_fold:start:before_install.4 travis_time:start:147f72db $ export reldir=latest travis_time:end:147f72db:start=1508642413253511381,finish=1508642413257287685,duration=3776304 travis_fold:end:before_install.4 travis_fold:start:before_install.5 travis_time:start:1ee783d0 $ export antsrrel=0.6.1 travis_time:end:1ee783d0:start=1508642413262154707,finish=1508642413266169289,duration=4014582 travis_fold:end:before_install.5 travis_fold:start:before_install.6 travis_time:start:26bddad7 $ if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get -y install libiomp5 ; fi Reading package lists... 0% Reading package lists... 100% Reading package lists... Done Building dependency tree... 0% Building dependency tree... 0% Building dependency tree... 50% Building dependency tree... 50% Building dependency tree Reading state information... 0% Reading state information... 0% Reading state information... Done The following NEW packages will be installed: libiomp5 0 upgraded, 1 newly installed, 0 to remove and 96 not upgraded. Need to get 187 kB of archives. After this operation, 666 kB of additional disk space will be used. 0% [Working] Get:1 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/universe amd64 libiomp5 amd64 0.20131209-1 [187 kB] 6% [1 libiomp5 13.6 kB/187 kB 7%] 100% [Working] Fetched 187 kB in 0s (18.3 MB/s) Selecting previously unselected package libiomp5. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 99068 files and directories currently installed.) Preparing to unpack .../libiomp5_0.20131209-1_amd64.deb ... Unpacking libiomp5 (0.20131209-1) ... Setting up libiomp5 (0.20131209-1) ... travis_time:end:26bddad7:start=1508642413270956327,finish=1508642414632865759,duration=1361909432 travis_fold:end:before_install.6 travis_fold:start:before_install.7 travis_time:start:3535fdca $ wget -O antsr_travis.sh http://bit.ly/antsr_travis_sh --2017-10-22 03:20:14-- http://bit.ly/antsr_travis_sh Resolving bit.ly (bit.ly)... 67.199.248.11, 67.199.248.10 Connecting to bit.ly (bit.ly)|67.199.248.11|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://gist.githubusercontent.com/muschellij2/183aca6ea4d326db549cdcc28e1ff395/raw/ [following] --2017-10-22 03:20:14-- https://gist.githubusercontent.com/muschellij2/183aca6ea4d326db549cdcc28e1ff395/raw/ Resolving gist.githubusercontent.com (gist.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ... Connecting to gist.githubusercontent.com (gist.githubusercontent.com)|151.101.0.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 817 [text/plain] Saving to: ‘antsr_travis.sh’ 0% [ ] 0 --.-K/s 100%[======================================>] 817 --.-K/s in 0s 2017-10-22 03:20:14 (160 MB/s) - ‘antsr_travis.sh’ saved [817/817] travis_time:end:3535fdca:start=1508642414637745207,finish=1508642414763317507,duration=125572300 travis_fold:end:before_install.7 travis_fold:start:before_install.8 travis_time:start:03d7aee2 $ chmod +x antsr_travis.sh travis_time:end:03d7aee2:start=1508642414768240560,finish=1508642414772774549,duration=4533989 travis_fold:end:before_install.8 travis_fold:start:before_install.9 travis_time:start:01db070e $ . ./antsr_travis.sh --2017-10-22 03:20:14-- http://bit.ly/travis_helpers Resolving bit.ly (bit.ly)... 67.199.248.11, 67.199.248.10 Connecting to bit.ly (bit.ly)|67.199.248.11|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://gist.githubusercontent.com/muschellij2/64f9104ccec09deb85d4928071b3c9e8/raw [following] --2017-10-22 03:20:14-- https://gist.githubusercontent.com/muschellij2/64f9104ccec09deb85d4928071b3c9e8/raw Resolving gist.githubusercontent.com (gist.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ... Connecting to gist.githubusercontent.com (gist.githubusercontent.com)|151.101.0.133|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 12484 (12K) [text/plain] Saving to: ‘travis_helpers.sh’ 0% [ ] 0 --.-K/s 100%[======================================>] 12,484 --.-K/s in 0.001s 2017-10-22 03:20:14 (15.6 MB/s) - ‘travis_helpers.sh’ saved [12484/12484] R version 3.4.2 (2017-01-27) -- "Short Summer" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/. CI is true Inside a CI service Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) also installing the dependencies ‘mime’, ‘curl’, ‘openssl’, ‘R6’, ‘httr’, ‘memoise’, ‘whisker’, ‘digest’, ‘rstudioapi’, ‘jsonlite’, ‘git2r’, ‘withr’ trying URL 'http://cran.rstudio.com/src/contrib/mime_0.5.tar.gz' Content type 'application/x-gzip' length 12634 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'http://cran.rstudio.com/src/contrib/curl_3.0.tar.gz' Content type 'application/x-gzip' length 412212 bytes (402 KB) ================================================== downloaded 402 KB trying URL 'http://cran.rstudio.com/src/contrib/openssl_0.9.7.tar.gz' Content type 'application/x-gzip' length 1243577 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'http://cran.rstudio.com/src/contrib/R6_2.2.2.tar.gz' Content type 'application/x-gzip' length 322959 bytes (315 KB) ================================================== downloaded 315 KB trying URL 'http://cran.rstudio.com/src/contrib/httr_1.3.1.tar.gz' Content type 'application/x-gzip' length 147593 bytes (144 KB) ================================================== downloaded 144 KB trying URL 'http://cran.rstudio.com/src/contrib/memoise_1.1.0.tar.gz' Content type 'application/x-gzip' length 11025 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'http://cran.rstudio.com/src/contrib/whisker_0.3-2.tar.gz' Content type 'application/x-gzip' length 27707 bytes (27 KB) ================================================== downloaded 27 KB trying URL 'http://cran.rstudio.com/src/contrib/digest_0.6.12.tar.gz' Content type 'application/x-gzip' length 120337 bytes (117 KB) ================================================== downloaded 117 KB trying URL 'http://cran.rstudio.com/src/contrib/rstudioapi_0.7.tar.gz' Content type 'application/x-gzip' length 39845 bytes (38 KB) ================================================== downloaded 38 KB trying URL 'http://cran.rstudio.com/src/contrib/jsonlite_1.5.tar.gz' Content type 'application/x-gzip' length 1096810 bytes (1.0 MB) ================================================== downloaded 1.0 MB trying URL 'http://cran.rstudio.com/src/contrib/git2r_0.19.0.tar.gz' Content type 'application/x-gzip' length 1155950 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'http://cran.rstudio.com/src/contrib/withr_2.0.0.tar.gz' Content type 'application/x-gzip' length 16956 bytes (16 KB) ================================================== downloaded 16 KB trying URL 'http://cran.rstudio.com/src/contrib/devtools_1.13.3.tar.gz' Content type 'application/x-gzip' length 486402 bytes (475 KB) ================================================== downloaded 475 KB * installing *source* package ‘mime’ ... ** package ‘mime’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c rawmatch.c -o rawmatch.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o mime.so rawmatch.o -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/mime/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (mime) * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ** libs rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o utils.o version.o winidn.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c callbacks.c -o callbacks.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c curl.c -o curl.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c download.c -o download.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c escape.c -o escape.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c fetch.c -o fetch.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c form.c -o form.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c getdate.c -o getdate.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c handle.c -o handle.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c ieproxy.c -o ieproxy.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c interrupt.c -o interrupt.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c multi.c -o multi.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c nslookup.c -o nslookup.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c reflist.c -o reflist.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c split.c -o split.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c ssl.c -o ssl.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c utils.c -o utils.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c version.c -o version.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c winidn.c -o winidn.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o utils.o version.o winidn.o -lcurl -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/curl/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (curl) * installing *source* package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.1.0.0 -l:libcrypto.so.1.0.0 ** libs rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o openssl.so gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c aes.c -o aes.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c base64.c -o base64.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c bignum.c -o bignum.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c cert.c -o cert.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c compatibility.c -o compatibility.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c diffie.c -o diffie.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c envelope.c -o envelope.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c error.c -o error.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c hash.c -o hash.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c info.c -o info.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c keygen.c -o keygen.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c keys.c -o keys.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c onload.c -o onload.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c openssh.c -o openssh.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c password.c -o password.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c pem.c -o pem.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c pkcs12.c -o pkcs12.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c pkcs7.c -o pkcs7.