BioC 3.1: CHECK report for edgeR on petty
This page was generated on 2015-10-09 09:33:41 -0700 (Fri, 09 Oct 2015).
edgeR 3.10.5
Yunshun Chen , Aaron Lun , Mark Robinson , Davis McCarthy , Gordon Smyth
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/edgeR | | Last Changed Rev: 109338 / Revision: 109384 | | Last Changed Date: 2015-10-07 17:40:28 -0700 (Wed, 07 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
| Package: edgeR |
| Version: 3.10.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz |
| StartedAt: 2015-10-08 22:47:51 -0700 (Thu, 08 Oct 2015) |
| EndedAt: 2015-10-08 22:49:57 -0700 (Thu, 08 Oct 2015) |
| EllapsedTime: 126.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: edgeR.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edgeR_3.10.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/edgeR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.10.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘edgeR’ can be installed ... [16s/19s] 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
romer.DGEList 11.815 0.312 12.139
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘edgeR-Tests.R’ [9s/11s]
Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
[9s/12s] 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: OK
edgeR.Rcheck/00install.out:
* installing *source* package ‘edgeR’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_compute_nbdev.cpp -o R_compute_nbdev.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_cr_adjust.cpp -o R_cr_adjust.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_levenberg.cpp -o R_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_loess_by_col.cpp -o R_loess_by_col.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_one_group.cpp -o R_one_group.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c R_simple_good_turing.cpp -o R_simple_good_turing.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c adj_coxreid.cpp -o adj_coxreid.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c fmm_spline.c -o fmm_spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c glm_levenberg.cpp -o glm_levenberg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c glm_one_group.cpp -o glm_one_group.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c init.cpp -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c interpolator.cpp -o interpolator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c matvec_check.cpp -o matvec_check.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c nbdev.cpp -o nbdev.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o edgeR.so 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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)
edgeR.Rcheck/edgeR-Ex.timings:
| name | user | system | elapsed
|
| DGEList | 0.021 | 0.001 | 0.022 |
|
| WLEB | 0.140 | 0.005 | 0.145 |
|
| adjustedProfileLik | 0.018 | 0.002 | 0.020 |
|
| aveLogCPM | 0.005 | 0.001 | 0.006 |
|
| binomTest | 0.004 | 0.000 | 0.004 |
|
| calcNormFactors | 0.01 | 0.00 | 0.01 |
|
| camera.DGEList | 0.285 | 0.005 | 0.290 |
|
| commonCondLogLikDerDelta | 0.009 | 0.000 | 0.009 |
|
| condLogLikDerSize | 0.002 | 0.000 | 0.002 |
|
| cpm | 0.005 | 0.001 | 0.007 |
|
| cutWithMinN | 0.005 | 0.000 | 0.005 |
|
| dglmStdResid | 0.023 | 0.002 | 0.025 |
|
| diffSpliceDGE | 0.173 | 0.005 | 0.179 |
|
| dim | 0.005 | 0.000 | 0.006 |
|
| dispBinTrend | 0.672 | 0.006 | 0.678 |
|
| dispCoxReid | 0.051 | 0.000 | 0.051 |
|
| dispCoxReidInterpolateTagwise | 0.054 | 0.004 | 0.057 |
|
| dispCoxReidSplineTrend | 1.267 | 0.003 | 1.271 |
|
| dropEmptyLevels | 0.002 | 0.001 | 0.002 |
|
| edgeRUsersGuide | 0.002 | 0.000 | 0.002 |
|
| equalizeLibSizes | 0.034 | 0.000 | 0.034 |
|
| estimateCommonDisp | 0.031 | 0.001 | 0.033 |
|
| estimateDisp | 0.431 | 0.002 | 0.434 |
|
| estimateExonGenewisedisp | 0.023 | 0.001 | 0.023 |
|
| estimateGLMCommonDisp | 0.101 | 0.000 | 0.102 |
|
| estimateGLMRobustDisp | 1.090 | 0.001 | 1.094 |
|
| estimateGLMTagwiseDisp | 0.289 | 0.001 | 0.291 |
|
| estimateGLMTrendedDisp | 0.218 | 0.001 | 0.220 |
|
| estimateTagwiseDisp | 0.000 | 0.000 | 0.001 |
|
| estimateTrendedDisp | 0.704 | 0.019 | 0.724 |
|
| exactTest | 0.023 | 0.001 | 0.023 |
|
| expandAsMatrix | 0.001 | 0.001 | 0.001 |
|
| getCounts | 0.017 | 0.000 | 0.016 |
|
| getPriorN | 0.004 | 0.000 | 0.004 |
|
| glmQLFTest | 0.682 | 0.007 | 0.699 |
|
| glmTreat | 0.041 | 0.001 | 0.043 |
|
| glmfit | 0.084 | 0.002 | 0.086 |
|
| goana | 0.001 | 0.000 | 0.001 |
|
| gof | 0.015 | 0.000 | 0.015 |
|
| goodTuring | 0.011 | 0.001 | 0.012 |
|
| loessByCol | 0.002 | 0.000 | 0.002 |
|
| maPlot | 0.027 | 0.002 | 0.033 |
|
| maximizeInterpolant | 0.003 | 0.000 | 0.002 |
|
| maximizeQuadratic | 0.002 | 0.000 | 0.002 |
|
| meanvar | 0.098 | 0.003 | 0.104 |
|
| mglm | 0.013 | 0.001 | 0.014 |
|
| movingAverageByCol | 0.002 | 0.000 | 0.002 |
|
| nbinomDeviance | 0.001 | 0.000 | 0.002 |
|
| plotBCV | 0.565 | 0.008 | 0.572 |
|
| plotExonUsage | 0.010 | 0.001 | 0.011 |
|
| plotMDS.DGEList | 0.039 | 0.002 | 0.042 |
|
| plotQLDisp | 0.744 | 0.008 | 0.773 |
|
| plotSmear | 0.516 | 0.005 | 0.522 |
|
| predFC | 0.026 | 0.002 | 0.028 |
|
| q2qnbinom | 0.003 | 0.000 | 0.003 |
|
| readDGE | 0.001 | 0.000 | 0.001 |
|
| roast.DGEList | 0.302 | 0.002 | 0.304 |
|
| romer.DGEList | 11.815 | 0.312 | 12.139 |
|
| spliceVariants | 0.028 | 0.001 | 0.028 |
|
| splitIntoGroups | 0.005 | 0.000 | 0.005 |
|
| subsetting | 0.029 | 0.001 | 0.031 |
|
| sumTechReps | 0.002 | 0.000 | 0.002 |
|
| systematicSubset | 0.001 | 0.001 | 0.002 |
|
| thinCounts | 0.001 | 0.000 | 0.002 |
|
| topTags | 0.037 | 0.002 | 0.039 |
|
| validDGEList | 0.004 | 0.001 | 0.005 |
|
| weightedCondLogLikDerDelta | 0.006 | 0.000 | 0.005 |
|
| zscoreNBinom | 0.001 | 0.000 | 0.001 |
|