##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstats.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  linear_summary.cpp:65:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  linear_summary.cpp:88:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstats.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstats.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstats
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MSstats’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c common.cpp -o common.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c comparison_contrasts.cpp -o comparison_contrasts.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linear_summary.cpp -o linear_summary.o
linear_summary.cpp:65:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
    if ((find_ref.length() != 0) & !(find_ref[0] == -1)) {
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                 &&
linear_summary.cpp:65:9: note: cast one or both operands to int to silence this warning
linear_summary.cpp:88:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
    if ((find_run_feature.length() != 0) & !(find_run_feature[0] == -1)) {
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                         &&
linear_summary.cpp:88:9: note: cast one or both operands to int to silence this warning
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c median_polish.cpp -o median_polish.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 18ms
INFO  [2024-11-09 08:05:35] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-09 08:05:35] ** Fractionation handled.
INFO  [2024-11-09 08:05:35] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-09 08:05:35] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-11-09 08:05:35] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-11-09 08:05:35] ** Use all features that the dataset originally has.
INFO  [2024-11-09 08:05:35] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-11-09 08:05:35] 
                    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  [2024-11-09 08:05:35]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-11-09 08:05:35]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-11-09 08:05:35] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-09 08:05:35] ** Fractionation handled.
INFO  [2024-11-09 08:05:35] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-09 08:05:35] ** Use all features that the dataset originally has.
INFO  [2024-11-09 08:05:35] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2024-11-09 08:05:35] 
                    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  [2024-11-09 08:05:35] 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  [2024-11-09 08:05:35]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-11-09 08:05:35]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-11-09 08:05:35] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-09 08:05:35] ** Fractionation handled.
INFO  [2024-11-09 08:05:35] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-09 08:05:35] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-11-09 08:05:35] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-11-09 08:05:35] ** Use all features that the dataset originally has.
INFO  [2024-11-09 08:05:35] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-11-09 08:05:35] 
                    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  [2024-11-09 08:05:35]  == Start the summarization per subplot...
INFO  [2024-11-09 08:05:36]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-11-09 08:05:36] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-09 08:05:36] ** Fractionation handled.
INFO  [2024-11-09 08:05:36] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-09 08:05:36] ** Use all features that the dataset originally has.
INFO  [2024-11-09 08:05:36] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2024-11-09 08:05:36] 
                    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  [2024-11-09 08:05:36] 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  [2024-11-09 08:05:36]  == Start the summarization per subplot...
INFO  [2024-11-09 08:05:37]  == Summarization is done.

test_dataProcess.R............    0 tests    
test_dataProcess.R............    1 tests OK 
test_dataProcess.R............    2 tests OK 2.2s
INFO  [2024-11-09 08:05:37] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-09 08:05:37] ** Fractionation handled.
INFO  [2024-11-09 08:05:37] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-09 08:05:37] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-11-09 08:05:37] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-11-09 08:05:37] ** Use all features that the dataset originally has.
INFO  [2024-11-09 08:05:37] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-11-09 08:05:37] 
                    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  [2024-11-09 08:05:37]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-11-09 08:05:37]  == Summarization is done.

test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    
test_groupComparison.R........    0 tests    INFO  [2024-11-09 08:05:38]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-11-09 08:05:38]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    INFO  [2024-11-09 08:05:38]  == Start to test and get inference in whole plot ...
INFO  [2024-11-09 08:05:39]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    
test_groupComparison.R........    1 tests OK 1.1s

test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    INFO  [2024-11-09 08:05:39] ** Features with one or two measurements across runs are removed.
INFO  [2024-11-09 08:05:39] ** Fractionation handled.
INFO  [2024-11-09 08:05:39] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-11-09 08:05:39] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-11-09 08:05:39] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-11-09 08:05:39] ** Use all features that the dataset originally has.
INFO  [2024-11-09 08:05:39] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-11-09 08:05:39] 
                    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  [2024-11-09 08:05:39]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-11-09 08:05:39]  == Summarization is done.

test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    
test_groupComparisonQCPlots.R.    0 tests    INFO  [2024-11-09 08:05:39]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-11-09 08:05:39]  == Comparisons for all proteins are done.

test_groupComparisonQCPlots.R.    0 tests    Test passed 🥳

test_groupComparisonQCPlots.R.    8 tests OK 0.2s
1ms

test_utils_groupcomparison_checks.R    0 tests    
test_utils_groupcomparison_checks.R    1 tests OK 
test_utils_groupcomparison_checks.R    1 tests OK 
test_utils_groupcomparison_checks.R    2 tests OK 
test_utils_groupcomparison_checks.R    2 tests OK 
test_utils_groupcomparison_checks.R    3 tests OK 
test_utils_groupcomparison_checks.R    3 tests OK 
test_utils_groupcomparison_checks.R    4 tests OK 
test_utils_groupcomparison_checks.R    4 tests OK 
test_utils_groupcomparison_checks.R    5 tests OK 4ms
All ok, 17 results (3.6s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  1.418   0.093   4.556