From 48883850aac2f3b5c6d7ff1b48789294878c5836 Mon Sep 17 00:00:00 2001 From: "sascha.manier@uni-saarland.de" Date: Tue, 19 Nov 2024 10:59:55 +0100 Subject: [PATCH 1/4] Fix Issue #288: Compilation fails: control reaches end of non-void function --- DESCRIPTION | 1 + src/pwiz/data/msdata/MSData.cpp | 2 ++ 2 files changed, 3 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index d0c0aaed7..ad1959550 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,6 +9,7 @@ Authors@R: c( person("Laurent", "Gatto", email="laurent.gatto@uclouvain.be", role=c("aut")), person("Qiakng", "Kou", email="qkou@umail.iu.edu", role=c("aut")), person("David","Rauh",email="drauh@ipb-halle.de", role=c("ctb")) + person("Sascha","Manier",email="sascha.manier@uni-saarland.de", role=c("ctb")) ) Description: mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a diff --git a/src/pwiz/data/msdata/MSData.cpp b/src/pwiz/data/msdata/MSData.cpp index 963bcb655..88c9589f5 100644 --- a/src/pwiz/data/msdata/MSData.cpp +++ b/src/pwiz/data/msdata/MSData.cpp @@ -1112,6 +1112,8 @@ PWIZ_API_DECL size_t SpectrumList::findAbbreviated(const string& abbreviatedId, if ((result >= 0 && result < size()) || s == 0) return result; } + + return size(); } From 24872950179ee83653f6cd911319b9934e05a40f Mon Sep 17 00:00:00 2001 From: "sascha.manier@uni-saarland.de" Date: Tue, 19 Nov 2024 12:51:01 +0100 Subject: [PATCH 2/4] Fixed typo in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ad1959550..69bc60d04 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,7 +8,7 @@ Authors@R: c( person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")), person("Laurent", "Gatto", email="laurent.gatto@uclouvain.be", role=c("aut")), person("Qiakng", "Kou", email="qkou@umail.iu.edu", role=c("aut")), - person("David","Rauh",email="drauh@ipb-halle.de", role=c("ctb")) + person("David","Rauh",email="drauh@ipb-halle.de", role=c("ctb")), person("Sascha","Manier",email="sascha.manier@uni-saarland.de", role=c("ctb")) ) Description: mzR provides a unified API to the common file formats and From 7bd8d491b31e39b3ab00dc57f568737ee7ab6389 Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Tue, 19 Nov 2024 17:38:44 +0100 Subject: [PATCH 3/4] Bump version. Thanks Sascha, this closes #288 --- DESCRIPTION | 2 +- NEWS | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 69bc60d04..5fdc53c99 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mzR Type: Package Title: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) -Version: 2.41.0 +Version: 2.41.1 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer Authors@R: c( person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")), diff --git a/NEWS b/NEWS index c0dd80691..d6cf359f2 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,7 @@ +CHANGES IN VERSION 2.41.1 +------------------------- +o Fix compilation error with stricter compiler checks + CHANGES IN VERSION 2.39.2 ------------------------- o Improve openMSfile and openIDfile manual page (contirbuted by From e91cfccefca398cb7471cc54356865853f04635b Mon Sep 17 00:00:00 2001 From: Steffen Neumann Date: Tue, 19 Nov 2024 17:40:24 +0100 Subject: [PATCH 4/4] attempt fix for github action --- .github/workflows/check-bioc.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index a351a0100..69e82e635 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -52,10 +52,9 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: fedora-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: macOS-latest, r: 'devel', bioc: '3.19'} - - { os: windows-latest, r: 'devel', bioc: '3.19'} + - { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { os: macOS-latest, r: 'devel', bioc: '3.21'} + - { os: windows-latest, r: 'devel', bioc: '3.21'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }}