BioC 2.13: CHECK report for edgeR on moscato1

Package: edgeR

Version: 3.4.2

Command: rm -rf edgeR.buildbin-libdir && mkdir edgeR.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=edgeR.buildbin-libdir edgeR_3.4.2.tar.gz >edgeR-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=edgeR.buildbin-libdir --install="check:edgeR-install.out" --force-multiarch --no-vignettes --timings edgeR_3.4.2.tar.gz && mv edgeR.buildbin-libdir/* edgeR.Rcheck/ && rmdir edgeR.buildbin-libdir

StartedAt: 2014-04-05 03:39:43 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:41:56 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 132.3 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/edgeR.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '3.4.2'
* 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 'edgeR' 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
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 'D:/biocbld/bbs-2.13-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/i386/edgeR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/x64/edgeR.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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'edgeR.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [9s] OK
** running examples for arch 'x64' ... [8s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'edgeR-Tests.R' [5s]
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 [6s] OK
** running tests for arch 'x64'
  Running 'edgeR-Tests.R' [9s]
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 [9s] 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/edgeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'edgeR' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_levenberg.cpp -o R_levenberg.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_one_group.cpp -o R_one_group.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/interpolator.cpp -o core/interpolator.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c core/fmm_spline.c -o core/fmm_spline.o
g++ -m32 -shared -s -static-libgcc -o edgeR.dll tmp.def R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lRlapack -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/i386
** R
** data
** 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 'edgeR' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_levenberg.cpp -o R_levenberg.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_one_group.cpp -o R_one_group.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/adj_coxreid.cpp -o core/adj_coxreid.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/glm_levenberg.cpp -o core/glm_levenberg.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/glm_one_group.cpp -o core/glm_one_group.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c core/interpolator.cpp -o core/interpolator.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I./core -I.     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c core/fmm_spline.c -o core/fmm_spline.o
g++ -m64 -shared -s -static-libgcc -o edgeR.dll tmp.def R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'edgeR' as edgeR_3.4.2.zip
* DONE (edgeR)

name	user	system	elapsed
DGEList	0.05	0.00	0.04
WLEB	0.16	0.04	0.21
adjustedProfileLik	0.01	0.00	0.01
aveLogCPM	0.02	0.00	0.02
binomTest	0	0	0
calcNormFactors	0.01	0.00	0.01
camera.DGEList	0.24	0.00	0.24
commonCondLogLikDerDelta	0.05	0.00	0.04
condLogLikDerSize	0	0	0
cpm	0	0	0
cutWithMinN	0	0	0
dglmStdResid	0.06	0.00	0.06
dim	0	0	0
dispBinTrend	0.65	0.00	0.66
dispCoxReid	0.05	0.00	0.05
dispCoxReidInterpolateTagwise	0.06	0.00	0.06
dispCoxReidSplineTrend	1.16	0.02	1.17
edgeRUsersGuide	0.01	0.00	0.01
equalizeLibSizes	0.05	0.00	0.05
estimateCommonDisp	0.06	0.00	0.06
estimateDisp	0.51	0.00	0.51
estimateExonGenewisedisp	0.05	0.00	0.05
estimateGLMCommonDisp	0.17	0.00	0.17
estimateGLMTagwiseDisp	0.45	0.00	0.45
estimateGLMTrendedDisp	0.30	0.00	0.29
estimateTagwiseDisp	0	0	0
estimateTrendedDisp	0.89	0.00	0.89
exactTest	0.03	0.00	0.03
expandAsMatrix	0	0	0
getCounts	0.02	0.00	0.02
getPriorN	0	0	0
glmfit	0.06	0.00	0.06
gof	0.02	0.00	0.02
goodTuring	0.01	0.00	0.01
loessByCol	0	0	0
maPlot	0.05	0.00	0.04
maximizeInterpolant	0	0	0
maximizeQuadratic	0	0	0
meanvar	0.08	0.00	0.07
mglm	0.04	0.00	0.05
movingAverageByCol	0	0	0
plotBCV	0.62	0.00	0.78
plotExonUsage	0.02	0.00	0.01
plotMDS.DGEList	0.06	0.00	0.06
plotSmear	0.53	0.00	0.53
predFC	0.03	0.00	0.04
q2qnbinom	0	0	0
readDGE	0	0	0
roast.DGEList	0.22	0.00	0.22
spliceVariants	0.03	0.00	0.03
splitIntoGroups	0	0	0
subsetting	0.03	0.00	0.03
systematicSubset	0	0	0
thinCounts	0	0	0
topTags	0.02	0.02	0.04
weightedCondLogLikDerDelta	0	0	0
zscoreNBinom	0	0	0

name	user	system	elapsed
DGEList	0.03	0.00	0.03
WLEB	0.17	0.00	0.17
adjustedProfileLik	0.01	0.00	0.02
aveLogCPM	0	0	0
binomTest	0	0	0
calcNormFactors	0	0	0
camera.DGEList	0.18	0.00	0.19
commonCondLogLikDerDelta	0	0	0
condLogLikDerSize	0	0	0
cpm	0.02	0.00	0.01
cutWithMinN	0.00	0.02	0.02
dglmStdResid	0.06	0.00	0.06
dim	0	0	0
dispBinTrend	0.80	0.00	0.79
dispCoxReid	0.13	0.00	0.12
dispCoxReidInterpolateTagwise	0.06	0.00	0.06
dispCoxReidSplineTrend	0.97	0.00	0.97
edgeRUsersGuide	0.01	0.00	0.02
equalizeLibSizes	0.03	0.00	0.03
estimateCommonDisp	0.04	0.02	0.05
estimateDisp	0.34	0.00	0.34
estimateExonGenewisedisp	0.04	0.00	0.04
estimateGLMCommonDisp	0.11	0.00	0.10
estimateGLMTagwiseDisp	0.26	0.00	0.27
estimateGLMTrendedDisp	0.22	0.00	0.22
estimateTagwiseDisp	0	0	0
estimateTrendedDisp	0.83	0.00	0.83
exactTest	0.03	0.00	0.03
expandAsMatrix	0	0	0
getCounts	0.01	0.00	0.01
getPriorN	0	0	0
glmfit	0.08	0.00	0.08
gof	0.01	0.00	0.01
goodTuring	0.02	0.00	0.02
loessByCol	0	0	0
maPlot	0.05	0.00	0.05
maximizeInterpolant	0.02	0.00	0.02
maximizeQuadratic	0	0	0
meanvar	0.09	0.00	0.09
mglm	0.06	0.00	0.06
movingAverageByCol	0	0	0
plotBCV	0.73	0.00	0.73
plotExonUsage	0.02	0.00	0.02
plotMDS.DGEList	0.03	0.00	0.03
plotSmear	0.52	0.02	0.53
predFC	0.03	0.00	0.04
q2qnbinom	0.02	0.00	0.01
readDGE	0	0	0
roast.DGEList	0.22	0.00	0.22
spliceVariants	0.03	0.00	0.03
splitIntoGroups	0.01	0.00	0.02
subsetting	0.03	0.00	0.03
systematicSubset	0.02	0.00	0.02
thinCounts	0	0	0
topTags	0.03	0.00	0.03
weightedCondLogLikDerDelta	0	0	0
zscoreNBinom	0.02	0.00	0.02