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BioC 3.4: CHECK report for edgeR on moscato1

This page was generated on 2016-09-21 03:42:35 -0700 (Wed, 21 Sep 2016).

Package 358/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edgeR 3.15.2
Yunshun Chen , Aaron Lun , Mark Robinson , Davis McCarthy , Gordon Smyth
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 119042 / Revision: 121152
Last Changed Date: 2016-06-29 18:47:59 -0700 (Wed, 29 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: edgeR
Version: 3.15.2
Command: rm -rf edgeR.buildbin-libdir edgeR.Rcheck && mkdir edgeR.buildbin-libdir edgeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=edgeR.buildbin-libdir edgeR_3.15.2.tar.gz >edgeR.Rcheck\00install.out 2>&1 && cp edgeR.Rcheck\00install.out edgeR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=edgeR.buildbin-libdir --install="check:edgeR-install.out" --force-multiarch --no-vignettes --timings edgeR_3.15.2.tar.gz
StartedAt: 2016-09-20 07:38:53 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:41:00 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 126.8 seconds
RetCode: 0
Status:  OK  
CheckDir: edgeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf edgeR.buildbin-libdir edgeR.Rcheck && mkdir edgeR.buildbin-libdir edgeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=edgeR.buildbin-libdir edgeR_3.15.2.tar.gz >edgeR.Rcheck\00install.out 2>&1 && cp edgeR.Rcheck\00install.out edgeR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=edgeR.buildbin-libdir --install="check:edgeR-install.out" --force-multiarch --no-vignettes --timings edgeR_3.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/edgeR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '3.15.2'
* 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 ... OK
* 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 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 'D:/biocbld/bbs-3.4-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/i386/edgeR.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
romer.DGEList 5.26      0    5.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
romer.DGEList  6.2   0.02    6.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'edgeR-Tests.R'
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 OK
** running tests for arch 'x64' ...
  Running 'edgeR-Tests.R'
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ... OK
 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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/edgeR.Rcheck/00check.log'
for details.


edgeR.Rcheck/00install.out:


install for i386

* installing *source* package 'edgeR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_cr_adjust.cpp -o R_cr_adjust.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_levenberg.cpp -o R_levenberg.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_loess_by_col.cpp -o R_loess_by_col.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_one_group.cpp -o R_one_group.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c adj_coxreid.cpp -o adj_coxreid.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fmm_spline.c -o fmm_spline.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_levenberg.cpp -o glm_levenberg.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_one_group.cpp -o glm_one_group.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c interpolator.cpp -o interpolator.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c matvec_check.cpp -o matvec_check.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c nbdev.cpp -o nbdev.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o edgeR.dll tmp.def R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/i386
** R
** 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
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_cr_adjust.cpp -o R_cr_adjust.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_levenberg.cpp -o R_levenberg.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_loess_by_col.cpp -o R_loess_by_col.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_one_group.cpp -o R_one_group.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c adj_coxreid.cpp -o adj_coxreid.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fmm_spline.c -o fmm_spline.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_levenberg.cpp -o glm_levenberg.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_one_group.cpp -o glm_one_group.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c interpolator.cpp -o interpolator.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c matvec_check.cpp -o matvec_check.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c nbdev.cpp -o nbdev.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o edgeR.dll tmp.def R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/edgeR.buildbin-libdir/edgeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'edgeR' as edgeR_3.15.2.zip
* DONE (edgeR)

