Wolfgang Kopp
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/motifcounter |
| git_branch: devel |
| git_last_commit: 08f5123 |
| git_last_commit_date: 2024-10-29 10:18:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 1315/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifcounter 1.31.0 (landing page) Wolfgang Kopp
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: motifcounter |
| Version: 1.31.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings motifcounter_1.31.0.tar.gz |
| StartedAt: 2025-01-25 00:19:12 -0500 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 00:23:31 -0500 (Sat, 25 Jan 2025) |
| EllapsedTime: 259.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifcounter.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings motifcounter_1.31.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/motifcounter.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.31.0’
* 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
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simulateClumpSizeDist 10.105 0.119 10.227
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/motifcounter.Rcheck/00check.log’
for details.
motifcounter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL motifcounter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘motifcounter’ ... ** this is package ‘motifcounter’ version ‘1.31.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Rbackground.c -o Rbackground.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Rcombinatorial.c -o Rcombinatorial.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Rcompoundpoisson.c -o Rcompoundpoisson.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Rminmaxscore.c -o Rminmaxscore.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Roption.c -o Roption.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Roverlap.c -o Roverlap.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Rscore1d.c -o Rscore1d.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Rsequence.c -o Rsequence.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c Rsimulate.c -o Rsimulate.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c background.c -o background.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c combinatorial.c -o combinatorial.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c compoundpoisson.c -o compoundpoisson.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c markovchain.c -o markovchain.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c markovchain_single.c -o markovchain_single.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c matrix.c -o matrix.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c mdist_register.c -o mdist_register.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c minmaxscore.c -o minmaxscore.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c overlap.c -o overlap.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c score1d.c -o score1d.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c score2d.c -o score2d.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c scorefunctions.c -o scorefunctions.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c sequence.c -o sequence.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -c simulate.c -o simulate.o gcc -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-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) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
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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
116.109 5.406 121.511
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.388 | 0.004 | 0.393 | |
| combinatorialDist | 0.251 | 0.020 | 0.271 | |
| compoundPoissonDist | 0.139 | 0.028 | 0.167 | |
| computeClumpStartProb | 0.114 | 0.011 | 0.124 | |
| generateDNAString | 0.067 | 0.016 | 0.082 | |
| generateDNAStringSet | 0.116 | 0.005 | 0.121 | |
| hitStrand | 0.067 | 0.002 | 0.069 | |
| lenSequences | 0.06 | 0.00 | 0.06 | |
| markovModel | 0.094 | 0.002 | 0.096 | |
| motifAndBackgroundValid | 0.063 | 0.001 | 0.064 | |
| motifEnrichment | 2.278 | 0.005 | 2.284 | |
| motifHitProfile | 0.064 | 0.002 | 0.067 | |
| motifHits | 0.071 | 0.002 | 0.073 | |
| motifValid | 0.002 | 0.000 | 0.002 | |
| motifcounter-package | 0.920 | 0.013 | 0.933 | |
| motifcounterOptions | 0 | 0 | 0 | |
| normalizeMotif | 0.002 | 0.001 | 0.002 | |
| numMotifHits | 0.513 | 0.003 | 0.516 | |
| probOverlapHit | 0.128 | 0.005 | 0.132 | |
| readBackground | 0.066 | 0.002 | 0.068 | |
| revcompMotif | 0.001 | 0.000 | 0.002 | |
| scoreDist | 0.065 | 0.002 | 0.066 | |
| scoreDistBf | 0.084 | 0.001 | 0.084 | |
| scoreDistEmpirical | 2.134 | 0.008 | 2.142 | |
| scoreHistogram | 0.177 | 0.010 | 0.186 | |
| scoreHistogramSingleSeq | 0.073 | 0.004 | 0.077 | |
| scoreProfile | 0.368 | 0.002 | 0.370 | |
| scoreSequence | 0.071 | 0.001 | 0.072 | |
| scoreStrand | 0.071 | 0.004 | 0.075 | |
| scoreThreshold | 0.075 | 0.000 | 0.075 | |
| sigLevel | 0.000 | 0.000 | 0.001 | |
| simulateClumpSizeDist | 10.105 | 0.119 | 10.227 | |
| simulateNumHitsDist | 1.709 | 0.009 | 1.718 | |