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c rand.c -o rand.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c rsa.c -o rsa.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c signing.c -o signing.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c ssl.c -o ssl.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c stream.c -o stream.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c write.c -o write.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o -l:libssl.so.1.0.0 -l:libcrypto.so.1.0.0 -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/openssl/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (openssl) * installing *source* package ‘R6’ ... ** package ‘R6’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (R6) * installing *source* package ‘whisker’ ... ** package ‘whisker’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (whisker) * installing *source* package ‘digest’ ... ** package ‘digest’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c aes.c -o aes.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c crc32.c -o crc32.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c digest.c -o digest.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c md5.c -o md5.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c pmurhash.c -o pmurhash.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c raes.c -o raes.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c sha1.c -o sha1.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c sha2.c -o sha2.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c sha256.c -o sha256.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c xxhash.c -o xxhash.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/digest/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (digest) * installing *source* package ‘rstudioapi’ ... ** package ‘rstudioapi’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rstudioapi) * installing *source* package ‘jsonlite’ ... ** package ‘jsonlite’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c base64.c -o base64.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c collapse_array.c -o collapse_array.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c collapse_object.c -o collapse_object.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c collapse_pretty.c -o collapse_pretty.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c escape_chars.c -o escape_chars.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c integer64_to_na.c -o integer64_to_na.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c is_datelist.c -o is_datelist.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c is_recordlist.c -o is_recordlist.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c is_scalarlist.c -o is_scalarlist.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c modp_numtoa.c -o modp_numtoa.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c null_to_na.c -o null_to_na.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c num_to_char.c -o num_to_char.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c parse.c -o parse.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c prettify.c -o prettify.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c push_parser.c -o push_parser.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c r-base64.c -o r-base64.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c register.c -o register.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c row_collapse.c -o row_collapse.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c transpose_list.c -o transpose_list.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c validate.c -o validate.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl.c -o yajl/yajl.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl_buf.c -o yajl/yajl_buf.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl_encode.c -o yajl/yajl_encode.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl_gen.c -o yajl/yajl_gen.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl_lex.c -o yajl/yajl_lex.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl_parser.c -o yajl/yajl_parser.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iyajl/api -I/home/travis/R-bin/include -fpic -g -O2 -c yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -L. -lstatyajl -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/jsonlite/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (jsonlite) * installing *source* package ‘git2r’ ... ** package ‘git2r’ successfully unpacked and MD5 sums checked checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of void*... 8 checking for library containing inflate... -lz checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for libssl... yes checking for library containing EVP_EncryptInit... none required checking for library containing SSL_library_init... none required checking for library containing OPENSSL_init_ssl... no checking for library containing libssh2_version... -lssh2 checking for gawk... gawk checking for curl-config... /home/travis/R-bin/bin/curl-config checking for the version of libcurl... 7.43.0 checking whether libcurl is usable... yes checking for curl_free... yes checking for struct stat.st_mtim... yes checking for struct stat.st_mtimespec... no checking for struct stat.st_mtime_nsec... no checking for struct stat.st_mtim.tv_nsec... yes checking for futimens... yes checking for qsort_r... yes checking for qsort_s... no ----- Results of the git2r package configure ----- OpenSSL to talk over HTTPS...........: yes LibSSH2 to enable the SSH transport..: yes -------------------------------------------------- configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r.c -o git2r.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_arg.c -o git2r_arg.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_blame.c -o git2r_blame.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_blob.c -o git2r_blob.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_branch.c -o git2r_branch.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_checkout.c -o git2r_checkout.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_clone.c -o git2r_clone.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_commit.c -o git2r_commit.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_config.c -o git2r_config.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_cred.c -o git2r_cred.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_diff.c -o git2r_diff.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_error.c -o git2r_error.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_graph.c -o git2r_graph.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_index.c -o git2r_index.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_libgit2.c -o git2r_libgit2.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_merge.c -o git2r_merge.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_note.c -o git2r_note.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_object.c -o git2r_object.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_odb.c -o git2r_odb.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_oid.c -o git2r_oid.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_push.c -o git2r_push.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_reference.c -o git2r_reference.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_reflog.c -o git2r_reflog.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_remote.c -o git2r_remote.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_repository.c -o git2r_repository.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_reset.c -o git2r_reset.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_revparse.c -o git2r_revparse.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_revwalk.c -o git2r_revwalk.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_signature.c -o git2r_signature.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_stash.c -o git2r_stash.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_status.c -o git2r_status.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_tag.c -o git2r_tag.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_transfer.c -o git2r_transfer.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c git2r_tree.c -o git2r_tree.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/annotated_commit.c -o libgit2/src/annotated_commit.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/apply.c -o libgit2/src/apply.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/attr_file.c -o libgit2/src/attr_file.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/attr.c -o libgit2/src/attr.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/attrcache.c -o libgit2/src/attrcache.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/blame_git.c -o libgit2/src/blame_git.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/blame.c -o libgit2/src/blame.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/blob.c -o libgit2/src/blob.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/branch.c -o libgit2/src/branch.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/buf_text.c -o libgit2/src/buf_text.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/buffer.c -o libgit2/src/buffer.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/cache.c -o libgit2/src/cache.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/checkout.c -o libgit2/src/checkout.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/cherrypick.c -o libgit2/src/cherrypick.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/clone.c -o libgit2/src/clone.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/commit_list.c -o libgit2/src/commit_list.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/commit.c -o libgit2/src/commit.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/config_cache.c -o libgit2/src/config_cache.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/config_file.c -o libgit2/src/config_file.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/config.c -o libgit2/src/config.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/crlf.c -o libgit2/src/crlf.