diff --git a/README.md b/README.md
index 2456f4da..3ee9e0d4 100644
--- a/README.md
+++ b/README.md
@@ -166,6 +166,14 @@ run the example:
 ``` r
 library(SSMSE) #load the package
 library(r4ss) #install using remotes::install_github("r4ss/r4ss)
+## 
+## Attaching package: 'r4ss'
+## The following object is masked from 'package:stats':
+## 
+##     profile
+## The following object is masked from 'package:base':
+## 
+##     jitter
 # library(foreach) #if using run_parallel = TRUE
 # library(doParallel) #if using run_parallel = TRUE
 ```
@@ -529,6 +537,8 @@ the results are stored.
 summary <- SSMSE_summary_all(run_res_path)
 ## Extracting results from 2 scenarios
 ## Starting h-1 with 5 iterations
+## Warning: The `ncols` argument of `SS_output()` is deprecated as of r4ss 1.46.0.
+## Input 'ncols' no longer needed.
 ## Starting h-ctl with 5 iterations
 ```
 
diff --git a/inst/bookdown/data/SSMSE_scalar.csv b/inst/bookdown/data/SSMSE_scalar.csv
index 95f9b303..1af36798 100644
--- a/inst/bookdown/data/SSMSE_scalar.csv
+++ b/inst/bookdown/data/SSMSE_scalar.csv
@@ -1,19 +1,19 @@
 "SSB_Unfished","Totbio_Unfished","SmryBio_Unfished","Recr_Unfished","SSB_Btgt","SPR_Btgt","F_Btgt","TotYield_Btgt","SSB_SPR","F_SPR","TotYield_SPR","SSB_MSY","SPR_MSY","F_MSY","TotYield_MSY","Ret_Catch_MSY","max_grad","depletion","alt_sigma_r","last_yr_early","first_yr_full","last_yr_full","first_yr_recent","max_bias_adj","params_on_bound","params_stuck_low","params_stuck_high","NatM_uniform_Fem_GP_1","L_at_Amin_Fem_GP_1","L_at_Amax_Fem_GP_1","VonBert_K_Fem_GP_1","CV_young_Fem_GP_1","CV_old_Fem_GP_1","Wtlen_1_Fem_GP_1","Wtlen_2_Fem_GP_1","Mat50._Fem_GP_1","Mat_slope_Fem_GP_1","Eggs.kg_inter_Fem_GP_1","Eggs.kg_slope_wt_Fem_GP_1","RecrDist_GP_1","RecrDist_Area_1","RecrDist_month_1","CohortGrowDev","FracFemale_GP_1","SR_LN_R0","SR_BH_steep","SR_sigmaR","SR_regime","SR_autocorr","Late_RecrDev_101","Late_RecrDev_102","Late_RecrDev_103","ForeRecr_104","ForeRecr_105","ForeRecr_106","LnQ_base_Survey_2","Size_DblN_peak_Fishery_1","Size_DblN_top_logit_Fishery_1","Size_DblN_ascend_se_Fishery_1","Size_DblN_descend_se_Fishery_1","Size_DblN_start_logit_Fishery_1","Size_DblN_end_logit_Fishery_1","Size_DblN_peak_Survey_2","Size_DblN_top_logit_Survey_2","Size_DblN_ascend_se_Survey_2","Size_DblN_descend_se_Survey_2","Size_DblN_start_logit_Survey_2","Size_DblN_end_logit_Survey_2","minage.sel.1_Fishery_1","maxage.sel.1_Fishery_1","minage.sel.1_Survey_2","maxage.sel.1_Survey_2","Catch_endyear","NLL_TOTAL","NLL_Catch","NLL_Equil_catch","NLL_Survey","NLL_Length_comp","NLL_Age_comp","NLL_Recruitment","NLL_InitEQ_Regime","NLL_Forecast_Recruitment","NLL_Parm_priors","NLL_Parm_softbounds","NLL_Parm_devs","NLL_Crash_Pen","Curr_Var_Adj_lcomp_flt_1_Fishery","Curr_Var_Adj_agecomp_flt_2_Survey","version","RunTime","model_run","hessian","Niterations","ForeRecr_101","ForeRecr_102","ForeRecr_103","Late_RecrDev_104","Late_RecrDev_105","Late_RecrDev_106","ForeRecr_107","Size_DblN_ascend_se_Fishery_1_dev_se","Size_DblN_ascend_se_Fishery_1_dev_autocorr","Size_DblN_ascend_se_Fishery_1_DEVadd_101","Size_DblN_ascend_se_Fishery_1_DEVadd_102","Size_DblN_ascend_se_Fishery_1_DEVadd_103","Size_DblN_ascend_se_Fishery_1_DEVadd_104","Size_DblN_ascend_se_Fishery_1_DEVadd_105","Size_DblN_ascend_se_Fishery_1_DEVadd_106","iteration","scenario"
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