| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:15 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the motifcounter package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1242/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifcounter 1.23.0 (landing page) Wolfgang Kopp
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: motifcounter |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings motifcounter_1.23.0.tar.gz |
| StartedAt: 2023-02-07 08:53:16 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 08:57:50 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 273.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: motifcounter.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings motifcounter_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/motifcounter.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.23.0’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 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 11.683 0.190 15.988
motifEnrichment 3.444 0.111 5.374
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(motifcounter)
>
> test_check("motifcounter")
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘motifcounter.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘motifcounter.Rmd’ using rmarkdown
Killed
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/motifcounter.Rcheck/00check.log’
for details.
motifcounter.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL motifcounter
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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]
143 | int mins, maxs, noscores;
| ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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]
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"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
Killed
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.183 | 0.036 | 0.426 | |
| combinatorialDist | 0.326 | 0.016 | 0.542 | |
| compoundPoissonDist | 0.216 | 0.028 | 0.244 | |
| computeClumpStartProb | 0.173 | 0.000 | 0.241 | |
| generateDNAString | 0.103 | 0.000 | 0.103 | |
| generateDNAStringSet | 0.154 | 0.000 | 0.170 | |
| hitStrand | 0.098 | 0.004 | 0.104 | |
| lenSequences | 0.087 | 0.012 | 0.152 | |
| markovModel | 0.142 | 0.004 | 0.146 | |
| motifAndBackgroundValid | 0.095 | 0.000 | 0.108 | |
| motifEnrichment | 3.444 | 0.111 | 5.374 | |
| motifHitProfile | 0.103 | 0.001 | 0.277 | |
| motifHits | 0.105 | 0.000 | 0.213 | |
| motifValid | 0.002 | 0.000 | 0.011 | |
| motifcounter-package | 1.139 | 0.012 | 1.211 | |
| motifcounterOptions | 0 | 0 | 0 | |
| normalizeMotif | 0.001 | 0.000 | 0.002 | |
| numMotifHits | 0.706 | 0.004 | 1.163 | |
| probOverlapHit | 0.180 | 0.004 | 0.184 | |
| readBackground | 0.093 | 0.000 | 0.142 | |
| revcompMotif | 0.002 | 0.000 | 0.002 | |
| scoreDist | 0.098 | 0.000 | 0.183 | |
| scoreDistBf | 0.120 | 0.000 | 0.244 | |
| scoreDistEmpirical | 2.812 | 0.004 | 3.305 | |
| scoreHistogram | 0.253 | 0.004 | 0.257 | |
| scoreHistogramSingleSeq | 0.100 | 0.004 | 0.103 | |
| scoreProfile | 0.553 | 0.000 | 0.594 | |
| scoreSequence | 0.122 | 0.000 | 0.257 | |
| scoreStrand | 0.099 | 0.000 | 0.147 | |
| scoreThreshold | 0.098 | 0.000 | 0.098 | |
| sigLevel | 0 | 0 | 0 | |
| simulateClumpSizeDist | 11.683 | 0.190 | 15.988 | |
| simulateNumHitsDist | 2.301 | 0.169 | 4.864 | |