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CHECK report for motifcounter on celaya2

This page was generated on 2019-04-09 13:18:01 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifcounter_1.7.0.tar.gz
StartedAt: 2019-04-09 03:43:25 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:50:06 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 401.3 seconds
RetCode: 0
Status:  OK 
CheckDir: motifcounter.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings motifcounter_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/motifcounter.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 12.463  0.207  12.671
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/motifcounter.Rcheck/00check.log’
for details.



Installation output

motifcounter.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL motifcounter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Roption.c -o Roption.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
    int mins, maxs, noscores;
                    ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c background.c -o background.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c markovchain_single.c -o markovchain_single.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c overlap.c -o overlap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c score1d.c -o score1d.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c score2d.c -o score2d.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
    int j, i, index, cindex, ds;
                     ^
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  int s, index, cindex;
                ^
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
    int s, index, cindex;
                  ^
3 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c sequence.c -o sequence.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c simulate.c -o simulate.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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-apple-darwin15.6.0 (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 
257.158   4.321 266.832 

Example timings

motifcounter.Rcheck/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.4900.0150.527
combinatorialDist0.3920.0380.430
compoundPoissonDist0.3540.0460.400
computeClumpStartProb0.2830.0520.335
generateDNAString0.1270.0020.129
generateDNAStringSet0.1620.0020.164
hitStrand0.0790.0020.081
lenSequences0.1420.0160.158
markovModel0.2210.0290.250
motifAndBackgroundValid0.0950.0010.098
motifEnrichment3.2830.0393.323
motifHitProfile0.0960.0030.099
motifHits0.1040.0050.110
motifValid0.0020.0010.002
motifcounter-package0.9260.0270.954
motifcounterOptions0.0000.0000.001
normalizeMotif0.0030.0010.003
numMotifHits0.7740.0140.787
probOverlapHit0.2410.0100.252
readBackground0.0780.0030.081
revcompMotif0.0020.0010.002
scoreDist0.0760.0010.076
scoreDistBf0.1050.0010.106
scoreDistEmpirical3.7920.0563.850
scoreHistogram0.3380.0150.353
scoreHistogramSingleSeq0.1130.0070.121
scoreProfile0.4380.0030.442
scoreSequence0.0850.0030.087
scoreStrand0.0820.0020.083
scoreThreshold0.0870.0010.087
sigLevel0.0010.0000.000
simulateClumpSizeDist12.463 0.20712.671
simulateNumHitsDist2.7480.0852.834