BioC 3.6: CHECK report for edgeR on malbec1

Package: edgeR

Version: 3.19.3

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.19.3.tar.gz

StartedAt: 2017-08-15 22:49:04 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:50:06 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 62.7 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘3.19.3’
* 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 
393c393
< [1,] 8.295172 8.338525 8.284484
---
> x 8.295172 8.338525 8.284484
395,397c395
< [1] "CompressedMatrix"
< attr(,"Dims")
< [1] 5 3
---
> [1] "compressedMatrix"
402d399
< 995 more rows ...
424c421
< 0.05545 0.09511 0.11623 0.11014 0.13329 0.16861 
---
> 0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
428c425
< 0.04203 0.08586 0.11280 0.11010 0.12369 0.37408 
---
> 0.04203 0.08586 0.11280 0.11010 0.12370 0.37410 
432c429
< 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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.056	0.000	0.055
WLEB	0.260	0.000	0.263
addPriorCount	0.000	0.000	0.002
adjustedProfileLik	0.024	0.004	0.026
aveLogCPM	0.024	0.000	0.024
binomTest	0.004	0.000	0.002
calcNormFactors	0.040	0.000	0.039
camera.DGEList	0.696	0.000	0.696
cbind	0	0	0
commonCondLogLikDerDelta	0.040	0.000	0.038
condLogLikDerSize	0.000	0.000	0.001
cpm	0.016	0.000	0.013
cutWithMinN	0.000	0.000	0.002
decidetestsDGE	0.116	0.000	0.116
dglmStdResid	0.024	0.000	0.025
diffSpliceDGE	0.064	0.004	0.068
dim	0.000	0.000	0.002
dispBinTrend	0.556	0.000	0.554
dispCoxReid	0.024	0.000	0.024
dispCoxReidInterpolateTagwise	0.024	0.000	0.024
dispCoxReidSplineTrend	0.664	0.000	0.667
dropEmptyLevels	0.004	0.000	0.001
edgeRUsersGuide	0.000	0.000	0.001
equalizeLibSizes	0.016	0.000	0.013
estimateCommonDisp	0.088	0.000	0.090
estimateDisp	0.348	0.000	0.349
estimateExonGenewisedisp	0.064	0.000	0.064
estimateGLMCommonDisp	0.048	0.000	0.047
estimateGLMRobustDisp	0.796	0.000	0.793
estimateGLMTagwiseDisp	0.136	0.000	0.137
estimateGLMTrendedDisp	0.116	0.000	0.115
estimateTagwiseDisp	0.092	0.000	0.090
estimateTrendedDisp	0.208	0.004	0.211
exactTest	0.068	0.000	0.068
expandAsMatrix	0.000	0.000	0.001
getCounts	0.008	0.000	0.007
getPriorN	0.004	0.000	0.002
gini	0	0	0
glmQLFTest	0.492	0.000	0.515
glmTreat	0.036	0.000	0.037
glmfit	0.028	0.000	0.032
goana	0.000	0.000	0.001
gof	0.008	0.000	0.008
goodTuring	0.004	0.000	0.005
loessByCol	0.000	0.000	0.002
maPlot	0.012	0.000	0.012
makeCompressedMatrix	0.000	0.000	0.003
maximizeInterpolant	0.000	0.000	0.001
maximizeQuadratic	0	0	0
meanvar	0.252	0.000	0.254
mglm	0.008	0.000	0.005
movingAverageByCol	0.000	0.000	0.001
nbinomDeviance	0	0	0
plotBCV	0.360	0.004	0.364
plotExonUsage	0.004	0.000	0.006
plotMDS.DGEList	0.036	0.000	0.039
plotQLDisp	0.320	0.000	0.323
plotSmear	0.476	0.004	0.476
predFC	0.012	0.000	0.012
q2qnbinom	0.000	0.000	0.001
readDGE	0	0	0
roast.DGEList	0.456	0.000	0.456
romer.DGEList	3.692	0.004	3.699
scaleOffset	0.004	0.000	0.000
spliceVariants	0.044	0.000	0.046
splitIntoGroups	0.004	0.000	0.002
subsetting	0.032	0.000	0.031
sumTechReps	0.000	0.000	0.001
systematicSubset	0.004	0.000	0.000
thinCounts	0.000	0.000	0.001
topTags	0.016	0.000	0.016
validDGEList	0.004	0.000	0.001
weightedCondLogLikDerDelta	0.012	0.000	0.011
zscoreNBinom	0	0	0