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/curl_stream.c -o libgit2/src/curl_stream.o In file included from /home/travis/R-bin/include/curl/curl.h:2363:0, from libgit2/src/curl_stream.c:10: libgit2/src/curl_stream.c: In function ‘curls_certificate’: /home/travis/R-bin/include/curl/typecheck-gcc.h:126:42: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] _curl_easy_getinfo_err_curl_slist(); \ ^ libgit2/src/curl_stream.c:157:13: note: in expansion of macro ‘curl_easy_getinfo’ if ((res = curl_easy_getinfo(s->handle, CURLINFO_CERTINFO, &certinfo)) != CURLE_OK) ^ gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/date.c -o libgit2/src/date.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/delta.c -o libgit2/src/delta.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/describe.c -o libgit2/src/describe.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_driver.c -o libgit2/src/diff_driver.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_file.c -o libgit2/src/diff_file.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_generate.c -o libgit2/src/diff_generate.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_parse.c -o libgit2/src/diff_parse.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_print.c -o libgit2/src/diff_print.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_stats.c -o libgit2/src/diff_stats.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_tform.c -o libgit2/src/diff_tform.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff_xdiff.c -o libgit2/src/diff_xdiff.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/diff.c -o libgit2/src/diff.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/errors.c -o libgit2/src/errors.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/fetch.c -o libgit2/src/fetch.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/fetchhead.c -o libgit2/src/fetchhead.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/filebuf.c -o libgit2/src/filebuf.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/fileops.c -o libgit2/src/fileops.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/filter.c -o libgit2/src/filter.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/fnmatch.c -o libgit2/src/fnmatch.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/global.c -o libgit2/src/global.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/graph.c -o libgit2/src/graph.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/hash.c -o libgit2/src/hash.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/hashsig.c -o libgit2/src/hashsig.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/ident.c -o libgit2/src/ident.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/idxmap.c -o libgit2/src/idxmap.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/ignore.c -o libgit2/src/ignore.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/index.c -o libgit2/src/index.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/indexer.c -o libgit2/src/indexer.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/iterator.c -o libgit2/src/iterator.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/merge_driver.c -o libgit2/src/merge_driver.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/merge_file.c -o libgit2/src/merge_file.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/merge.c -o libgit2/src/merge.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/message.c -o libgit2/src/message.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/mwindow.c -o libgit2/src/mwindow.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/netops.c -o libgit2/src/netops.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/notes.c -o libgit2/src/notes.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/object_api.c -o libgit2/src/object_api.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/object.c -o libgit2/src/object.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/odb_loose.c -o libgit2/src/odb_loose.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/odb_mempack.c -o libgit2/src/odb_mempack.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/odb_pack.c -o libgit2/src/odb_pack.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/odb.c -o libgit2/src/odb.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/offmap.c -o libgit2/src/offmap.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/oid.c -o libgit2/src/oid.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/oidarray.c -o libgit2/src/oidarray.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/oidmap.c -o libgit2/src/oidmap.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/openssl_stream.c -o libgit2/src/openssl_stream.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/pack-objects.c -o libgit2/src/pack-objects.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/pack.c -o libgit2/src/pack.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/patch_generate.c -o libgit2/src/patch_generate.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/patch_parse.c -o libgit2/src/patch_parse.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/patch.c -o libgit2/src/patch.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/path.c -o libgit2/src/path.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/pathspec.c -o libgit2/src/pathspec.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/pool.c -o libgit2/src/pool.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/posix.c -o libgit2/src/posix.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/pqueue.c -o libgit2/src/pqueue.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/proxy.c -o libgit2/src/proxy.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/push.c -o libgit2/src/push.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/rebase.c -o libgit2/src/rebase.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/refdb_fs.c -o libgit2/src/refdb_fs.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/refdb.c -o libgit2/src/refdb.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/reflog.c -o libgit2/src/reflog.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/refs.c -o libgit2/src/refs.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/refspec.c -o libgit2/src/refspec.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/remote.c -o libgit2/src/remote.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/repository.c -o libgit2/src/repository.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/reset.c -o libgit2/src/reset.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/revert.c -o libgit2/src/revert.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/revparse.c -o libgit2/src/revparse.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/revwalk.c -o libgit2/src/revwalk.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/settings.c -o libgit2/src/settings.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/sha1_lookup.c -o libgit2/src/sha1_lookup.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/signature.c -o libgit2/src/signature.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/socket_stream.c -o libgit2/src/socket_stream.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/sortedcache.c -o libgit2/src/sortedcache.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/stash.c -o libgit2/src/stash.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/status.c -o libgit2/src/status.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/strmap.c -o libgit2/src/strmap.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/submodule.c -o libgit2/src/submodule.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/sysdir.c -o libgit2/src/sysdir.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/tag.c -o libgit2/src/tag.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/thread-utils.c -o libgit2/src/thread-utils.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/tls_stream.c -o libgit2/src/tls_stream.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/trace.c -o libgit2/src/trace.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transaction.c -o libgit2/src/transaction.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transport.c -o libgit2/src/transport.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/tree-cache.c -o libgit2/src/tree-cache.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/tree.c -o libgit2/src/tree.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/tsort.c -o libgit2/src/tsort.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/util.c -o libgit2/src/util.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/varint.c -o libgit2/src/varint.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/vector.c -o libgit2/src/vector.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/worktree.c -o libgit2/src/worktree.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/zstream.c -o libgit2/src/zstream.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/auth.c -o libgit2/src/transports/auth.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/cred_helpers.c -o libgit2/src/transports/cred_helpers.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/cred.c -o libgit2/src/transports/cred.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/git.c -o libgit2/src/transports/git.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/http.c -o libgit2/src/transports/http.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/local.c -o libgit2/src/transports/local.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/smart_pkt.c -o libgit2/src/transports/smart_pkt.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/smart_protocol.c -o libgit2/src/transports/smart_protocol.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/smart.c -o libgit2/src/transports/smart.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/transports/ssh.c -o libgit2/src/transports/ssh.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/unix/map.c -o libgit2/src/unix/map.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/unix/realpath.c -o libgit2/src/unix/realpath.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/xdiff/xdiffi.c -o libgit2/src/xdiff/xdiffi.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/xdiff/xemit.c -o libgit2/src/xdiff/xemit.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/xdiff/xhistogram.c -o libgit2/src/xdiff/xhistogram.