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

nameusersystemelapsed
DGEList0.010.000.02
WLEB0.030.000.03
adjustedProfileLik000
aveLogCPM000
binomTest000
calcNormFactors000
camera.DGEList0.160.000.16
commonCondLogLikDerDelta000
condLogLikDerSize000
cpm0.010.000.01
cutWithMinN000
dglmStdResid0.000.010.02
diffSpliceDGE0.060.000.06
dim000
dispBinTrend0.490.000.49
dispCoxReid0.030.000.03
dispCoxReidInterpolateTagwise0.030.000.03
dispCoxReidSplineTrend0.760.000.76
dropEmptyLevels000
edgeRUsersGuide000
equalizeLibSizes0.030.000.03
estimateCommonDisp0.040.000.03
estimateDisp0.260.000.27
estimateExonGenewisedisp0.010.000.01
estimateGLMCommonDisp0.060.000.06
estimateGLMRobustDisp0.640.000.64
estimateGLMTagwiseDisp0.140.000.14
estimateGLMTrendedDisp0.110.000.11
estimateTagwiseDisp0.050.000.05
estimateTrendedDisp0.30.00.3
exactTest0.010.000.01
expandAsMatrix000
getCounts000
getPriorN000
gini0.020.000.02
glmQLFTest0.510.000.51
glmTreat0.020.000.02
glmfit0.050.000.04
goana000
gof0.010.000.02
goodTuring000
loessByCol0.020.000.02
maPlot0.030.000.03
maximizeInterpolant000
maximizeQuadratic000
meanvar0.080.000.07
mglm0.010.000.02
movingAverageByCol000
nbinomDeviance000
plotBCV0.450.000.45
plotExonUsage0.020.000.02
plotMDS.DGEList0.020.020.03
plotQLDisp0.530.000.53
plotSmear0.450.000.45
predFC0.010.000.02
q2qnbinom000
readDGE000
roast.DGEList0.130.000.12
romer.DGEList5.260.005.26
spliceVariants0.020.000.01
splitIntoGroups000
subsetting0.000.010.02
sumTechReps000
systematicSubset000
thinCounts0.010.000.01
topTags0.020.000.02
validDGEList000
weightedCondLogLikDerDelta000
zscoreNBinom000

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

nameusersystemelapsed
DGEList0.030.000.03
WLEB0.030.000.04
adjustedProfileLik000
aveLogCPM0.020.000.01
binomTest000
calcNormFactors000
camera.DGEList0.170.000.17
commonCondLogLikDerDelta000
condLogLikDerSize000
cpm0.020.000.02
cutWithMinN000
dglmStdResid0.010.000.01
diffSpliceDGE0.110.000.11
dim000
dispBinTrend0.550.000.69
dispCoxReid0.040.000.05
dispCoxReidInterpolateTagwise0.050.000.04
dispCoxReidSplineTrend0.90.00.9
dropEmptyLevels000
edgeRUsersGuide000
equalizeLibSizes0.020.000.02
estimateCommonDisp0.030.000.03
estimateDisp0.310.000.31
estimateExonGenewisedisp0.030.000.03
estimateGLMCommonDisp0.080.000.08
estimateGLMRobustDisp0.760.000.77
estimateGLMTagwiseDisp0.180.000.17
estimateGLMTrendedDisp0.140.000.14
estimateTagwiseDisp0.030.000.04
estimateTrendedDisp0.350.000.34
exactTest0.010.000.01
expandAsMatrix000
getCounts000
getPriorN000
gini000
glmQLFTest0.470.000.47
glmTreat0.030.000.03
glmfit0.040.000.05
goana000
gof0.020.000.01
goodTuring000
loessByCol0.010.000.02
maPlot0.040.000.03
maximizeInterpolant000
maximizeQuadratic000
meanvar0.070.000.08
mglm0.020.000.01
movingAverageByCol000
nbinomDeviance000
plotBCV0.480.000.48
plotExonUsage000
plotMDS.DGEList0.030.000.03
plotQLDisp0.520.010.53
plotSmear0.440.000.44
predFC0.020.000.01
q2qnbinom000
readDGE000
roast.DGEList0.150.000.16
romer.DGEList6.200.026.21
spliceVariants0.010.000.01
splitIntoGroups000
subsetting0.020.000.01
sumTechReps000
systematicSubset000
thinCounts000
topTags0.030.000.04
validDGEList000
weightedCondLogLikDerDelta000
zscoreNBinom000