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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MSstats_4.15.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstats.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.15.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstats’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘MSstatsConvert:::.standardizeColnames’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotHeatmap : <anonymous>: no visible global function definition for
  ‘col2rgb’
.plotProfile: no visible binding for global variable ‘newABUNDANCE’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
.setCensoredByThreshold: no visible binding for global variable
  ‘any_censored’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘DetectionQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘LibQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalPGQValue’
DIANNtoMSstatsFormat: no visible binding for global variable
  ‘GlobalQValue’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘ref’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘LABEL’
MSstatsPrepareForSummarization: no visible binding for global variable
  ‘RUN’
SDRFtoAnnotation: no visible binding for global variable
  ‘..extract_cols’
extractSDRF: no visible binding for global variable ‘..extract_cols’
validateAnnotation: no visible binding for global variable
  ‘BioReplicate’
validateAnnotation: no visible binding for global variable ‘Condition’
Undefined global functions or variables:
  ..extract_cols BioReplicate Condition DetectionQValue GlobalPGQValue
  GlobalQValue LABEL LibPGQValue LibQValue RUN any_censored col2rgb
  newABUNDANCE ref zip
Consider adding
  importFrom("grDevices", "col2rgb")
  importFrom("utils", "zip")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) MSstatsSummarizationOutput.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MSstatsSummarizationOutput.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MSstatsSummarizationOutput.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'dot-documentFunction.Rd':
  ‘removeFewMeasurements’ ‘useUniquePeptide’ ‘summaryforMultipleRows’
  ‘removeProtein_with1Feature’ ‘removeProtein_with1Peptide’
  ‘removeOxidationMpeptides’ ‘removeMpeptides’ ‘use_log_file’ ‘append’
  ‘verbose’ ‘log_file_path’

Documented arguments not in \usage in Rd file 'dot-getContrast.Rd':
  ‘contrast_matrix’

Documented arguments not in \usage in Rd file 'dot-getSingleProteinForProfile.Rd':
  ‘dataProcess’

Documented arguments not in \usage in Rd file 'dot-getWideTable.Rd':
  ‘vector’

Undocumented arguments in Rd file 'modelBasedQCPlots.Rd'
  ‘displayDeprecationMessage’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MSstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MSstatsSummarizeSingleLinear
> ### Title: Linear model-based summarization for a single protein
> ### Aliases: MSstatsSummarizeSingleLinear
> 
> ### ** Examples
> 
> raw = DDARawData 
> method = "linear"
> cens = NULL
> impute = FALSE 
> # currently, MSstats only supports MBimpute = FALSE for linear summarization
> MSstatsConvert::MSstatsLogsSettings(FALSE)
> input = MSstatsPrepareForDataProcess(raw, 2, NULL)
INFO  [2025-01-25 00:29:42] ** Features with one or two measurements across runs are removed.
INFO  [2025-01-25 00:29:42] ** Fractionation handled.
INFO  [2025-01-25 00:29:42] ** Updated quantification data to make balanced design. Missing values are marked by NA
> input = MSstatsNormalize(input, "EQUALIZEMEDIANS")
> input = MSstatsMergeFractions(input)
> input = MSstatsHandleMissing(input, "TMP", TRUE, "NA", 0.999)
INFO  [2025-01-25 00:29:42] ** Log2 intensities under cutoff = 13.456  were considered as censored missing values.
INFO  [2025-01-25 00:29:42] ** Log2 intensities = NA were considered as censored missing values.
> input = MSstatsSelectFeatures(input, "all")
INFO  [2025-01-25 00:29:42] ** Use all features that the dataset originally has.
> input = MSstatsPrepareForSummarization(input, method, impute, cens, FALSE)
> input_split = split(input, input$PROTEIN)
> single_protein_summary = MSstatsSummarizeSingleLinear(input_split[[1]])
Warning in get_linear_summary(single_protein, cf, counts, label) :
  subscript out of bounds (index 0 >= vector size 0)