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/xdiff/xmerge.c -o libgit2/src/xdiff/xmerge.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/xdiff/xpatience.c -o libgit2/src/xdiff/xpatience.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/xdiff/xprepare.c -o libgit2/src/xdiff/xprepare.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/src/xdiff/xutils.c -o libgit2/src/xdiff/xutils.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser -I/home/travis/R-bin/include -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DGIT_OPENSSL -DGIT_SHA1_OPENSSL -DGIT_SSH -DGIT_CURL -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -I/home/travis/R-bin/include -I/home/travis/R-bin/include -fpic -g -O2 -c libgit2/deps/http-parser/http_parser.c -o libgit2/deps/http-parser/http_parser.o ar rcs libmygit.a libgit2/src/annotated_commit.o libgit2/src/apply.o libgit2/src/attr_file.o libgit2/src/attr.o libgit2/src/attrcache.o libgit2/src/blame_git.o libgit2/src/blame.o libgit2/src/blob.o libgit2/src/branch.o libgit2/src/buf_text.o libgit2/src/buffer.o libgit2/src/cache.o libgit2/src/checkout.o libgit2/src/cherrypick.o libgit2/src/clone.o libgit2/src/commit_list.o libgit2/src/commit.o libgit2/src/config_cache.o libgit2/src/config_file.o libgit2/src/config.o libgit2/src/crlf.o libgit2/src/curl_stream.o libgit2/src/date.o libgit2/src/delta.o libgit2/src/describe.o libgit2/src/diff_driver.o libgit2/src/diff_file.o libgit2/src/diff_generate.o libgit2/src/diff_parse.o libgit2/src/diff_print.o libgit2/src/diff_stats.o libgit2/src/diff_tform.o libgit2/src/diff_xdiff.o libgit2/src/diff.o libgit2/src/errors.o libgit2/src/fetch.o libgit2/src/fetchhead.o libgit2/src/filebuf.o libgit2/src/fileops.o libgit2/src/filter.o libgit2/src/fnmatch.o libgit2/src/global.o libgit2/src/graph.o libgit2/src/hash.o libgit2/src/hashsig.o libgit2/src/ident.o libgit2/src/idxmap.o libgit2/src/ignore.o libgit2/src/index.o libgit2/src/indexer.o libgit2/src/iterator.o libgit2/src/merge_driver.o libgit2/src/merge_file.o libgit2/src/merge.o libgit2/src/message.o libgit2/src/mwindow.o libgit2/src/netops.o libgit2/src/notes.o libgit2/src/object_api.o libgit2/src/object.o libgit2/src/odb_loose.o libgit2/src/odb_mempack.o libgit2/src/odb_pack.o libgit2/src/odb.o libgit2/src/offmap.o libgit2/src/oid.o libgit2/src/oidarray.o libgit2/src/oidmap.o libgit2/src/openssl_stream.o libgit2/src/pack-objects.o libgit2/src/pack.o libgit2/src/patch_generate.o libgit2/src/patch_parse.o libgit2/src/patch.o libgit2/src/path.o libgit2/src/pathspec.o libgit2/src/pool.o libgit2/src/posix.o libgit2/src/pqueue.o libgit2/src/proxy.o libgit2/src/push.o libgit2/src/rebase.o libgit2/src/refdb_fs.o libgit2/src/refdb.o libgit2/src/reflog.o libgit2/src/refs.o libgit2/src/refspec.o libgit2/src/remote.o libgit2/src/repository.o libgit2/src/reset.o libgit2/src/revert.o libgit2/src/revparse.o libgit2/src/revwalk.o libgit2/src/settings.o libgit2/src/sha1_lookup.o libgit2/src/signature.o libgit2/src/socket_stream.o libgit2/src/sortedcache.o libgit2/src/stash.o libgit2/src/status.o libgit2/src/strmap.o libgit2/src/submodule.o libgit2/src/sysdir.o libgit2/src/tag.o libgit2/src/thread-utils.o libgit2/src/tls_stream.o libgit2/src/trace.o libgit2/src/transaction.o libgit2/src/transport.o libgit2/src/tree-cache.o libgit2/src/tree.o libgit2/src/tsort.o libgit2/src/util.o libgit2/src/varint.o libgit2/src/vector.o libgit2/src/worktree.o libgit2/src/zstream.o libgit2/src/transports/auth.o libgit2/src/transports/cred_helpers.o libgit2/src/transports/cred.o libgit2/src/transports/git.o libgit2/src/transports/http.o libgit2/src/transports/local.o libgit2/src/transports/smart_pkt.o libgit2/src/transports/smart_protocol.o libgit2/src/transports/smart.o libgit2/src/transports/ssh.o libgit2/src/unix/map.o libgit2/src/unix/realpath.o libgit2/src/xdiff/xdiffi.o libgit2/src/xdiff/xemit.o libgit2/src/xdiff/xhistogram.o libgit2/src/xdiff/xmerge.o libgit2/src/xdiff/xpatience.o libgit2/src/xdiff/xprepare.o libgit2/src/xdiff/xutils.o libgit2/deps/http-parser/http_parser.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o git2r.so git2r.o git2r_arg.o git2r_blame.o git2r_blob.o git2r_branch.o git2r_checkout.o git2r_clone.o git2r_commit.o git2r_config.o git2r_cred.o git2r_diff.o git2r_error.o git2r_graph.o git2r_index.o git2r_libgit2.o git2r_merge.o git2r_note.o git2r_object.o git2r_odb.o git2r_oid.o git2r_push.o git2r_reference.o git2r_reflog.o git2r_remote.o git2r_repository.o git2r_reset.o git2r_revparse.o git2r_revwalk.o git2r_signature.o git2r_stash.o git2r_status.o git2r_tag.o git2r_transfer.o git2r_tree.o -L. -lmygit -lssh2 -lssl -lcrypto -lz -L/home/travis/R-bin/lib -lcurl -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/git2r/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (git2r) * installing *source* package ‘withr’ ... ** package ‘withr’ successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (withr) * installing *source* package ‘httr’ ... ** package ‘httr’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (httr) * installing *source* package ‘memoise’ ... ** package ‘memoise’ successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (memoise) * installing *source* package ‘devtools’ ... ** package ‘devtools’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (devtools) The downloaded source packages are in ‘/tmp/Rtmp4VJifZ/downloaded_packages’ Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT` Downloading GitHub repo muschellij2/ghtravis@master from URL https://api.github.com/repos/muschellij2/ghtravis/zipball/master Installing ghtravis Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT` trying URL 'https://cloud.r-project.org/src/contrib/yaml_2.1.14.tar.gz' Content type 'application/x-gzip' length 81095 bytes (79 KB) ================================================== downloaded 79 KB Installing yaml '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp7FkEW3/devtools34c734e6bbce/yaml' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘yaml’ ... ** package ‘yaml’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c api.c -o api.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c dumper.c -o dumper.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c emitter.c -o emitter.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c implicit.c -o implicit.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c loader.c -o loader.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c parser.c -o parser.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c r-ext.c -o r-ext.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c reader.c -o reader.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c scanner.c -o scanner.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c writer.c -o writer.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r-ext.o reader.o scanner.o writer.o -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/yaml/libs ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (yaml) Downloading GitHub repo muschellij2/desc@master from URL https://api.github.com/repos/muschellij2/desc/zipball/master Installing desc trying URL 'https://cloud.r-project.org/src/contrib/assertthat_0.2.0.tar.gz' Content type 'application/x-gzip' length 11612 bytes (11 KB) ================================================== downloaded 11 KB Installing assertthat '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp7FkEW3/devtools34c77d9e2436/assertthat' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘assertthat’ ... ** package ‘assertthat’ successfully unpacked and MD5 sums checked ** R ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (assertthat) trying URL 'https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz' Content type 'application/x-gzip' length 658694 bytes (643 KB) ================================================== downloaded 643 KB Installing crayon '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp7FkEW3/devtools34c753e7c565/crayon' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘crayon’ ... ** package ‘crayon’ successfully unpacked and MD5 sums checked ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (crayon) trying URL 'https://cloud.r-project.org/src/contrib/rprojroot_1.2.tar.gz' Content type 'application/x-gzip' length 42063 bytes (41 KB) ================================================== downloaded 41 KB Installing rprojroot trying URL 'https://cloud.r-project.org/src/contrib/backports_1.1.1.tar.gz' Content type 'application/x-gzip' length 10090 bytes ================================================== downloaded 10090 bytes Installing backports '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp7FkEW3/devtools34c76740205f/backports' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘backports’ ... ** package ‘backports’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c dotsElt.c -o dotsElt.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c dotsLength.c -o dotsLength.o gcc -std=gnu99 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o backports.so dotsElt.o dotsLength.o init.o -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/backports/libs ** R ** tests ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (backports) '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp7FkEW3/devtools34c750526c83/rprojroot' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘rprojroot’ ... ** package ‘rprojroot’ successfully unpacked and MD5 sums checked ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rprojroot) '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp7FkEW3/devtools34c721c18c24/muschellij2-desc-d35a9db' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘desc’ ... ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (desc) '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp7FkEW3/devtools34c71e8c37b6/muschellij2-ghtravis-7829289' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘ghtravis’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (ghtravis) Using bundled GitHub PAT. Please add your own PAT to the env var `GITHUB_PAT` ghtravis version 0.8.5#!