BioC 3.5: CHECK report for edgeR on malbec2

Package: edgeR

Version: 3.18.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.18.1.tar.gz

StartedAt: 2017-08-15 22:44:46 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:45:51 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 64.4 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/edgeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.18.1’
* 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 for sufficient/correct file permissions ... 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
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ...95c95
< 0.02428 0.36369 0.55662 0.54319 0.78889 1.00000 
---
> 0.02428 0.36370 0.55660 0.54320 0.78890 1.00000 
98c98
< 0.02428 0.36369 0.55662 0.54319 0.78889 1.00000 
---
> 0.02428 0.36370 0.55660 0.54320 0.78890 1.00000 
270c270
< 0.09353 0.11082 0.15463 0.19006 0.23050 0.52006 
---
> 0.09353 0.11080 0.15460 0.19010 0.23050 0.52010 
421c421
< 0.05545 0.09511 0.11623 0.11014 0.13329 0.16861 
---
> 0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
425c425
< 0.04203 0.08586 0.11280 0.11010 0.12369 0.37408 
---
> 0.04203 0.08586 0.11280 0.11010 0.12370 0.37410 
429c429
< 0.05545 0.09511 0.11623 0.11014 0.13329 0.16861 
---
> 0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
 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

* installing *source* package ‘edgeR’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_add_prior_count.cpp -o R_add_prior_count.o
In file included from matvec_check.h:1:0,
                 from R_add_prior_count.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_add_repeat_matrices.cpp -o R_add_repeat_matrices.o
In file included from matvec_check.h:1:0,
                 from R_add_repeat_matrices.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_calculate_cpm.cpp -o R_calculate_cpm.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_check_counts.cpp -o R_check_counts.o
In file included from matvec_check.h:1:0,
                 from R_check_counts.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
In file included from matvec_check.h:1:0,
                 from R_check_poisson_bound.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_compute_apl.cpp -o R_compute_apl.o
In file included from glm.h:5:0,
                 from R_compute_apl.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_compute_nbdev.cpp -o R_compute_nbdev.o
In file included from R_compute_nbdev.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
In file included from R_exact_test_by_deviance.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
In file included from glm.h:5:0,
                 from R_get_one_way_fitted.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
In file included from glm.h:5:0,
                 from R_initialize_levenberg.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_levenberg.cpp -o R_levenberg.o
In file included from glm.h:5:0,
                 from R_levenberg.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_loess_by_col.cpp -o R_loess_by_col.o
In file included from R_loess_by_col.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
In file included from R_maximize_interpolant.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_one_group.cpp -o R_one_group.o
In file included from glm.h:5:0,
                 from R_one_group.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_simple_good_turing.cpp -o R_simple_good_turing.o
In file included from R_simple_good_turing.cpp:9:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c add_prior.cpp -o add_prior.o
In file included from matvec_check.h:1:0,
                 from add_prior.h:3,
                 from add_prior.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c adj_coxreid.cpp -o adj_coxreid.o
In file included from glm.h:5:0,
                 from adj_coxreid.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fmm_spline.c -o fmm_spline.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c glm_levenberg.cpp -o glm_levenberg.o
In file included from glm.h:5:0,
                 from glm_levenberg.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c glm_one_group.cpp -o glm_one_group.o
In file included from glm.h:5:0,
                 from glm_one_group.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
In file included from init.cpp:1:0:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interpolator.cpp -o interpolator.o
In file included from interpolator.h:4:0,
                 from interpolator.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matvec_check.cpp -o matvec_check.o
In file included from matvec_check.h:1:0,
                 from matvec_check.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nbdev.cpp -o nbdev.o
In file included from glm.h:5:0,
                 from nbdev.cpp:1:
utils.h:79:14: warning: ‘LNtwo’ defined but not used [-Wunused-variable]
 const double LNtwo=std::log(2), one_million=1000000, LNmillion=std::log(one_million);
              ^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_add_repeat_matrices.o R_ave_log_cpm.o R_calculate_cpm.o R_check_counts.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_get_one_way_fitted.o R_initialize_levenberg.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 add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)

name	user	system	elapsed
DGEList	0.076	0.000	0.074
WLEB	0.440	0.004	0.444
addPriorCount	0.004	0.000	0.002
adjustedProfileLik	0.024	0.000	0.024
aveLogCPM	0.020	0.000	0.022
binomTest	0.004	0.000	0.001
calcNormFactors	0.04	0.00	0.04
camera.DGEList	0.692	0.000	0.691
commonCondLogLikDerDelta	0.036	0.000	0.037
condLogLikDerSize	0	0	0
cpm	0.016	0.000	0.013
cutWithMinN	0.000	0.000	0.001
decidetestsDGE	0.112	0.000	0.115
dglmStdResid	0.028	0.000	0.025
diffSpliceDGE	0.068	0.000	0.067
dim	0.004	0.000	0.002
dispBinTrend	0.508	0.000	0.510
dispCoxReid	0.02	0.00	0.02
dispCoxReidInterpolateTagwise	0.024	0.000	0.025
dispCoxReidSplineTrend	0.592	0.008	0.598
dropEmptyLevels	0.000	0.000	0.001
edgeRUsersGuide	0.004	0.000	0.001
equalizeLibSizes	0.012	0.000	0.014
estimateCommonDisp	0.092	0.000	0.091
estimateDisp	0.340	0.000	0.338
estimateExonGenewisedisp	0.064	0.000	0.067
estimateGLMCommonDisp	0.044	0.000	0.046
estimateGLMRobustDisp	0.736	0.000	0.736
estimateGLMTagwiseDisp	0.144	0.000	0.142
estimateGLMTrendedDisp	0.108	0.000	0.107
estimateTagwiseDisp	0.092	0.000	0.093
estimateTrendedDisp	0.212	0.000	0.212
exactTest	0.068	0.000	0.069
expandAsMatrix	0.000	0.000	0.001
getCounts	0.008	0.000	0.007
getPriorN	0.000	0.000	0.002
gini	0	0	0
glmQLFTest	0.584	0.000	0.596
glmTreat	0.044	0.000	0.044
glmfit	0.048	0.000	0.048
goana	0	0	0
gof	0.012	0.000	0.013
goodTuring	0.008	0.000	0.010
loessByCol	0.000	0.000	0.003
maPlot	0.020	0.000	0.019
makeCompressedMatrix	0.008	0.000	0.007
maximizeInterpolant	0.000	0.000	0.001
maximizeQuadratic	0.004	0.000	0.002
meanvar	0.408	0.004	0.410
mglm	0.012	0.000	0.010
movingAverageByCol	0.000	0.000	0.001
nbinomDeviance	0.000	0.000	0.001
plotBCV	0.576	0.000	0.574
plotExonUsage	0.008	0.000	0.008
plotMDS.DGEList	0.060	0.004	0.064
plotQLDisp	0.372	0.000	0.370
plotSmear	0.416	0.000	0.416
predFC	0.008	0.004	0.012
q2qnbinom	0.000	0.000	0.001
readDGE	0	0	0
roast.DGEList	0.440	0.000	0.438
romer.DGEList	3.768	0.004	3.775
scaleOffset	0.000	0.000	0.001
spliceVariants	0.044	0.000	0.042
splitIntoGroups	0.000	0.000	0.002
subsetting	0.028	0.008	0.034
sumTechReps	0	0	0
systematicSubset	0.004	0.000	0.001
thinCounts	0	0	0
topTags	0.016	0.000	0.016
validDGEList	0.004	0.000	0.002
weightedCondLogLikDerDelta	0.008	0.000	0.010
zscoreNBinom	0	0	0