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CHECK report for motifcounter on malbec2

This page was generated on 2019-04-09 11:47:42 -0400 (Tue, 09 Apr 2019).

Package 1022/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifcounter 1.7.0
Wolfgang Kopp
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/motifcounter
Branch: master
Last Commit: 31de589
Last Changed Date: 2018-10-30 11:54:37 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

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

Command output

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###
### 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
###
##############################################################################
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* 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.



Installation output

motifcounter.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

motifcounter.Rcheck/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.3850.0080.411
combinatorialDist0.3880.0160.409
compoundPoissonDist0.2620.0150.280
computeClumpStartProb0.1620.0240.190
generateDNAString0.0960.0030.100
generateDNAStringSet0.1530.0000.156
hitStrand0.1030.0000.106
lenSequences0.0890.0000.089
markovModel0.1410.0040.145
motifAndBackgroundValid0.0940.0000.097
motifEnrichment3.9500.0084.081
motifHitProfile0.0980.0040.101
motifHits0.0990.0040.103
motifValid0.0020.0000.002
motifcounter-package1.3600.0121.411
motifcounterOptions000
normalizeMotif0.0020.0000.002
numMotifHits0.6880.0080.701
probOverlapHit0.1800.0040.190
readBackground0.0750.0030.078
revcompMotif0.0020.0000.002
scoreDist0.0820.0000.082
scoreDistBf0.1300.0000.149
scoreDistEmpirical3.4930.0083.578
scoreHistogram0.2690.0000.269
scoreHistogramSingleSeq0.1100.0000.111
scoreProfile0.5550.0000.559
scoreSequence0.0980.0040.102
scoreStrand0.1010.0000.102
scoreThreshold0.1040.0000.104
sigLevel000
simulateClumpSizeDist13.844 0.07914.195
simulateNumHitsDist2.2710.0082.326