/bin/bash # https://gist.github.com/muschellij2/64f9104ccec09deb85d4928071b3c9e8 export cran_set='options(repos = "http://cran.rstudio.com"); ' # we may be able to change to remotes export ig_package=devtools export devtools_source='library(ghtravis); ' export devtools_source=${devtools_source}' '${cran_set} R --version install_gh() { str=${ig_package}'::install_github("' str=${str}"${1}" str=${str}'");' Rscript -e "${str}" } install_gh_no_dep() { str=${ig_package}'::install_github("' str=${str}"${1}" str=${str}'", upgrade_dependencies = FALSE);' Rscript -e "${str}" } r_install_if_missing() { str=${cran_set} str=${str}'if (!requireNamespace("'${1}'", ' str=${str}'quietly = TRUE))' str=${str}'install.packages("'${1}'")' Rscript -e "${str}" } if [[ -n "${CI}" ]]; then echo "CI is ${CI}" echo "Inside a CI service" fi # installing devtools r_install_if_missing ${ig_package} # x=`Rscript -e 'res=!requireNamespace("ghtravis"); cat(res*1)'` # if [ ${x} -eq 1 ] # then if [[ -n "${CI}" ]]; then install_gh_no_dep muschellij2/ghtravis fi # fi str='packageVersion(pkg = "ghtravis")' str='as.character('${str}')' str='c("ghtravis version", '${str}')' str='cat('${str}', sep=" ")' Rscript --vanilla -e "${str}" # wget to tempdir, source, then remove file wget_remove() { tfile=`tempfile` wget -O ${tfile} ${1} source ${tfile} rm ${tfile} } install_missing_remote_deps() { packs="\"${1}\"" shift for i in $@ do packs="${packs}, \"${i}\"" done packs="c(${packs})" echo "Installing repos ${packs}" str=${devtools_source} str=${str}'packs = install_missing_remote_deps(' str=${str}'remotes = '"${packs}"', ' str=${str}'dependencies = c("Imports", "Depends"));' Rscript -e "${str}" } # get filename extension get_ext() { file=`basename ${1}` ext=`echo "${file}" | awk -F . '{print $NF}'` if [ "$ext" == "gz" ] then ext=tar.gz fi echo "$ext" } # make temporary file with extension # of file passed in temp_with_ext() { ext=`get_ext ${1}` tfile=`tempfile` echo "${tfile}.${ext}" } # wget the tarball # then install wget_r_install() { tfile=`temp_with_ext ${1}` echo "Installing ${1}" wget -O ${tfile} ${1} &> /dev/null; # shift so install args can be passed shift R CMD INSTALL ${tfile} $* } # change .travis.yml to deploy with API key deploy_travis() { api_key="${1}" if [[ -n "${api_key}" ]]; then api_key=${DEPLOY_KEY} fi str=${devtools_source} str=${str}'deploy_travis(api_key = c("'${api_key}'"));' Rscript -e "${str}" } # args deployed_tarball package user tag [version optional] # deployed_tarball ITKR stnava latest # args deployed_tarball package user tag [version optional] deployed_tarball() { str=${devtools_source} str=${str}'res = deployed_tarball(' str=${str}' user="'${2}'"' str=${str}', package="'${1}'"' str=${str}', tag="'${3}'"' str=${str}', version="'${4}'"' str=${str}');' echo "${str}" >&2 res=`Rscript --vanilla -e "${str} cat(res)"` echo "$res" } # Binary install Package gh_binary_install() { packs="\"${1}\"" shift for i in $@ do packs="${packs}, \"${i}\"" done packs="c(${packs})" echo "Installing repos ${packs}" str=${devtools_source} str=${str}'install_remote_binaries(' str=${str}'remotes = '"${packs}"'); ' Rscript -e "${str}" } # gh_binary_install() { # package=${1} # version=${3} # str=${devtools_source} # str=${str}'res = set_update_var(version = "'${version}'",' # str=${str}'package = "'${package}'"); cat(res)' # update_package=`Rscript -e "${str}"` # echo "Update Variable for ${package} is: ${update_package}" # tarball=`deployed_tarball $*` # echo "${package} tarball is ${tarball}" # wget_r_install $tarball # drop_remote $package # } remote_binary_install() { packs="\"${1}\"" shift for i in $@ do packs="${packs}, \"${i}\"" done if [[ -n "${packs}" ]]; then echo "Installing ${packs}" else echo "Installing all package binaries in Remotes" fi packs="c(${packs})" str=${devtools_source} str=${str}'install_remote_binaries(' str=${str}'package = '"${packs}"'); ' Rscript -e "${str}" } drop_remote() { str=${devtools_source} packs="\"${1}\"" shift for i in $@ do packs="${packs}, \"${i}\"" done packs="c(${packs})" str=${str}' drop_remotes(drop_remotes = '"${packs}"');' Rscript -e "${str}" } install_remotes_no_dep() { packs="\"${1}\"" shift for i in $@ do packs="${packs}, \"${i}\"" done packs="c(${packs})" str=${devtools_source} str=${str}'install_remotes_no_dep(package = '"${packs}"');' Rscript -e "${str}" } install_nodep_and_drop() { install_remotes_no_dep ${1} drop_remote ${1} } install_build_with_tag() { # delete so no overwrite of linux build if [ "$TRAVIS_OS_NAME" = "osx" ]; then rm -f *.tar.gz fi packname=`Rscript -e 'cat(read.dcf("DESCRIPTION")[, "Package"])'` cd ../; if [ ${#TRAVIS_TAG} -gt 0 ]; then R CMD INSTALL --debug --build ${packname} ; fi; } install_build() { packname=`Rscript -e 'cat(read.dcf("DESCRIPTION")[, "Package"])'` cd ../ travis_wait 100 R CMD INSTALL --build ${packname} } cmake_setup() { # cmake_url=https://cmake.org/files/ # v${cmake_version}/cmake-${cmake_version}.0 cmake_url="https://muschellij2.github.io" cmake_url=${cmake_url}"/cmake_versions/" cmake_url=${cmake_url}"cmake-${cmake_version}.0" if [ "$TRAVIS_OS_NAME" = "linux" ]; then cmake_opts="--no-check-certificate" cmake_system="Linux" cmake_url=${cmake_url}-${cmake_system}-x86_64.sh # making so no output { wget -O cmake.sh ${cmake_opts} ${cmake_url} ; sh cmake.sh --skip-license --prefix=${HOME} ; rm cmake.sh ; } &> /dev/null; export PATH=${HOME}/bin:$PATH ; echo "export PATH=${HOME}/bin:$PATH ;" fi if [ "$TRAVIS_OS_NAME" = "osx" ]; then run_dir=$PWD ; cd ~/ ; cmake_opts="" ; cmake_system="Darwin" ; cmake_url=${cmake_url}-${cmake_system}-x86_64.tar.gz ; # making so no output { wget -O cmake.tar.gz ${cmake_opts} ${cmake_url}; tar -xf cmake.tar.gz &> /dev/null ; cmake_dir=`basename ${cmake_url}` ; cmake_dir=`echo $cmake_dir | awk '{ gsub(/.tar.gz/,""); print }'` ; cmake_dir=${PWD}/${cmake_dir}/CMake.app/Contents ; export PATH=${cmake_dir}/bin:$PATH ; } &> /dev/null echo "export PATH=${cmake_dir}/bin:$PATH ;" rm cmake.tar.gz ; cd ${run_dir} ; fi } export_clang_cxx() { echo "export CC=clang ;" echo "export CXX=clang++ ;" echo "export CXX1X=clang++ ;" echo "export CXX1XSTD=-std=c++11 ;" echo "export CXX11=clang++ ;" } clang_cxx() { mkdir -p ~/.R x=`clang --version` echo "clang --version returns: ${x}" x=`clang++ --version` echo "clang++ --version returns: ${x}" x=`export_clang_cxx`; eval ${x}; CCACHER="" if [[ -n "${CCACHE}" ]]; then CCACHER="\$(CCACHE) " echo "CCACHE=${CCACHE}" >> ~/.R/Makevars fi echo "CC=${CCACHER}${CC}" >> ~/.R/Makevars echo "CXX=${CCACHER}${CXX}" >> ~/.R/Makevars echo "CXX1X=${CCACHER}${CXX1X}" >> ~/.R/Makevars echo "CXX1XSTD=${CXX1XSTD}" >> ~/.R/Makevars echo "CXX11=${CCACHER}${CXX11}" >> ~/.R/Makevars # clang doesn't do well with openmp # if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then # echo "SHLIB_OPENMP_CXXFLAGS=" >> ~/.R/Makevars; # fi } cat_desc_elements(){ if [[ -n "${1}" ]]; then str='ghtravis::cat_desc_elements("'${1}'")' else str='ghtravis::cat_desc_elements()' fi pkg=`Rscript --vanilla -e "${str}"` echo "$pkg" } cat_desc_elements_remote(){ str='ghtravis::cat_desc_elements_remote(repo = "'${1}'")' pkg=`Rscript --vanilla -e "${str}"` echo "$pkg" } package_name(){ str='x=ghtravis::read_dcf("DESCRIPTION")$dcf;' str=${str}'cat(x$Package);' pkg=`Rscript --vanilla -e "${str}"` echo $pkg } package_version(){ str='x=ghtravis::read_dcf("DESCRIPTION")$dcf;' str=${str}'cat(x$Version);' pkg=`Rscript --vanilla -e "${str}"` echo $pkg } tarball_name(){ str='x=ghtravis::read_dcf("DESCRIPTION")$dcf;' str=${str}'x=paste0(x$Package, "_", ' str=${str}'x$Version, ".tar.gz");' str=${str}'cat(x);' tarball=`Rscript --vanilla -e "${str}"` echo $tarball } remove_neuroc_packages() { # so only does it if it's in a CI - just in case if [[ -z "${CI}" ]]; then echo "Not in CI - must run remove_neuroc_packages_force"; exit 1; fi remove_neuroc_packages_force $@ } # remove_neuroc_packages_force table_path USER # if table_path is empty, then will use default users remove_neuroc_packages_force() { install_gh muschellij2/neuroc.deps str='packageVersion(pkg = "neuroc.deps")' str='as.character('${str}')' str='c("neuroc.deps version", '${str}')' str='cat('${str}', sep=" ")' Rscript --vanilla -e "${str}" table_path="${1}" user="${2}" if [[ -z "${user}" ]]; then if [[ -n "${PROJECT_NAME}" ]] then user="${PROJECT_NAME}" else user="neuroconductor" fi fi fcn="neuroc.deps::remove_neuroc_packages" if [[ -z "${table_path}" ]]; then str=${fcn}'(user = "'${user}'");' else str=${fcn}'(table_path = "'${table_path}'");' fi Rscript -e "${str}" } remove_package() { packs="\"${1}\"" shift for i in $@ do packs="${packs}, \"${i}\"" done packs="c(${packs})" echo "Removing packages: ${packs}" str='packs = '"${packs}"';' str=${str}'check = packs %in% utils::installed.packages();' str=${str}' if (any(check)) utils::remove.packages(packs[check]);' Rscript -e "${str}" } jags_install() { # if [[ "${TRAVIS_OS_NAME}" = "linux" ]]; # then wget -O jags.tar.gz https://ayera.