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BioC 2.14: CHECK report for COMPASS on moscato2

This page was generated on 2014-10-08 08:56:27 -0700 (Wed, 08 Oct 2014).

Package 182/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.2.1
Kevin Ushey
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/COMPASS
Last Changed Rev: 90176 / Revision: 95116
Last Changed Date: 2014-05-09 15:54:26 -0700 (Fri, 09 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: COMPASS
Version: 1.2.1
Command: rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COMPASS.buildbin-libdir COMPASS_1.2.1.tar.gz >COMPASS-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=COMPASS.buildbin-libdir --install="check:COMPASS-install.out" --force-multiarch --no-vignettes --timings COMPASS_1.2.1.tar.gz
StartedAt: 2014-10-08 00:09:24 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:12:28 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 183.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: COMPASS.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COMPASS.buildbin-libdir COMPASS_1.2.1.tar.gz >COMPASS-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=COMPASS.buildbin-libdir --install="check:COMPASS-install.out" --force-multiarch --no-vignettes --timings COMPASS_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/COMPASS.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-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 '1.2.1'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
draw_polar_legend: no visible binding for global variable 'trtLabels'
plot.COMPASSResult: multiple local function definitions for 'order_fun'
  with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'shinyCOMPASS':
shinyCOMPASS
  Code: function(x, dir = NULL, meta.vars, facet1 = "None", facet2 =
                 "None", facet3 = "None", main = "Heatmap of
                 Ag-Specificity Posterior Probabilities", launch =
                 TRUE, ...)
  Docs: function(x, dir = NULL, meta.vars, facet1 = "None", facet2 =
                 "None", facet3 = "None", main = NA, launch = TRUE,
                 ...)
  Mismatches in argument default values:
    Name: 'main' Code: "Heatmap of Ag-Specificity Posterior Probabilities" Docs: NA

* 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 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 'E:/biocbld/bbs-2.14-bioc/meat/COMPASS.buildbin-libdir/COMPASS/libs/i386/COMPASS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.14-bioc/meat/COMPASS.buildbin-libdir/COMPASS/libs/x64/COMPASS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  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' ... [11s] WARNING
Found the following significant warnings:

  Warning: '.local' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
GetThresholdedIntensities 6.03   0.06    6.16
** running examples for arch 'x64' ... [15s] WARNING
Found the following significant warnings:

  Warning: '.local' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
GetThresholdedIntensities 7.47   0.06     8.7
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [3s]
 [3s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [3s]
 [4s] 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

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/COMPASS.Rcheck/00check.log'
for details.

COMPASS.Rcheck/00install.out:


install for i386

* installing *source* package 'COMPASS' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c COMPASS_init.c -o COMPASS_init.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c CellCounts.cpp -o CellCounts.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c CellCounts_character.cpp -o CellCounts_character.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c digamma.c -o digamma.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mat2vec.c -o mat2vec.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c melt_dataframe.c -o melt_dataframe.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c melt_matrix.c -o melt_matrix.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c samplePuPs.cpp -o samplePuPs.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transpose_list.c -o transpose_list.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatealphas_Exp.cpp -o updatealphas_Exp.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatealphau.cpp -o updatealphau.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatebeta_RW.cpp -o updatebeta_RW.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updategammak_noPu.cpp -o updategammak_noPu.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
g++ -m32 -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 -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lRlapack -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-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
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c COMPASS_init.c -o COMPASS_init.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c CellCounts.cpp -o CellCounts.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c CellCounts_character.cpp -o CellCounts_character.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c digamma.c -o digamma.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mat2vec.c -o mat2vec.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c melt_dataframe.c -o melt_dataframe.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c melt_matrix.c -o melt_matrix.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c samplePuPs.cpp -o samplePuPs.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transpose_list.c -o transpose_list.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatealphas_Exp.cpp -o updatealphas_Exp.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatealphau.cpp -o updatealphau.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updatebeta_RW.cpp -o updatebeta_RW.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updategammak_noPu.cpp -o updategammak_noPu.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utils.c -o utils.o
g++ -m64 -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 -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lRlapack -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/COMPASS.buildbin-libdir/COMPASS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COMPASS' as COMPASS_1.2.1.zip
* DONE (COMPASS)

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

nameusersystemelapsed
COMPASS0.30.00.3
COMPASSContainer0.030.000.03
COMPASSContainerFromGatingSet000
CellCounts0.660.020.67
Combinations000
FunctionalityScore0.010.000.02
GetThresholdedIntensities6.030.066.16
PolyfunctionalityScore000
Posterior000
SimpleCOMPASS000
TotalCellCounts0.030.000.03
UniqueCombinations000
merge.COMPASSContainer0.020.000.01
pheatmap2.170.002.17
plot.COMPASSResult0.140.000.14
print.COMPASSContainer000
print.COMPASSResult000
shinyCOMPASS000
shinyCOMPASSDeps0.490.090.68
subset.COMPASSContainer0.010.000.02
summary.COMPASSContainer000
summary.COMPASSResult000
transpose_list000

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

nameusersystemelapsed
COMPASS0.340.000.34
COMPASSContainer0.050.000.05
COMPASSContainerFromGatingSet000
CellCounts0.840.000.84
Combinations000
FunctionalityScore000
GetThresholdedIntensities7.470.068.70
PolyfunctionalityScore000
Posterior0.020.000.02
SimpleCOMPASS000
TotalCellCounts0.030.000.03
UniqueCombinations000
merge.COMPASSContainer0.020.000.02
pheatmap2.290.002.29
plot.COMPASSResult0.20.00.2
print.COMPASSContainer000
print.COMPASSResult000
shinyCOMPASS000
shinyCOMPASSDeps0.620.110.75
subset.COMPASSContainer0.020.000.01
summary.COMPASSContainer000
summary.COMPASSResult000
transpose_list000