Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:16:04 -0400 (Thu, 12 Apr 2018).
Package 888/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
motifcounter 1.2.1 Wolfgang Kopp
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: motifcounter |
Version: 1.2.1 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings motifcounter_1.2.1.tar.gz |
StartedAt: 2018-04-12 01:14:45 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 01:18:44 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 239.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: motifcounter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings motifcounter_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/motifcounter.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘motifcounter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘motifcounter’ version ‘1.2.1’ * 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 ... NOTE Found the following hidden files and directories: .zenodo.json These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘motifcounter’ 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 loading without being on the library search path ... 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 Examples with CPU or elapsed time > 5s user system elapsed simulateClumpSizeDist 36.532 0.108 36.655 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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 ‘/home/biocbuild/bbs-3.6-bioc/meat/motifcounter.Rcheck/00check.log’ for details.
motifcounter.Rcheck/00install.out
* installing *source* package ‘motifcounter’ ... ** libs gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rbackground.c -o Rbackground.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rcombinatorial.c -o Rcombinatorial.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rcompoundpoisson.c -o Rcompoundpoisson.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rminmaxscore.c -o Rminmaxscore.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Roption.c -o Roption.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Roverlap.c -o Roverlap.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rscore1d.c -o Rscore1d.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rsequence.c -o Rsequence.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rsimulate.c -o Rsimulate.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c background.c -o background.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c combinatorial.c -o combinatorial.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c compoundpoisson.c -o compoundpoisson.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c markovchain.c -o markovchain.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c markovchain_single.c -o markovchain_single.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c matrix.c -o matrix.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c mdist_register.c -o mdist_register.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c minmaxscore.c -o minmaxscore.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c overlap.c -o overlap.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c score1d.c -o score1d.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c score2d.c -o score2d.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c scorefunctions.c -o scorefunctions.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c sequence.c -o sequence.o gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c simulate.c -o simulate.o g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -fopenmp -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/motifcounter.Rcheck/motifcounter/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 (motifcounter)
motifcounter.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(motifcounter) > > test_check("motifcounter") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 831 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 117.448 7.336 124.992
motifcounter.Rcheck/motifcounter-Ex.timings
name | user | system | elapsed | |
clumpSizeDist | 0.340 | 0.012 | 0.349 | |
combinatorialDist | 0.376 | 0.008 | 0.386 | |
compoundPoissonDist | 0.264 | 0.000 | 0.265 | |
computeClumpStartProb | 0.116 | 0.000 | 0.116 | |
generateDNAString | 0.076 | 0.000 | 0.075 | |
generateDNAStringSet | 0.112 | 0.000 | 0.112 | |
lenSequences | 0.048 | 0.004 | 0.050 | |
markovModel | 0.244 | 0.004 | 0.246 | |
motifAndBackgroundValid | 0.048 | 0.000 | 0.048 | |
motifEnrichment | 3.140 | 0.024 | 3.166 | |
motifHitProfile | 0.084 | 0.000 | 0.082 | |
motifHits | 0.048 | 0.000 | 0.051 | |
motifValid | 0.000 | 0.000 | 0.001 | |
motifcounter-package | 1.024 | 0.008 | 1.030 | |
motifcounterOptions | 0 | 0 | 0 | |
normalizeMotif | 0.004 | 0.000 | 0.002 | |
numMotifHits | 0.676 | 0.012 | 0.688 | |
probOverlapHit | 0.128 | 0.000 | 0.130 | |
readBackground | 0.048 | 0.000 | 0.048 | |
revcompMotif | 0.000 | 0.000 | 0.001 | |
scoreDist | 0.052 | 0.004 | 0.052 | |
scoreDistBf | 0.084 | 0.000 | 0.084 | |
scoreDistEmpirical | 2.556 | 0.008 | 2.565 | |
scoreHistogram | 0.140 | 0.000 | 0.139 | |
scoreHistogramSingleSeq | 0.052 | 0.000 | 0.052 | |
scoreProfile | 0.384 | 0.000 | 0.386 | |
scoreSequence | 0.084 | 0.004 | 0.089 | |
scoreStrand | 0.092 | 0.000 | 0.089 | |
scoreThreshold | 0.084 | 0.000 | 0.083 | |
sigLevel | 0.000 | 0.000 | 0.001 | |
simulateClumpSizeDist | 36.532 | 0.108 | 36.655 | |
simulateNumHitsDist | 1.652 | 0.004 | 1.656 | |