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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1292/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifcounter 1.29.0  (landing page)
Wolfgang Kopp
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/motifcounter
git_branch: devel
git_last_commit: a85abf5
git_last_commit_date: 2024-04-30 10:57:02 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for motifcounter on palomino6

To the developers/maintainers of the motifcounter package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifcounter.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: motifcounter
Version: 1.29.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifcounter.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings motifcounter_1.29.0.tar.gz
StartedAt: 2024-07-16 01:57:38 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 02:03:03 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 324.8 seconds
RetCode: 0
Status:   OK  
CheckDir: motifcounter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifcounter.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings motifcounter_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'motifcounter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'motifcounter' version '1.29.0'
* 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 whether package 'motifcounter' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/motifcounter/libs/x64/motifcounter.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
simulateClumpSizeDist 6.23   0.33    6.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck/00check.log'
for details.


Installation output

motifcounter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL motifcounter
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'motifcounter' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rbackground.c -o Rbackground.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rcombinatorial.c -o Rcombinatorial.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rminmaxscore.c -o Rminmaxscore.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Roption.c -o Roption.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Roverlap.c -o Roverlap.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rscore1d.c -o Rscore1d.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rsequence.c -o Rsequence.o
Rsequence.c: In function 'RscoreHistogram':
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
  143 |     int mins, maxs, noscores;
      |                     ^~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rsimulate.c -o Rsimulate.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c background.c -o background.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c combinatorial.c -o combinatorial.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c compoundpoisson.c -o compoundpoisson.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c markovchain.c -o markovchain.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c markovchain_single.c -o markovchain_single.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix.c -o matrix.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mdist_register.c -o mdist_register.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c minmaxscore.c -o minmaxscore.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c overlap.c -o overlap.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c score1d.c -o score1d.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c score2d.c -o score2d.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c: In function 'getPositionWeights':
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
   84 |     int j, i, index, cindex, ds;
      |                      ^~~~~~
scorefunctions.c: In function 'hitSequence':
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  119 |   int s, index, cindex;
      |                 ^~~~~~
scorefunctions.c: In function 'scoreSequence':
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
  159 |     int s, index, cindex;
      |                   ^~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sequence.c -o sequence.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DIN_R   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
gcc -shared -s -static-libgcc -o motifcounter.dll tmp.def 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-motifcounter/00new/motifcounter/libs/x64
** 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
** 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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
> 
> proc.time()
   user  system elapsed 
 165.92   59.68  226.48 

Example timings

motifcounter.Rcheck/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.150.030.18
combinatorialDist0.150.060.22
compoundPoissonDist0.220.060.32
computeClumpStartProb0.080.060.14
generateDNAString0.040.000.04
generateDNAStringSet0.10.00.1
hitStrand0.040.020.06
lenSequences0.070.020.08
markovModel0.110.010.12
motifAndBackgroundValid0.040.000.05
motifEnrichment2.850.092.94
motifHitProfile0.030.030.06
motifHits0.050.020.07
motifValid000
motifcounter-package0.640.040.68
motifcounterOptions000
normalizeMotif0.000.020.02
numMotifHits0.400.000.41
probOverlapHit0.140.060.20
readBackground0.070.000.06
revcompMotif000
scoreDist0.060.000.06
scoreDistBf0.080.000.08
scoreDistEmpirical2.420.082.52
scoreHistogram0.140.020.15
scoreHistogramSingleSeq0.060.010.08
scoreProfile0.270.020.28
scoreSequence0.040.010.07
scoreStrand0.050.020.06
scoreThreshold0.050.010.06
sigLevel000
simulateClumpSizeDist6.230.336.56
simulateNumHitsDist1.590.241.83