Multiple platform build/check report for BioC 3.11 - CHECK report for COMPASS on tokay2

Package: COMPASS

Version: 1.26.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COMPASS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings COMPASS_1.26.0.tar.gz

StartedAt: 2020-10-17 02:51:29 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 02:56:05 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 276.0 seconds

RetCode: 0

Status: OK

CheckDir: COMPASS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COMPASS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings COMPASS_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/COMPASS.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'COMPASS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COMPASS' version '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'COMPASS' can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'BiocStyle' 'rmarkdown'
  All declared Imports should be used.
':::' call which should be '::': 'flowWorkspace:::.getNodeInd'
  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
.CellCounts: no visible binding for global variable
  '_COMPASS_CellCounts'
COMPASSfitToCountsTable: no visible binding for global variable
  'population'
COMPASSfitToCountsTable: no visible binding for global variable 'Count'
COMPASSfitToCountsTable: no visible binding for global variable 'id'
CellCounts_character: no visible binding for global variable
  '_COMPASS_CellCounts_character'
GetThresholdedIntensities : <anonymous>: no visible global function
  definition for 'gh_pop_is_bool_gate'
Undefined global functions or variables:
  Count _COMPASS_CellCounts _COMPASS_CellCounts_character
  gh_pop_is_bool_gate id population
* checking Rd files ... OK
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/COMPASS/libs/i386/COMPASS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/COMPASS/libs/x64/COMPASS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
GetThresholdedIntensities 4.29    0.3       7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
GetThresholdedIntensities 4.62   0.34   12.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/COMPASS.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/COMPASS_1.26.0.tar.gz && rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=COMPASS.buildbin-libdir COMPASS_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL COMPASS_1.26.0.zip && rm COMPASS_1.26.0.tar.gz COMPASS_1.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  908k  100  908k    0     0  2255k      0 --:--:-- --:--:-- --:--:-- 2288k

install for i386

* installing *source* package 'COMPASS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c COMPASS_init.c -o COMPASS_init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CellCounts.cpp -o CellCounts.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CellCounts_character.cpp -o CellCounts_character.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c digamma.c -o digamma.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mat2vec.c -o mat2vec.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c melt_dataframe.c -o melt_dataframe.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c melt_matrix.c -o melt_matrix.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c samplePuPs.cpp -o samplePuPs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transpose_list.c -o transpose_list.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatealphas_Exp.cpp -o updatealphas_Exp.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatealphau.cpp -o updatealphau.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatebeta_RW.cpp -o updatebeta_RW.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updategammak_noPu.cpp -o updategammak_noPu.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o COMPASS.dll tmp.def COMPASS_init.o CellCounts.o CellCounts_character.o RcppExports.o digamma.o mat2vec.o melt_dataframe.o melt_matrix.o samplePuPs.o transpose_list.o updatealphas_Exp.o updatealphau.o updatealphau_noPu_Exp.o updatebeta_RW.o updategammak_noPu.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/COMPASS.buildbin-libdir/00LOCK-COMPASS/00new/COMPASS/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'COMPASS'
    finding HTML links ... done
    COMPASS-package                         html  
    COMPASS                                 html  
    COMPASSContainer-data                   html  
    COMPASSContainer                        html  
    COMPASSContainerFromGatingSet           html  
    COMPASSDescription                      html  
    COMPASSResult-accessors                 html  
    COMPASSResult-data                      html  
    COMPASSfitToCountsTable                 html  
    CellCounts                              html  
    Combinations                            html  
    FunctionalityScore                      html  
    GetThresholdedIntensities               html  
    PolyfunctionalityScore                  html  
    Posterior                               html  
    Response                                html  
    SimpleCOMPASS                           html  
    TotalCellCounts                         html  
    UniqueCombinations                      html  
    categories                              html  
    getCounts                               html  
    markers                                 html  
    melt_                                   html  
    merge.COMPASSContainer                  html  
    metadata                                html  
    pheatmap                                html  
    plot.COMPASSResult                      html  
    plot2                                   html  
    plotCOMPASSResultStack                  html  
    print.COMPASSContainer                  html  
    print.COMPASSResult                     html  
    scores                                  html  
    select_compass_pops                     html  
    shinyCOMPASS                            html  
    shinyCOMPASSDeps                        html  
    subset.COMPASSContainer                 html  
    summary.COMPASSContainer                html  
    summary.COMPASSResult                   html  
    translate_marker_names                  html  
    transpose_list                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'COMPASS' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c COMPASS_init.c -o COMPASS_init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CellCounts.cpp -o CellCounts.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CellCounts_character.cpp -o CellCounts_character.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c digamma.c -o digamma.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mat2vec.c -o mat2vec.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c melt_dataframe.c -o melt_dataframe.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c melt_matrix.c -o melt_matrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c samplePuPs.cpp -o samplePuPs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transpose_list.c -o transpose_list.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatealphas_Exp.cpp -o updatealphas_Exp.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatealphau.cpp -o updatealphau.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updatebeta_RW.cpp -o updatebeta_RW.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c updategammak_noPu.cpp -o updategammak_noPu.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o COMPASS.dll tmp.def COMPASS_init.o CellCounts.o CellCounts_character.o RcppExports.o digamma.o mat2vec.o melt_dataframe.o melt_matrix.o samplePuPs.o transpose_list.o updatealphas_Exp.o updatealphau.o updatealphau_noPu_Exp.o updatebeta_RW.o updategammak_noPu.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/COMPASS.buildbin-libdir/COMPASS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COMPASS' as COMPASS_1.26.0.zip
* DONE (COMPASS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'COMPASS' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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.

