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BioC 3.4: CHECK report for COMPASS on tokay1

This page was generated on 2017-04-15 16:18:30 -0400 (Sat, 15 Apr 2017).

Package 248/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.12.0
Greg Finak
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/COMPASS
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: COMPASS
Version: 1.12.0
Command: rm -rf COMPASS.buildbin-libdir COMPASS.Rcheck && mkdir COMPASS.buildbin-libdir COMPASS.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COMPASS.buildbin-libdir COMPASS_1.12.0.tar.gz >COMPASS.Rcheck\00install.out 2>&1 && cp COMPASS.Rcheck\00install.out COMPASS-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=COMPASS.buildbin-libdir --install="check:COMPASS-install.out" --force-multiarch --no-vignettes --timings COMPASS_1.12.0.tar.gz
StartedAt: 2017-04-14 21:39:13 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:41:44 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 151.1 seconds
RetCode: 0
Status:  OK  
CheckDir: COMPASS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf COMPASS.buildbin-libdir COMPASS.Rcheck && mkdir COMPASS.buildbin-libdir COMPASS.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COMPASS.buildbin-libdir COMPASS_1.12.0.tar.gz >COMPASS.Rcheck\00install.out 2>&1 && cp COMPASS.Rcheck\00install.out COMPASS-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=COMPASS.buildbin-libdir --install="check:COMPASS-install.out" --force-multiarch --no-vignettes --timings COMPASS_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/COMPASS.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.12.0'
* 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 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: '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
.COMPASS.discrete: no visible global function definition for 'median'
.MakeComparableTwoCOMPASSResults : .consolidateColumns : <anonymous>:
  no visible global function definition for 'na.omit'
.polarLegend: no visible global function definition for 'head'
.polarLegend: no visible global function definition for 'colorRamp'
.polarLegend: no visible global function definition for 'rgb'
.polarLegend: no visible global function definition for 'rgb2hsv'
.polarLegend: no visible global function definition for 'hsv'
COMPASS: no visible global function definition for 'sessionInfo'
COMPASS: multiple local function definitions for '.drop_degree_one'
  with different formal arguments
COMPASSContainerFromGatingSet: no visible global function definition
  for 'pData'
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous> :
  <anonymous>: no visible global function definition for 'na.omit'
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous> :
  <anonymous>: no visible global function definition for 'parameters'
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for 'na.omit'
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for 'parameters'
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for 'getData'
COMPASSContainerFromGatingSet: no visible global function definition
  for 'parameters'
COMPASSContainerFromGatingSet: no visible global function definition
  for 'na.omit'
COMPASSContainerFromGatingSet: no visible global function definition
  for 'getSingleCellExpression'
GetThresholdedIntensities: no visible global function definition for
  'parameters'
GetThresholdedIntensities : .check_match : <anonymous>: no visible
  global function definition for 'na.omit'
GetThresholdedIntensities: no visible global function definition for
  'exprs'
GetThresholdedIntensities : <anonymous>: no visible global function
  definition for 'getData'
MakeComparable: no visible global function definition for 'combn'
TotalCellCounts: no visible global function definition for 'setNames'
cluster_mat: no visible global function definition for 'as.dist'
cluster_mat: no visible global function definition for 'cor'
cluster_mat: no visible global function definition for 'dist'
cluster_mat: no visible global function definition for 'hclust'
draw_polar_legend: no visible binding for global variable 'trtLabels'
generate_annotation_colours: no visible global function definition for
  'hsv'
generate_annotation_colours: no visible global function definition for
  'runif'
generate_row_annotation_colours: no visible global function definition
  for 'hsv'
heatmap_motor : <anonymous>: no visible global function definition for
  'pdf'
heatmap_motor : <anonymous>: no visible global function definition for
  'png'
heatmap_motor : <anonymous>: no visible global function definition for
  'jpeg'
heatmap_motor : <anonymous>: no visible global function definition for
  'tiff'
heatmap_motor : <anonymous>: no visible global function definition for
  'bmp'
heatmap_motor: no visible global function definition for 'dev.off'
kmeans_pheatmap: no visible binding for global variable 'sd'
kmeans_pheatmap: no visible global function definition for 'kmeans'
lo: no visible global function definition for 'strwidth'
pheatmap: no visible global function definition for 'kmeans'
plot.COMPASSResult: no visible global function definition for 'is'
plot2: no visible global function definition for 'colorRamp'
plot2: no visible global function definition for 'rgb2hsv'
plot2: no visible global function definition for 'hsv'
scale_colours: no visible global function definition for 'rainbow'
scale_rows: no visible binding for global variable 'sd'
scale_vec_colours: no visible global function definition for 'rainbow'
shinyCOMPASS: no visible global function definition for 'runApp'
shinyCOMPASSDeps: no visible global function definition for
  'installed.packages'
summary.COMPASSContainer: no visible global function definition for
  'hist'
Undefined global functions or variables:
  as.dist bmp colorRamp combn cor dev.off dist exprs getData
  getSingleCellExpression hclust head hist hsv installed.packages is
  jpeg kmeans median na.omit pData parameters pdf png rainbow rgb
  rgb2hsv runApp runif sd sessionInfo setNames strwidth tiff trtLabels
Consider adding
  importFrom("grDevices", "bmp", "colorRamp", "dev.off", "hsv", "jpeg",
             "pdf", "png", "rainbow", "rgb", "rgb2hsv", "tiff")
  importFrom("graphics", "hist", "strwidth")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "kmeans",
             "median", "na.omit", "runif", "sd", "setNames")
  importFrom("utils", "combn", "head", "installed.packages",
             "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 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-3.4-bioc/meat/COMPASS.buildbin-libdir/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)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
GetThresholdedIntensities 3.61   0.16    5.22
** running examples for arch 'x64' ... OK
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/COMPASS.Rcheck/00check.log'
for details.