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Source/JAGS-4.3.0.tar.gz jags_dir=`tar -tf jags.tar.gz | head -n 1` tar -xvf jags.tar.gz rm jags.tar.gz cd ${jags_dir} prefix=/usr ; if [[ "${TRAVIS_OS_NAME}" = "osx" ]]; then prefix=/usr/local ; fi ./configure --prefix=${prefix} && sudo make && sudo make install cd ../ sudo rm -rf ${jags_dir} # else # brew install jags; # fi } fftw_install() { # if [[ "${TRAVIS_OS_NAME}" = "linux" ]]; # then # sudo apt-get install -y libfftw3-dev ; # apt-get install -y libfftw3-dev ; # fi if [[ "${TRAVIS_OS_NAME}" = "osx" ]]; then brew install -y fftw ; fi } gsl_install() { if [[ "${TRAVIS_OS_NAME}" = "osx" ]]; then brew install -y gsl ; fi } ffmpeg_install() { if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then sudo apt-get -qq update ; sudo apt-get install -y software-properties-common ; sudo add-apt-repository -y ppa:mc3man/trusty-media ; sudo apt-get -qq update ; sudo apt-get install -y ffmpeg ; fi if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then brew install -y ffmpeg imagemagick; fi } check_fail() { str="message(devtools::check_failures(path = '" ; str=${str}"${RCHECK_DIR}" ; str=${str}"'))" ; Rscript -e "${str}" } check_warnings() { grep -q -R "WARNING" "${RCHECK_DIR}/00check.log" ; if [[ $? -eq 0 ]]; then exit 1; fi } install_deps() { deps="${1}" if [[ -z "${CI}" ]]; then deps="TRUE"; fi str='deps <- devtools::dev_package_deps(dependencies = ' str=${str}"${deps});" str=${str}'devtools::install_deps(dependencies = ' str=${str}"${deps});" str=${str}'if (!all(deps$package %in% installed.packages())) {' str=${str}' message("missing: ", paste(setdiff(deps$package, ' str=${str}'installed.packages()), collapse=", "));' str=${str}' q(status = 1, save = "no")' str=${str}'}' Rscript -e "${str}" } install_deps_no_suggests() { install_deps "NA" } no_open_mp() { if [ "$TRAVIS_OS_NAME" == "osx" ]; then mkdir -p ~/.R ; echo "SHLIB_OPENMP_CXXFLAGS = " >> ~/.R/Makevars ; echo "SHLIB_OPENMP_CFLAGS= " >> ~/.R/Makevars ; echo "SHLIB_OPENMP_CPPFLAGS = " >> ~/.R/Makevars ; fi } start_xvfb() { if [ "$TRAVIS_OS_NAME" == "osx" ]; then (sudo Xvfb :99 -ac -screen 0 1024x768x8; echo ok) & fi if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sh -e /etc/init.d/xvfb start ; fi } # if [ "$TRAVIS_OS_NAME" = "osx" ]; # then # brew install fftw # fi # "DEB": "libfftw3-dev", # 6 "OSX/brew": "fftw", # 7 "RPM": "fftw-devel"ANTSR_TRAVIS VERSION 0.4 cmake: /home/travis/R-bin/lib/libcurl.so.4: no version information available (required by cmake) cmake version 3.2.2 CMake suite maintained and supported by Kitware (kitware.com/cmake). export PATH=/home/travis/bin:/home/travis/bin:/home/travis/R-bin/bin:/home/travis/bin:/home/travis/.local/bin:/opt/pyenv/shims:/home/travis/.phpenv/shims:/home/travis/perl5/perlbrew/bin:/home/travis/.nvm/versions/node/v6.9.4/bin:/home/travis/.kiex/elixirs/elixir-1.3.2/bin:/home/travis/.kiex/bin:/home/travis/.rvm/gems/ruby-2.4.1/bin:/home/travis/.rvm/gems/ruby-2.4.1@global/bin:/home/travis/.rvm/rubies/ruby-2.4.1/bin:/home/travis/gopath/bin:/home/travis/.gimme/versions/go1.7.4.linux.amd64/bin:/usr/local/phantomjs/bin:/usr/local/phantomjs:/usr/local/neo4j-3.2.1/bin:/usr/local/clang-3.9.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/ghc/bin:/home/travis/.rvm/bin:/home/travis/.phpenv/bin:/opt/pyenv/bin ; cmake version 3.4.0 CMake suite maintained and supported by Kitware (kitware.com/cmake). clang --version returns: clang version 3.9.0 (tags/RELEASE_390/final) Target: x86_64-unknown-linux-gnu Thread model: posix InstalledDir: /usr/local/clang-3.9.0/bin clang++ --version returns: clang version 3.9.0 (tags/RELEASE_390/final) Target: x86_64-unknown-linux-gnu Thread model: posix InstalledDir: /usr/local/clang-3.9.0/bin Installing Missing Deps Installing repos c("stnava/ITKR", "stnava/ANTsRCore", "stnava/ANTsR") Repositories are given, overriding path name installed 1 Rcpp FALSE 4 RcppEigen FALSE 5 tools TRUE 6 magrittr FALSE 7 stats TRUE 8 utils TRUE 9 methods TRUE 10 graphics TRUE 11 grDevices TRUE 12 magic FALSE 14 psych FALSE 15 rsvd FALSE All installed dependencies are tools,stats,utils,methods,graphics,grDevices All missing dependencies are Rcpp,RcppEigen,magrittr,magic,psych,rsvd Installing packages into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) also installing the dependencies ‘abind’, ‘mnormt’ trying URL 'http://cran.rstudio.com/src/contrib/abind_1.4-5.tar.gz' Content type 'application/x-gzip' length 21810 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'http://cran.rstudio.com/src/contrib/mnormt_1.5-5.tar.gz' Content type 'application/x-gzip' length 37169 bytes (36 KB) ================================================== downloaded 36 KB trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.13.tar.gz' Content type 'application/x-gzip' length 3751669 bytes (3.6 MB) ================================================== downloaded 3.6 MB trying URL 'http://cran.rstudio.com/src/contrib/RcppEigen_0.3.3.3.0.tar.gz' Content type 'application/x-gzip' length 1634023 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'http://cran.rstudio.com/src/contrib/magrittr_1.5.tar.gz' Content type 'application/x-gzip' length 200504 bytes (195 KB) ================================================== downloaded 195 KB trying URL 'http://cran.rstudio.com/src/contrib/magic_1.5-6.tar.gz' Content type 'application/x-gzip' length 203897 bytes (199 KB) ================================================== downloaded 199 KB trying URL 'http://cran.rstudio.com/src/contrib/psych_1.7.8.tar.gz' Content type 'application/x-gzip' length 3311758 bytes (3.2 MB) ================================================== downloaded 3.2 MB trying URL 'http://cran.rstudio.com/src/contrib/rsvd_0.6.tar.gz' Content type 'application/x-gzip' length 1555349 bytes (1.5 MB) ================================================== downloaded 1.5 MB * installing *source* package ‘abind’ ... ** package ‘abind’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (abind) * installing *source* package ‘mnormt’ ... ** package ‘mnormt’ successfully unpacked and MD5 sums checked ** libs gfortran -fpic -g -O2 -c biv-nt.f -o biv-nt.o gfortran -fpic -g -O2 -c sadmvnt.f -o sadmvnt.o clang -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o mnormt.so biv-nt.o sadmvnt.o -lgfortran -lm -lquadmath -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/mnormt/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (mnormt) * installing *source* package ‘Rcpp’ ... ** package ‘Rcpp’ successfully unpacked and MD5 sums checked ** libs clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -c Date.cpp -o Date.o clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -c Module.cpp -o Module.o clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -c Rcpp_init.cpp -o Rcpp_init.o clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -c api.cpp -o api.o clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -c attributes.cpp -o attributes.o clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -c barrier.cpp -o barrier.o clang++ -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/Rcpp/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rcpp) * installing *source* package ‘magrittr’ ... ** package ‘magrittr’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (magrittr) * installing *source* package ‘rsvd’ ... ** package ‘rsvd’ successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (rsvd) * installing *source* package ‘RcppEigen’ ... ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked ** libs clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/home/travis/R-bin/include -I../inst/include -fpic -g -O2 -c RcppEigen.cpp -o RcppEigen.o clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/home/travis/R-bin/include -I../inst/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/home/travis/R-bin/include -I../inst/include -fpic -g -O2 -c fastLm.cpp -o fastLm.o clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/home/travis/R-bin/include -fpic -g -O2 -c init.c -o init.o clang++ -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o init.o -L/home/travis/R-bin/lib/R/lib -lRlapack -L/home/travis/R-bin/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RcppEigen/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RcppEigen) * installing *source* package ‘magic’ ... ** package ‘magic’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (magic) * installing *source* package ‘psych’ ... ** package ‘psych’ successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (psych) The downloaded source packages are in ‘/tmp/RtmpLMOHAP/downloaded_packages’ Done Installing Missing Deps Installing repos c("stnava/ITKR") [1] "stnava/ITKR" OK (HTTP 200).OK (HTTP 200).Table is tag_name zipball_url 7 latest https://api.github.com/repos/stnava/ITKR/zipball/latest 13 v0.4.12 https://api.github.com/repos/stnava/ITKR/zipball/v0.4.12 3 latest https://api.github.com/repos/stnava/ITKR/zipball/latest 5 latest https://api.github.com/repos/stnava/ITKR/zipball/latest 8 v0.0.0 https://api.github.com/repos/stnava/ITKR/zipball/v0.0.0 NA NA.1 NA.2 NA.3 NA.4 NA.5 NA.6 NA.7 tarball_url 7 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Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113 Connecting to github.com (github.com)|192.30.253.112|:443... connected. 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HTTP request sent, awaiting response... 200 OK Length: 22056409 (21M) [application/octet-stream] Saving to: ‘/tmp/RtmpXcGfnt/ITKR_0.4.12_R_x86_64-pc-linux-gnu.tar.gz’ 0% [ ] 0 --.-K/s 0% [ ] 181,812 823KB/s 2% [ ] 564,788 1.25MB/s 5% [=> ] 1,156,660 1.70MB/s 9% [==> ] 2,001,460 2.21MB/s 14% [====> ] 3,123,764 2.75MB/s 20% [=======> ] 4,620,852 3.40MB/s 29% [==========> ] 6,587,956 4.15MB/s 41% [===============> ] 9,129,524 5.03MB/s 56% [====================> ] 12,428,852 6.09MB/s 75% [============================> ] 16,662,833 7.34MB/s 100%[======================================>] 22,056,409 8.93MB/s in 2.4s 2017-10-22 03:23:39 (8.93 MB/s) - ‘/tmp/RtmpXcGfnt/ITKR_0.4.12_R_x86_64-pc-linux-gnu.tar.gz’ saved [22056409/22056409] Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) * installing *binary* package ‘ITKR’ ... * DONE (ITKR) Rewriting new remotes: stnava/ANTsR, stnava/ANTsRCore Installing repos c("stnava/ANTsRCore") [1] "stnava/ANTsRCore" OK (HTTP 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https://github.com/ANTsX/ANTsR/releases/download/latest/ANTsR_0.6_R_x86_64-pc-linux-gnu.tar.gz 2 https://github.com/ANTsX/ANTsR/releases/download/beta/ANTsR_0.4.0_R_x86_64-pc-linux-gnu.tar.gz 25 https://github.com/ANTsX/ANTsR/releases/download/v0.3/ANTsR_1.0_R_x86_64-pc-linux-gnu.tar.gz NA NA.1 NA.2 NA.3 NA.4 NA.5 NA.6 NA.7 NA.8 NA.9 NA.10 NA.11 NA.12 NA.13 NA.14 NA.15 NA.16 NA.17 NA.18 NA.19 NA.20 NA.21 NA.22 NA.23 Installing ANTsR package binaries --2017-10-22 03:24:36-- https://github.com/ANTsX/ANTsR/releases/download/test/ANTsR_0.6.1_R_x86_64-pc-linux-gnu.tar.gz Resolving github.com (github.com)... 192.30.253.113, 192.30.253.112 Connecting to github.com (github.com)|192.30.253.113|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/5782626/23fa6366-8685-11e7-9820-b5a9048cbd01?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20171022%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20171022T032436Z&X-Amz-Expires=300&X-Amz-Signature=29fe9e7f866da7853abc821540b570e264641e0e0c6525590776a46f529f0c73&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DANTsR_0.6.1_R_x86_64-pc-linux-gnu.tar.gz&response-content-type=application%2Foctet-stream [following] --2017-10-22 03:24:36-- https://github-production-release-asset-2e65be.s3.amazonaws.com/5782626/23fa6366-8685-11e7-9820-b5a9048cbd01?