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: 2017-10-17 22:53:05 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:54:15 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 69.7 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 3.4.2 (2017-09-28)
* 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	0.075
WLEB	0.368	0.000	0.372
addPriorCount	0.000	0.000	0.001
adjustedProfileLik	0.016	0.004	0.019
aveLogCPM	0.024	0.000	0.022
binomTest	0.000	0.000	0.002
calcNormFactors	0.040	0.000	0.043
camera.DGEList	0.76	0.00	0.76
commonCondLogLikDerDelta	0.044	0.000	0.042
condLogLikDerSize	0	0	0
cpm	0.016	0.000	0.014
cutWithMinN	0.004	0.000	0.002
decidetestsDGE	0.116	0.000	0.118
dglmStdResid	0.040	0.000	0.039
diffSpliceDGE	0.116	0.000	0.118
dim	0.004	0.000	0.003
dispBinTrend	0.584	0.004	0.589
dispCoxReid	0.036	0.004	0.040
dispCoxReidInterpolateTagwise	0.04	0.00	0.04
dispCoxReidSplineTrend	0.692	0.000	0.693
dropEmptyLevels	0.004	0.000	0.002
edgeRUsersGuide	0.000	0.000	0.001
equalizeLibSizes	0.012	0.000	0.016
estimateCommonDisp	0.092	0.004	0.096
estimateDisp	0.368	0.000	0.369
estimateExonGenewisedisp	0.068	0.000	0.069
estimateGLMCommonDisp	0.048	0.000	0.047
estimateGLMRobustDisp	0.800	0.000	0.801
estimateGLMTagwiseDisp	0.132	0.000	0.128
estimateGLMTrendedDisp	0.104	0.000	0.104
estimateTagwiseDisp	0.088	0.000	0.087
estimateTrendedDisp	0.208	0.000	0.209
exactTest	0.076	0.000	0.074
expandAsMatrix	0	0	0
getCounts	0.008	0.000	0.008
getPriorN	0.000	0.000	0.002
gini	0.000	0.000	0.001
glmQLFTest	0.504	0.000	0.507
glmTreat	0.028	0.000	0.027
glmfit	0.028	0.000	0.031
goana	0	0	0
gof	0.004	0.004	0.008
goodTuring	0.008	0.000	0.007
loessByCol	0.000	0.000	0.002
maPlot	0.012	0.000	0.012
makeCompressedMatrix	0.000	0.004	0.004
maximizeInterpolant	0	0	0
maximizeQuadratic	0.004	0.000	0.001
meanvar	0.264	0.000	0.266
mglm	0.004	0.000	0.006
movingAverageByCol	0.004	0.000	0.001
nbinomDeviance	0.000	0.000	0.001
plotBCV	0.36	0.00	0.36
plotExonUsage	0.008	0.000	0.008
plotMDS.DGEList	0.048	0.000	0.046
plotQLDisp	0.336	0.000	0.334
plotSmear	0.536	0.004	0.541
predFC	0.012	0.000	0.012
q2qnbinom	0.000	0.000	0.001
readDGE	0.000	0.000	0.001
roast.DGEList	0.456	0.008	0.465
romer.DGEList	4.292	0.000	4.296
scaleOffset	0.000	0.000	0.001
spliceVariants	0.040	0.000	0.042
splitIntoGroups	0.004	0.000	0.002
subsetting	0.036	0.000	0.034
sumTechReps	0	0	0
systematicSubset	0	0	0
thinCounts	0.004	0.000	0.001
topTags	0.016	0.000	0.017
validDGEList	0.000	0.004	0.002
weightedCondLogLikDerDelta	0.008	0.000	0.009
zscoreNBinom	0	0	0