Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:47:42 -0400 (Tue, 09 Apr 2019).
Package 1022/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
motifcounter 1.7.0 Wolfgang Kopp
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: motifcounter |
Version: 1.7.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings motifcounter_1.7.0.tar.gz |
StartedAt: 2019-04-09 02:08:50 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:13:27 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 276.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: motifcounter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings motifcounter_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/motifcounter.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘1.7.0’ * 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 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 ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed simulateClumpSizeDist 13.844 0.079 14.195 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/motifcounter.Rcheck/00check.log’ for details.
motifcounter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL motifcounter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘motifcounter’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rsequence.c -o Rsequence.o Rsequence.c: In function ‘RscoreHistogram’: Rsequence.c:143:21: warning: unused variable ‘noscores’ [-Wunused-variable] int mins, maxs, noscores; ^˜˜˜˜˜˜˜ gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c scorefunctions.c -o scorefunctions.o scorefunctions.c: In function ‘getPositionWeights’: scorefunctions.c:84:22: warning: unused variable ‘cindex’ [-Wunused-variable] int j, i, index, cindex, ds; ^˜˜˜˜˜ scorefunctions.c: In function ‘hitSequence’: scorefunctions.c:119:17: warning: unused variable ‘cindex’ [-Wunused-variable] int s, index, cindex; ^˜˜˜˜˜ scorefunctions.c: In function ‘scoreSequence’: scorefunctions.c:159:19: warning: unused variable ‘cindex’ [-Wunused-variable] int s, index, cindex; ^˜˜˜˜˜ gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c simulate.c -o simulate.o gcc -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-motifcounter/00new/motifcounter/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (motifcounter)
motifcounter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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: 841 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 154.382 8.688 164.889
motifcounter.Rcheck/motifcounter-Ex.timings
name | user | system | elapsed | |
clumpSizeDist | 0.385 | 0.008 | 0.411 | |
combinatorialDist | 0.388 | 0.016 | 0.409 | |
compoundPoissonDist | 0.262 | 0.015 | 0.280 | |
computeClumpStartProb | 0.162 | 0.024 | 0.190 | |
generateDNAString | 0.096 | 0.003 | 0.100 | |
generateDNAStringSet | 0.153 | 0.000 | 0.156 | |
hitStrand | 0.103 | 0.000 | 0.106 | |
lenSequences | 0.089 | 0.000 | 0.089 | |
markovModel | 0.141 | 0.004 | 0.145 | |
motifAndBackgroundValid | 0.094 | 0.000 | 0.097 | |
motifEnrichment | 3.950 | 0.008 | 4.081 | |
motifHitProfile | 0.098 | 0.004 | 0.101 | |
motifHits | 0.099 | 0.004 | 0.103 | |
motifValid | 0.002 | 0.000 | 0.002 | |
motifcounter-package | 1.360 | 0.012 | 1.411 | |
motifcounterOptions | 0 | 0 | 0 | |
normalizeMotif | 0.002 | 0.000 | 0.002 | |
numMotifHits | 0.688 | 0.008 | 0.701 | |
probOverlapHit | 0.180 | 0.004 | 0.190 | |
readBackground | 0.075 | 0.003 | 0.078 | |
revcompMotif | 0.002 | 0.000 | 0.002 | |
scoreDist | 0.082 | 0.000 | 0.082 | |
scoreDistBf | 0.130 | 0.000 | 0.149 | |
scoreDistEmpirical | 3.493 | 0.008 | 3.578 | |
scoreHistogram | 0.269 | 0.000 | 0.269 | |
scoreHistogramSingleSeq | 0.110 | 0.000 | 0.111 | |
scoreProfile | 0.555 | 0.000 | 0.559 | |
scoreSequence | 0.098 | 0.004 | 0.102 | |
scoreStrand | 0.101 | 0.000 | 0.102 | |
scoreThreshold | 0.104 | 0.000 | 0.104 | |
sigLevel | 0 | 0 | 0 | |
simulateClumpSizeDist | 13.844 | 0.079 | 14.195 | |
simulateNumHitsDist | 2.271 | 0.008 | 2.326 | |