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20171022%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20171022T032436Z&X-Amz-Expires=300&X-Amz-Signature=29fe9e7f866da7853abc821540b570e264641e0e0c6525590776a46f529f0c73&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DANTsR_0.6.1_R_x86_64-pc-linux-gnu.tar.gz&response-content-type=application%2Foctet-stream Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.18.40 Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.18.40|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 28468211 (27M) [application/octet-stream] Saving to: ‘/tmp/RtmpIYYyoX/ANTsR_0.6.1_R_x86_64-pc-linux-gnu.tar.gz’ 0% [ ] 0 --.-K/s 0% [ ] 216,628 980KB/s 2% [ ] 634,420 1.40MB/s 4% [> ] 1,295,924 1.90MB/s 7% [==> ] 2,270,772 2.50MB/s 12% [===> ] 3,593,780 3.16MB/s 18% [======> ] 5,351,988 3.92MB/s 26% [=========> ] 7,667,252 4.81MB/s 37% [=============> ] 10,696,244 5.88MB/s 51% [===================> ] 14,741,698 7.20MB/s 70% [==========================> ] 20,164,987 8.86MB/s 97% [=====================================> ] 27,750,816 11.1MB/s 100%[======================================>] 28,468,211 11.3MB/s in 2.4s 2017-10-22 03:24:39 (11.3 MB/s) - ‘/tmp/RtmpIYYyoX/ANTsR_0.6.1_R_x86_64-pc-linux-gnu.tar.gz’ saved [28468211/28468211] Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) * installing *binary* package ‘ANTsR’ ... * DONE (ANTsR) Rewriting new remotes: Package: LESYMAP Title: Leions to Symptom Mapping in R Version: 0.0.0.9003 Date: 2017-06-07 Authors@R: person("Dorian", "Pustina", email='dorian.pustina@uphs.upenn.edu', role = c("aut", "cre")) Description: LESYMAP maps the specific brain areas responsible for cognitive deficits by taking a series of lesion maps and a vector of behavioral scores. Both univariate (t-test, Brunner-Munzel, regression) and multivariate (sparse canonical corelations) tests are available. LESYMAP is built to run both real and simulated lesion-to-symptom mapping analyses. License: Apache License 2.0 Encoding: UTF-8 LazyData: true Depends: R (>= 3.0), ANTsR Imports: ANTsRCore, graphics, lmPerm, nparcomp, Rcpp, stats, utils LinkingTo: Rcpp, RcppArmadillo NeedsCompilation: yes RoxygenNote: 6.0.1.9000 Reordering Remotes Remote order: NULL Package: LESYMAP Title: Leions to Symptom Mapping in R Version: 0.0.0.9003 Date: 2017-06-07 Authors@R: person("Dorian", "Pustina", email='dorian.pustina@uphs.upenn.edu', role = c("aut", "cre")) Description: LESYMAP maps the specific brain areas responsible for cognitive deficits by taking a series of lesion maps and a vector of behavioral scores. Both univariate (t-test, Brunner-Munzel, regression) and multivariate (sparse canonical corelations) tests are available. LESYMAP is built to run both real and simulated lesion-to-symptom mapping analyses. License: Apache License 2.0 Encoding: UTF-8 LazyData: true Depends: R (>= 3.0), ANTsR Imports: ANTsRCore, graphics, lmPerm, nparcomp, Rcpp, stats, utils LinkingTo: Rcpp, RcppArmadillo NeedsCompilation: yes RoxygenNote: 6.0.1.9000 travis_time:end:01db070e:start=1508642414777363639,finish=1508642685651528098,duration=270874164459 travis_fold:end:before_install.9 travis_fold:start:before_install.10 travis_time:start:08063436 $ rm antsr_travis.sh travis_time:end:08063436:start=1508642685662129192,finish=1508642685670845324,duration=8716132 travis_fold:end:before_install.10 travis_fold:start:before_install.11 travis_time:start:34db0cb6 $ cat DESCRIPTION Package: LESYMAP Title: Leions to Symptom Mapping in R Version: 0.0.0.9003 Date: 2017-06-07 Authors@R: person("Dorian", "Pustina", email='dorian.pustina@uphs.upenn.edu', role = c("aut", "cre")) Description: LESYMAP maps the specific brain areas responsible for cognitive deficits by taking a series of lesion maps and a vector of behavioral scores. Both univariate (t-test, Brunner-Munzel, regression) and multivariate (sparse canonical corelations) tests are available. LESYMAP is built to run both real and simulated lesion-to-symptom mapping analyses. License: Apache License 2.0 Encoding: UTF-8 LazyData: true Depends: R (>= 3.0), ANTsR Imports: ANTsRCore, graphics, lmPerm, nparcomp, Rcpp, stats, utils LinkingTo: Rcpp, RcppArmadillo NeedsCompilation: yes RoxygenNote: 6.0.1.9000 travis_time:end:34db0cb6:start=1508642685681446579,finish=1508642685689154431,duration=7707852 travis_fold:end:before_install.11 travis_fold:start:R-dependencies Installing package dependencies Installing *binary* R packages: devtools Installing apt packages: r-cran-devtools travis_time:start:0093b898 $ sudo apt-get install -y r-cran-devtools Reading package lists... 0% Reading package lists... 100% Reading package lists... Done Building dependency tree... 0% Building dependency tree... 0% Building dependency tree... 50% Building dependency tree... 50% Building dependency tree Reading state information... 0% Reading state information... 0% Reading state information... Done The following additional packages will be installed: curl libcurl3 libcurl4-openssl-dev libpaper-utils libpaper1 r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-curl r-cran-digest r-cran-foreign r-cran-git2r r-cran-httr r-cran-jsonlite r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-nnet r-cran-openssl r-cran-r6 r-cran-rpart r-cran-rstudioapi r-cran-spatial r-cran-survival r-cran-whisker r-cran-withr r-doc-html r-recommended Suggested packages: libcurl4-doc libcurl3-dbg ess r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra The following packages will be REMOVED: libcurl4-gnutls-dev The following NEW packages will be installed: libcurl4-openssl-dev libpaper-utils libpaper1 r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-curl r-cran-devtools r-cran-digest r-cran-foreign r-cran-git2r r-cran-httr r-cran-jsonlite r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-nnet r-cran-openssl r-cran-r6 r-cran-rpart r-cran-rstudioapi r-cran-spatial r-cran-survival r-cran-whisker r-cran-withr r-doc-html r-recommended The following packages will be upgraded: curl libcurl3 2 upgraded, 35 newly installed, 1 to remove and 93 not upgraded. Need to get 44.6 MB of archives. After this operation, 75.7 MB of additional disk space will be used. 0% [Working] Get:1 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 curl amd64 7.35.0-1ubuntu2.11 [123 kB] 0% [1 curl 8,046 B/123 kB 7%] [Connecting to ppa.launchpad.net (91.189.95.83)] 1% [Connecting to ppa.launchpad.net (91.189.95.83)] Get:2 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 libcurl3 amd64 7.35.0-1ubuntu2.11 [174 kB] 1% [2 libcurl3 7,168 B/174 kB 4%] [Connecting to ppa.launchpad.net (91.189.95.8 2% [Connecting to ppa.launchpad.net (91.189.95.83)] Get:3 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libpaper1 amd64 1.1.24+nmu2ubuntu3 [13.4 kB] 2% [3 libpaper1 13.4 kB/13.4 kB 100%] [Connecting to ppa.launchpad.net (91.189. 2% [Connecting to ppa.launchpad.net (91.189.95.83)] Get:4 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty-updates/main amd64 libcurl4-openssl-dev amd64 7.35.0-1ubuntu2.11 [245 kB] 2% [4 libcurl4-openssl-dev 8,192 B/245 kB 3%] [Connecting to ppa.launchpad.net 3% [Connecting to ppa.launchpad.net (91.189.95.83)] Get:5 http://us-central1.gce.archive.ubuntu.com/ubuntu trusty/main amd64 libpaper-utils amd64 1.1.24+nmu2ubuntu3 [8,244 B] 3% [5 libpaper-utils 8,244 B/8,244 B 100%] [Connecting to ppa.launchpad.net (91 4% [Connecting to ppa.launchpad.net (91.189.95.83)] Get:6 http://ppa.launchpad.net/marutter/c2d4u/ubuntu trusty/main amd64 r-cran-curl amd64 3.0-1cran1ppa0trusty0 [363 kB] 4% [6 r-cran-curl 7,472 B/363 kB 2%] Get:7 https://cloud.r-project.org/bin/linux/ubuntu trusty/ r-base-core 3.4.2-1trusty1 [23.1 MB] 4% [7 r-base-core 0 B/23.1 MB 0%] [6 r-cran-curl 12.6 kB/363 kB 3%] 23% [7 r-base-core 10.3 MB/23.1 MB 45%] Get:8 http://ppa.launchpad.net/marutter/c2d4u/ubuntu trusty/main amd64 r-cran-jsonlite amd64 1.5-1cran1ppa0trusty0 [582 kB] 34% [7 r-base-core 16.2 MB/23.1 MB 70%] [8 r-cran-jsonlite 1,032 B/582 kB 0%] 47% [8 r-cran-jsonlite 174 kB/582 kB 30%] Get:9 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http://ppa.launchpad.net/marutter/c2d4u/ubuntu trusty/main amd64 r-cran-mime amd64 0.5-1cran2ppa0trusty1 [25.5 kB] 60% [18 r-cran-mime 7,474 B/25.5 kB 29%] Get:19 https://cloud.r-project.org/bin/linux/ubuntu trusty/ r-cran-matrix 1.2-11-1trusty0 [2,375 kB] 60% [19 r-cran-matrix 0 B/2,375 kB 0%] [18 r-cran-mime 12.6 kB/25.5 kB 49%] 62% [19 r-cran-matrix 1,031 kB/2,375 kB 43%] [Connecting to ppa.launchpad.net ( 65% [Connecting to ppa.launchpad.net (91.189.95.83)] Get:20 https://cloud.r-project.org/bin/linux/ubuntu trusty/ r-cran-nlme 3.1.131-3trusty0 [2,197 kB] 65% [20 r-cran-nlme 7,240 B/2,197 kB 0%] [Connecting to ppa.launchpad.net (91.1 69% [Waiting for headers] Get:21 http://ppa.launchpad.net/marutter/c2d4u/ubuntu trusty/main amd64 r-cran-openssl amd64 0.9.7-1cran1ppa0trusty0 [516 kB] 69% [21 r-cran-openssl 7,472 B/516 kB 1%] Get:22 https://cloud.r-project.org/bin/linux/ubuntu trusty/ r-cran-mgcv 1.8-22-1cran1trusty0 [2,511 kB] 69% [22 r-cran-mgcv 0 B/2,511 kB 0%] [21 r-cran-openssl 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(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 99073 files and directories currently installed.) Removing libcurl4-gnutls-dev:amd64 (7.35.0-1ubuntu2.10) ... Processing triggers for man-db (2.6.7.1-1ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 99049 files and directories currently installed.) Preparing to unpack .../curl_7.35.0-1ubuntu2.11_amd64.deb ... Unpacking curl (7.35.0-1ubuntu2.11) over (7.35.0-1ubuntu2.10) ... Preparing to unpack .../libcurl3_7.35.0-1ubuntu2.11_amd64.deb ... Unpacking libcurl3:amd64 (7.35.0-1ubuntu2.11) over (7.35.0-1ubuntu2.10) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../libpaper1_1.1.24+nmu2ubuntu3_amd64.deb ... Unpacking libpaper1:amd64 (1.1.24+nmu2ubuntu3) ... Selecting previously unselected package libcurl4-openssl-dev:amd64. Preparing to unpack .../libcurl4-openssl-dev_7.35.0-1ubuntu2.11_amd64.deb ... Unpacking libcurl4-openssl-dev:amd64 (7.35.0-1ubuntu2.11) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../libpaper-utils_1.1.24+nmu2ubuntu3_amd64.deb ... Unpacking libpaper-utils (1.1.24+nmu2ubuntu3) ... Selecting previously unselected package r-base-core. Preparing to unpack .../r-base-core_3.4.2-1trusty1_amd64.deb ... Unpacking r-base-core (3.4.2-1trusty1) ... Selecting previously unselected package r-base-dev. Preparing to unpack .../r-base-dev_3.4.2-1trusty1_all.deb ... Unpacking r-base-dev (3.4.2-1trusty1) ... Selecting previously unselected package r-cran-boot. Preparing to unpack .../r-cran-boot_1.3-20-1trusty0_all.deb ... Unpacking r-cran-boot (1.3-20-1trusty0) ... Selecting previously unselected package r-cran-mass. Preparing to unpack .../r-cran-mass_7.3-47-1trusty0_amd64.deb ... Unpacking r-cran-mass (7.3-47-1trusty0) ... Selecting previously unselected package r-cran-class. Preparing to unpack .../r-cran-class_7.3-14-2trusty0_amd64.deb ... Unpacking r-cran-class (7.3-14-2trusty0) ... Selecting previously unselected package r-cran-cluster. Preparing to unpack .../r-cran-cluster_2.0.6-2trusty0_amd64.deb ... Unpacking r-cran-cluster (2.0.6-2trusty0) ... Selecting previously unselected package r-cran-codetools. Preparing to unpack .../r-cran-codetools_0.2-15-1cran1trusty0_all.deb ... Unpacking r-cran-codetools (0.2-15-1cran1trusty0) ... Selecting previously unselected package r-cran-curl. Preparing to unpack .../r-cran-curl_3.0-1cran1ppa0trusty0_amd64.deb ... Unpacking r-cran-curl (3.0-1cran1ppa0trusty0) ... Selecting previously unselected package r-cran-jsonlite. Preparing to unpack .../r-cran-jsonlite_1.5-1cran1ppa0trusty0_amd64.deb ... Unpacking r-cran-jsonlite (1.5-1cran1ppa0trusty0) ... 