##############################################################################
##############################################################################
###
### 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_4.13.0.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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘4.13.0’
* 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 ... 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’
Undefined global functions or variables:
  ..extract_cols 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 ... WARNING
Undocumented code objects:
  ‘example_SDRF’
Undocumented data sets:
  ‘example_SDRF’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
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’

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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstats.Rcheck/00check.log’
for details.

##############################################################################
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###
### 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 27ms
INFO  [2024-07-06 02:58:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-07-06 02:58:05] ** Fractionation handled.
INFO  [2024-07-06 02:58:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-07-06 02:58:05] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-07-06 02:58:05] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-07-06 02:58:05] ** Use all features that the dataset originally has.
INFO  [2024-07-06 02:58:05] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-07-06 02:58:05] 
                    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  [2024-07-06 02:58:05]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-07-06 02:58:05]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-07-06 02:58:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-07-06 02:58:05] ** Fractionation handled.
INFO  [2024-07-06 02:58:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-07-06 02:58:05] ** Use all features that the dataset originally has.
INFO  [2024-07-06 02:58:05] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2024-07-06 02:58:05] 
                    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  [2024-07-06 02:58:05] 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  [2024-07-06 02:58:05]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-07-06 02:58:05]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-07-06 02:58:05] ** Features with one or two measurements across runs are removed.
INFO  [2024-07-06 02:58:05] ** Fractionation handled.
INFO  [2024-07-06 02:58:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-07-06 02:58:05] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-07-06 02:58:05] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-07-06 02:58:05] ** Use all features that the dataset originally has.
INFO  [2024-07-06 02:58:05] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-07-06 02:58:05] 
                    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  [2024-07-06 02:58:05]  == Start the summarization per subplot...
INFO  [2024-07-06 02:58:07]  == Summarization is done.

test_dataProcess.R............    0 tests    INFO  [2024-07-06 02:58:07] ** Features with one or two measurements across runs are removed.
INFO  [2024-07-06 02:58:07] ** Fractionation handled.
INFO  [2024-07-06 02:58:07] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-07-06 02:58:07] ** Use all features that the dataset originally has.
INFO  [2024-07-06 02:58:07] 
 # proteins: 6
 # peptides per protein: 11-32
 # features per peptide: 1-1
INFO  [2024-07-06 02:58:07] 
                    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  [2024-07-06 02:58:07] 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  [2024-07-06 02:58:07]  == Start the summarization per subplot...
INFO  [2024-07-06 02:58:09]  == Summarization is done.

test_dataProcess.R............    0 tests    
test_dataProcess.R............    1 tests OK 
test_dataProcess.R............    2 tests OK 4.2s
INFO  [2024-07-06 02:58:09] ** Features with one or two measurements across runs are removed.
INFO  [2024-07-06 02:58:09] ** Fractionation handled.
INFO  [2024-07-06 02:58:09] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-07-06 02:58:09] ** Log2 intensities under cutoff = 3.776  were considered as censored missing values.
INFO  [2024-07-06 02:58:09] ** Log2 intensities = NA were considered as censored missing values.
INFO  [2024-07-06 02:58:09] ** Use all features that the dataset originally has.
INFO  [2024-07-06 02:58:09] 
 # proteins: 2
 # peptides per protein: 2-2
 # features per peptide: 3-3
INFO  [2024-07-06 02:58:09] 
                    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  [2024-07-06 02:58:09]  == Start the summarization per subplot...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-07-06 02:58:09]  == 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  [2024-07-06 02:58:09]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
INFO  [2024-07-06 02:58:09]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    INFO  [2024-07-06 02:58:09]  == Start to test and get inference in whole plot ...
INFO  [2024-07-06 02:58:11]  == Comparisons for all proteins are done.

test_groupComparison.R........    0 tests    
test_groupComparison.R........    1 tests OK 2.2s
1ms
All ok, 4 results (6.5s)
> 
> proc.time()
   user  system elapsed 
  1.724   0.138   8.182