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: get_linear_summary(single_protein, cf, counts, label)
 2: MSstatsSummarizeSingleLinear(input_split[[1]])
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
   3: MSstatsSummarizeWithSingleCore(input, method, impute, censored_symbol,     remove50missing, equal_variance)
   4: MSstatsSummarizeWithMultipleCores(input, summaryMethod, MBimpute,     censoredInt, remove50missing, equalFeatureVar, numberOfCores)
   5: doTryCatch(return(expr), name, parentenv, handler)
   6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7: tryCatchList(expr, classes, parentenv, handlers)
   8: tryCatch(MSstatsSummarizeWithMultipleCores(input, summaryMethod,     MBimpute, censoredInt, remove50missing, equalFeatureVar,     numberOfCores), error = function(e) {    print(e)    NULL})
   9: dataProcess(DDARawData, use_log_file = FALSE, summaryMethod = "linear")
  10: eval(expr, envir = e)
  11: eval(expr, envir = e)
  12: FUN(X[[i]], ...)
  13: lapply(basename(testfiles), run_test_file, at_home = at_home,     verbose = verbose, color = color, remove_side_effects = remove_side_effects,     ...)
  14: run_test_dir(testdir, at_home = at_home, cluster = cluster, ...)
  15: tinytest::test_package("MSstats")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstats.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MSstats
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘MSstats’ ...
** this is package ‘MSstats’ version ‘4.15.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -DR_NO_REMAP -c common.cpp -o common.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -DR_NO_REMAP -c comparison_contrasts.cpp -o comparison_contrasts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -DR_NO_REMAP -c linear_summary.cpp -o linear_summary.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -DR_NO_REMAP -c median_polish.cpp -o median_polish.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-MSstats/00new/MSstats/libs
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstats)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if ( requireNamespace("tinytest", quietly=TRUE) ){
+   tinytest::test_package("MSstats")
+ }

Attaching package: 'MSstats'

The following object is masked from 'package:grDevices':

    savePlot


test_MSstatsdev.R.............    1 tests OK 47ms
INFO  [2025-01-25 00:29:46] ** Features with one or two measurements across runs are removed.
INFO  [2025-01-25 00:29:46] ** Fractionation handled.
INFO  [2025-01-25 00:29:46] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-01-25 00:29:46] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2025-01-25 00:29:46] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2025-01-25 00:29:46] ** Use all features that the dataset originally has.
INFO  [2025-01-25 00:29:46] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2025-01-25 00:29:46] 
                    1 2 3 4 5 6 7 8 9 10
             # runs 3 3 3 3 3 3 3 3 3  3
    # bioreplicates 3 3 3 3 3 3 3 3 3  3
 # tech. replicates 1 1 1 1 1 1 1 1 1  1
INFO  [2025-01-25 00:29:46]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-01-25 00:29:46]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2025-01-25 00:29:46] ** Features with one or two measurements across runs are removed.
INFO  [2025-01-25 00:29:46] ** Fractionation handled.
INFO  [2025-01-25 00:29:46] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-01-25 00:29:46] ** Use all features that the dataset originally has.
INFO  [2025-01-25 00:29:46] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2025-01-25 00:29:46] 
                    C1 C2 C3 C4 C5 C6
             # runs  3  3  3  3  3  3
    # bioreplicates  1  1  1  1  1  1
 # tech. replicates  3  3  3  3  3  3
INFO  [2025-01-25 00:29:46] Some features are completely missing in at least one condition:  
 D.GPLTGTYR_23_23_NA_NA,
 F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA,
 G.PLTGTYR_8_8_NA_NA,
 H.SFNVEYDDSQDK_465_465_NA_NA,
 K.AVVQDPALKPL_156_156_NA_NA ...
INFO  [2025-01-25 00:29:46]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: get_linear_summary(single_protein, cf, counts, label)
 2: MSstatsSummarizeSingleLinear(single_protein, equal_variance)
 3: MSstatsSummarizeWithSingleCore(input, method, impute, censored_symbol,     remove50missing, equal_variance)
 4: MSstatsSummarizeWithMultipleCores(input, summaryMethod, MBimpute,     censoredInt, remove50missing, equalFeatureVar, numberOfCores)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: tryCatch(MSstatsSummarizeWithMultipleCores(input, summaryMethod,     MBimpute, censoredInt, remove50missing, equalFeatureVar,     numberOfCores), error = function(e) {    print(e)    NULL})
 9: dataProcess(DDARawData, use_log_file = FALSE, summaryMethod = "linear")
10: eval(expr, envir = e)
11: eval(expr, envir = e)
12: FUN(X[[i]], ...)
13: lapply(basename(testfiles), run_test_file, at_home = at_home,     verbose = verbose, color = color, remove_side_effects = remove_side_effects,     ...)
14: run_test_dir(testdir, at_home = at_home, cluster = cluster, ...)
15: tinytest::test_package("MSstats")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)