> library(testthat)
> library(COMPASS)
> if (file.exists("testthat")) {
+   test_dir("testthat")
+ }
v |  OK F W S | Context

/ |   0       | COMPASS Interface
- |   1       | COMPASS Interface
v |   1       | COMPASS Interface [0.6 s]

/ |   0       | test plotCOMPASSResultStack
- |   1       | test plotCOMPASSResultStack
x |   4 2     | test plotCOMPASSResultStack [62.9 s]
--------------------------------------------------------------------------------
test-COMPASSPlot.R:96: failure: only COMPASSResults with the same markers can be stacked
`plotCOMPASSResultStack(...)` threw an error.
Message: object not specified
Class:   simpleError/error/condition
Backtrace:
  1. testthat::expect_error(...) test-COMPASSPlot.R:96:2
  6. COMPASS::plotCOMPASSResultStack(...)
  7. COMPASS:::mergeMatricesForPlotCOMPASSResultStack(...)
  8. base::as.matrix.noquote(catsMerged[, "Counts"])
 10. base::NextMethod("as.matrix", x)

test-COMPASSPlot.R:199: error: mergeMatricesForPlotCOMPASSResultStack merges mean_gamma matrices correctly
object not specified
Backtrace:
 1. COMPASS:::mergeMatricesForPlotCOMPASSResultStack(...) test-COMPASSPlot.R:199:2
 2. base::as.matrix.noquote(catsMerged[, "Counts"])
 4. base::NextMethod("as.matrix", x)
--------------------------------------------------------------------------------

/ |   0       | CellCounts
v |   7       | CellCounts

/ |   0       | FS, PFS
v |   8       | FS, PFS

/ |   0       | test COMPASSContainerFromGatingSet
- |   0   1   | test COMPASSContainerFromGatingSet
\ |   0   2   | test COMPASSContainerFromGatingSet
x |   0 1 3   | test COMPASSContainerFromGatingSet [7.2 s]
--------------------------------------------------------------------------------
test-GatingSet2COMPASS.R:5: warning: (unknown)
'clone' is deprecated.
Use 'gs_clone' instead.
See help("Deprecated")

test-GatingSet2COMPASS.R:6: warning: (unknown)
'clone' is deprecated.
Use 'gs_clone' instead.
See help("Deprecated")

test-GatingSet2COMPASS.R:8: warning: (unknown)
'GatingSetList' is deprecated.
Use 'merge_list_to_gs' instead.
See help("Deprecated")

test-GatingSet2COMPASS.R:8: error: (unknown)
'rbind2' is defunct.
Use 'merge_list_to_gs' instead.
See help("Defunct")
Backtrace:
 1. methods::rbind2(GatingSetList(list(gs1, gs2))) test-GatingSet2COMPASS.R:8:0
 2. flowWorkspace::rbind2(GatingSetList(list(gs1, gs2)))
 3. base::.Defunct("merge_list_to_gs")
--------------------------------------------------------------------------------

== Results =====================================================================
Duration: 71.0 s

OK:       20
Failed:   3
Warnings: 3
Skipped:  0
> 
> proc.time()
   user  system elapsed 
  67.43    1.50   73.29


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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.

> library(testthat)
> library(COMPASS)
> if (file.exists("testthat")) {
+   test_dir("testthat")
+ }
v |  OK F W S | Context

/ |   0       | COMPASS Interface
- |   1       | COMPASS Interface
v |   1       | COMPASS Interface [0.5 s]

/ |   0       | test plotCOMPASSResultStack
- |   1       | test plotCOMPASSResultStack
\ |   4 2     | test plotCOMPASSResultStack
x |   4 2     | test plotCOMPASSResultStack [62.9 s]
--------------------------------------------------------------------------------
test-COMPASSPlot.R:96: failure: only COMPASSResults with the same markers can be stacked
`plotCOMPASSResultStack(...)` threw an error.
Message: object not specified
Class:   simpleError/error/condition
Backtrace:
  1. testthat::expect_error(...) test-COMPASSPlot.R:96:2
  6. COMPASS::plotCOMPASSResultStack(...)
  7. COMPASS:::mergeMatricesForPlotCOMPASSResultStack(...)
  8. base::as.matrix.noquote(catsMerged[, "Counts"])
 10. base::NextMethod("as.matrix", x)

test-COMPASSPlot.R:199: error: mergeMatricesForPlotCOMPASSResultStack merges mean_gamma matrices correctly
object not specified
Backtrace:
 1. COMPASS:::mergeMatricesForPlotCOMPASSResultStack(...) test-COMPASSPlot.R:199:2
 2. base::as.matrix.noquote(catsMerged[, "Counts"])
 4. base::NextMethod("as.matrix", x)
--------------------------------------------------------------------------------