COMPASS.Rcheck/00install.out:


install for i386

* installing *source* package 'COMPASS' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c COMPASS_init.c -o COMPASS_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellCounts.cpp -o CellCounts.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellCounts_character.cpp -o CellCounts_character.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c digamma.c -o digamma.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mat2vec.c -o mat2vec.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c melt_dataframe.c -o melt_dataframe.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c melt_matrix.c -o melt_matrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c samplePuPs.cpp -o samplePuPs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transpose_list.c -o transpose_list.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatealphas_Exp.cpp -o updatealphas_Exp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatealphau.cpp -o updatealphau.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatebeta_RW.cpp -o updatebeta_RW.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updategammak_noPu.cpp -o updategammak_noPu.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/g++ -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˜1.4-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/COMPASS.buildbin-libdir/COMPASS/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'COMPASS' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c COMPASS_init.c -o COMPASS_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellCounts.cpp -o CellCounts.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c CellCounts_character.cpp -o CellCounts_character.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c digamma.c -o digamma.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mat2vec.c -o mat2vec.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c melt_dataframe.c -o melt_dataframe.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c melt_matrix.c -o melt_matrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c samplePuPs.cpp -o samplePuPs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transpose_list.c -o transpose_list.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatealphas_Exp.cpp -o updatealphas_Exp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatealphau.cpp -o updatealphau.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updatebeta_RW.cpp -o updatebeta_RW.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c updategammak_noPu.cpp -o updategammak_noPu.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/g++ -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˜1.4-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/COMPASS.buildbin-libdir/COMPASS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COMPASS' as COMPASS_1.12.0.zip
* DONE (COMPASS)

COMPASS.Rcheck/examples_i386/COMPASS-Ex.timings:

nameusersystemelapsed
COMPASS0.260.020.28
COMPASSContainer0.020.010.03
COMPASSContainerFromGatingSet000
CellCounts0.590.020.61
Combinations000
FunctionalityScore000
GetThresholdedIntensities3.610.165.22
PolyfunctionalityScore000
Posterior0.010.000.01
SimpleCOMPASS000
TotalCellCounts0.020.000.02
UniqueCombinations0.010.000.01
merge.COMPASSContainer0.020.000.02
pheatmap1.420.031.45
plot.COMPASSResult0.060.030.09
print.COMPASSContainer000
print.COMPASSResult000
scores000
shinyCOMPASS000
shinyCOMPASSDeps0.760.301.09
subset.COMPASSContainer000
summary.COMPASSContainer000
summary.COMPASSResult000
transpose_list000

COMPASS.Rcheck/examples_x64/COMPASS-Ex.timings:

nameusersystemelapsed
COMPASS0.220.020.23
COMPASSContainer0.030.000.03
COMPASSContainerFromGatingSet000
CellCounts0.520.010.53
Combinations000
FunctionalityScore000
GetThresholdedIntensities3.290.133.43
PolyfunctionalityScore000
Posterior000
SimpleCOMPASS000
TotalCellCounts0.020.000.02
UniqueCombinations0.010.000.01
merge.COMPASSContainer0.020.000.02
pheatmap1.400.011.42
plot.COMPASSResult0.100.020.11
print.COMPASSContainer000
print.COMPASSResult000
scores0.010.000.02
shinyCOMPASS000
shinyCOMPASSDeps0.830.281.10
subset.COMPASSContainer000
summary.COMPASSContainer000
summary.COMPASSResult000
transpose_list000