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Preparing to unpack .../r-cran-memoise_1.1.0-1cran1ppa0trusty0_all.deb ... Unpacking r-cran-memoise (1.1.0-1cran1ppa0trusty0) ... Selecting previously unselected package r-cran-whisker. Preparing to unpack .../r-cran-whisker_0.3-2-1cran1precise0_all.deb ... Unpacking r-cran-whisker (0.3-2-1cran1precise0) ... Selecting previously unselected package r-cran-rstudioapi. Preparing to unpack .../r-cran-rstudioapi_0.7-1cran1ppa0trusty0_all.deb ... Unpacking r-cran-rstudioapi (0.7-1cran1ppa0trusty0) ... Selecting previously unselected package r-cran-git2r. Preparing to unpack .../r-cran-git2r_0.19.0-1cran1ppa0trusty0_amd64.deb ... Unpacking r-cran-git2r (0.19.0-1cran1ppa0trusty0) ... Selecting previously unselected package r-cran-withr. Preparing to unpack .../r-cran-withr_2.0.0-1cran1ppa0trusty0_all.deb ... Unpacking r-cran-withr (2.0.0-1cran1ppa0trusty0) ... Selecting previously unselected package r-cran-devtools. Preparing to unpack .../r-cran-devtools_1.13.2-1cran1ppa0trusty0_all.deb ... 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Processing triggers for libc-bin (2.19-0ubuntu6.13) ... travis_time:end:0093b898:start=1508642685698380945,finish=1508642705842751619,duration=20144370674 travis_time:start:030e2cc0 $ Rscript -e 'deps <- devtools::dev_package_deps(dependencies = NA);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}' trying URL 'https://cloud.r-project.org/src/contrib/lmPerm_2.1.0.tar.gz' Content type 'application/x-gzip' length 417035 bytes (407 KB) ================================================== downloaded 407 KB Installing lmPerm '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpDiqijy/devtools41e6129c7da9/lmPerm' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘lmPerm’ ... ** package ‘lmPerm’ successfully unpacked and MD5 sums checked ** libs clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c lmPerm.c -o lmPerm.o clang -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o lmPerm.so lmPerm.o -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/lmPerm/libs ** R ** data ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (lmPerm) trying URL 'https://cloud.r-project.org/src/contrib/nparcomp_2.6.tar.gz' Content type 'application/x-gzip' length 33095 bytes (32 KB) ================================================== downloaded 32 KB Installing nparcomp trying URL 'https://cloud.r-project.org/src/contrib/multcomp_1.4-7.tar.gz' Content type 'application/x-gzip' length 607663 bytes (593 KB) ================================================== downloaded 593 KB Installing multcomp trying URL 'https://cloud.r-project.org/src/contrib/mvtnorm_1.0-6.tar.gz' Content type 'application/x-gzip' length 159232 bytes (155 KB) ================================================== downloaded 155 KB Installing mvtnorm '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpDiqijy/devtools41e6150c80dc/mvtnorm' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘mvtnorm’ ... ** package ‘mvtnorm’ successfully unpacked and MD5 sums checked ** libs clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c miwa.c -o miwa.o gfortran -fpic -g -O2 -c mvt.f -o mvt.o clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I/home/travis/R-bin/include -fpic -g -O2 -c mvtnorm-init.c -o mvtnorm-init.o gfortran -fpic -g -O2 -c tvpack.f -o tvpack.o clang -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o mvtnorm.so C_FORTRAN_interface.o miwa.o mvt.o mvtnorm-init.o tvpack.o -lgfortran -lm -lquadmath -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/mvtnorm/libs ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (mvtnorm) trying URL 'https://cloud.r-project.org/src/contrib/sandwich_2.4-0.tar.gz' Content type 'application/x-gzip' length 1280592 bytes (1.2 MB) ================================================== downloaded 1.2 MB Installing sandwich trying URL 'https://cloud.r-project.org/src/contrib/zoo_1.8-0.tar.gz' Content type 'application/x-gzip' length 839729 bytes (820 KB) ================================================== downloaded 820 KB Installing zoo '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL '/tmp/RtmpDiqijy/devtools41e65f71ed85/zoo' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘zoo’ ... ** package ‘zoo’ successfully unpacked and MD5 sums checked ** libs clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include -I/home/travis/R-bin/include -fpic -g -O2 -c coredata.c -o coredata.o clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include -I/home/travis/R-bin/include -fpic -g -O2 -c init.c -o init.o clang -I/home/travis/R-bin/lib/R/include -DNDEBUG -I../inst/include -I/home/travis/R-bin/include -fpic -g -O2 -c lag.c -o lag.o clang -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o zoo.so coredata.o init.o lag.o -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/zoo/libs ** R ** demo ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (zoo) '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpDiqijy/devtools41e65588b678/sandwich' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘sandwich’ ... ** package ‘sandwich’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (sandwich) trying URL 'https://cloud.r-project.org/src/contrib/TH.data_1.0-8.tar.gz' Content type 'application/x-gzip' length 4963504 bytes (4.7 MB) ================================================== downloaded 4.7 MB Installing TH.data '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpDiqijy/devtools41e64c0530e1/TH.data' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘TH.data’ ... ** package ‘TH.data’ successfully unpacked and MD5 sums checked ** data *** moving datasets to lazyload DB ** demo ** inst ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (TH.data) '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpDiqijy/devtools41e6791ccb70/multcomp' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘multcomp’ ... ** package ‘multcomp’ successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (multcomp) Skipping install of 'mvtnorm' from a cran remote, the SHA1 (1.0-6) has not changed since last install. Use `force = TRUE` to force installation '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpDiqijy/devtools41e61b407315/nparcomp' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘nparcomp’ ... ** package ‘nparcomp’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (nparcomp) trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.8.100.1.0.tar.gz' Content type 'application/x-gzip' length 1312598 bytes (1.3 MB) ================================================== downloaded 1.3 MB Installing RcppArmadillo '/home/travis/R-bin/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpDiqijy/devtools41e67429210d/RcppArmadillo' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘RcppArmadillo’ ... ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether clang++ accepts -g... yes checking how to run the C++ preprocessor... clang++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether clang++ accepts -g... (cached) yes checking whether g++ version is sufficient... checking LAPACK_LIBS... fallback LAPACK from R 3.3.0 or later used checking for macOS... not found as on Linux checking for OpenMP... found configure: creating ./config.status config.status: creating inst/include/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs clang++ -std=gnu++11 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/home/travis/R-bin/include -I../inst/include -fopenmp -fpic -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o clang++ -std=gnu++11 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/home/travis/R-bin/include -I../inst/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I/home/travis/R-bin/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/home/travis/R-bin/include -I../inst/include -fopenmp -fpic -g -O2 -c fastLm.cpp -o fastLm.o clang++ -std=gnu++11 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -L/home/travis/R-bin/lib/R/lib -lRlapack -L/home/travis/R-bin/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/travis/R-bin/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RcppArmadillo/libs ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Error: package or namespace load failed for ‘RcppArmadillo’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/RcppArmadillo/libs/RcppArmadillo.so': libomp.so: cannot open shared object file: No such file or directory Error: loading failed Execution halted ERROR: loading failed * removing ‘/usr/local/lib/R/site-library/RcppArmadillo’ Installation failed: Command failed (1) missing: RcppArmadillo travis_time:end:030e2cc0:start=1508642705851189606,finish=1508642758428130130,duration=52576940524  The command "Rscript -e 'deps <- devtools::dev_package_deps(dependencies = NA);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during . Your build has been stopped.