/ |   0       | CellCounts
v |   7       | CellCounts

/ |   0       | FS, PFS
v |   8       | FS, PFS

/ |   0       | test COMPASSContainerFromGatingSet
- |   0   1   | test COMPASSContainerFromGatingSet
/ |   0 1 3   | test COMPASSContainerFromGatingSet
x |   0 1 3   | test COMPASSContainerFromGatingSet [2.1 s]
--------------------------------------------------------------------------------
test-GatingSet2COMPASS.R:5: warning: (unknown)
'clone' is deprecated.
Use 'gs_clone' instead.
See help("Deprecated")

test-GatingSet2COMPASS.R:6: warning: (unknown)
'clone' is deprecated.
Use 'gs_clone' instead.
See help("Deprecated")

test-GatingSet2COMPASS.R:8: warning: (unknown)
'GatingSetList' is deprecated.
Use 'merge_list_to_gs' instead.
See help("Deprecated")

test-GatingSet2COMPASS.R:8: error: (unknown)
'rbind2' is defunct.
Use 'merge_list_to_gs' instead.
See help("Defunct")
Backtrace:
 1. methods::rbind2(GatingSetList(list(gs1, gs2))) test-GatingSet2COMPASS.R:8:0
 2. flowWorkspace::rbind2(GatingSetList(list(gs1, gs2)))
 3. base::.Defunct("merge_list_to_gs")
--------------------------------------------------------------------------------

== Results =====================================================================
Duration: 65.6 s

OK:       20
Failed:   3
Warnings: 3
Skipped:  0
> 
> proc.time()
   user  system elapsed 
  66.59    1.18   67.79

name	user	system	elapsed
COMPASS	0.28	0.03	0.32
COMPASSContainer	0.07	0.00	0.06
COMPASSContainerFromGatingSet	0	0	0
CellCounts	0.53	0.02	0.54
Combinations	0	0	0
FunctionalityScore	0.00	0.01	0.02
GetThresholdedIntensities	4.29	0.30	7.00
PolyfunctionalityScore	0	0	0
Posterior	0.01	0.00	0.01
Response	0	0	0
SimpleCOMPASS	3.39	0.06	3.45
TotalCellCounts	0.03	0.00	0.03
UniqueCombinations	0	0	0
getCounts	0.03	0.00	0.03
merge.COMPASSContainer	0.02	0.00	0.02
pheatmap	1.28	0.03	1.31
plot.COMPASSResult	0.08	0.00	0.08
plotCOMPASSResultStack	0	0	0
print.COMPASSContainer	0	0	0
print.COMPASSResult	0	0	0
scores	0.01	0.00	0.01
select_compass_pops	0	0	0
shinyCOMPASS	0	0	0
shinyCOMPASSDeps	3.10	0.79	3.89
subset.COMPASSContainer	0	0	0
summary.COMPASSContainer	0	0	0
summary.COMPASSResult	0	0	0
translate_marker_names	0.00	0.02	0.02
transpose_list	0	0	0

name	user	system	elapsed
COMPASS	0.26	0.01	0.28
COMPASSContainer	0.08	0.00	0.07
COMPASSContainerFromGatingSet	0	0	0
CellCounts	0.62	0.02	0.50
Combinations	0	0	0
FunctionalityScore	0.02	0.00	0.02
GetThresholdedIntensities	4.62	0.34	12.12
PolyfunctionalityScore	0	0	0
Posterior	0	0	0
Response	0	0	0
SimpleCOMPASS	2.97	0.00	2.97
TotalCellCounts	0.03	0.00	0.03
UniqueCombinations	0	0	0
getCounts	0.02	0.00	0.02
merge.COMPASSContainer	0.01	0.00	0.01
pheatmap	1.07	0.02	1.08
plot.COMPASSResult	0.08	0.00	0.08
plotCOMPASSResultStack	0	0	0
print.COMPASSContainer	0	0	0
print.COMPASSResult	0	0	0
scores	0	0	0
select_compass_pops	0.02	0.00	0.01
shinyCOMPASS	0	0	0
shinyCOMPASSDeps	2.57	0.95	3.61
subset.COMPASSContainer	0	0	0
summary.COMPASSContainer	0.00	0.02	0.02
summary.COMPASSResult	0	0	0
translate_marker_names	0	0	0
transpose_list	0	0	0

CHECK report for COMPASS on tokay2

Summary

Command output

Installation output

Tests output

Example timings