| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:27 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1272/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifcounter 1.23.0 (landing page) Wolfgang Kopp
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| 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/site-library --timings motifcounter_1.23.0.tar.gz |
| StartedAt: 2023-04-11 21:44:41 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 21:49:17 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 276.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifcounter.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running 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/site-library --timings motifcounter_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/motifcounter.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 22.04.2 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 loading without being on the library search path ... OK
* checking 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 9.939 0.408 10.346
* 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 ...
‘motifcounter.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/motifcounter.Rcheck/00check.log’
for details.
motifcounter.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL motifcounter
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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/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 version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
>
> proc.time()
user system elapsed
128.535 4.640 134.745
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.130 | 0.020 | 0.151 | |
| combinatorialDist | 0.233 | 0.032 | 0.265 | |
| compoundPoissonDist | 0.166 | 0.004 | 0.171 | |
| computeClumpStartProb | 0.112 | 0.000 | 0.112 | |
| generateDNAString | 0.07 | 0.00 | 0.07 | |
| generateDNAStringSet | 0.109 | 0.000 | 0.110 | |
| hitStrand | 0.065 | 0.008 | 0.073 | |
| lenSequences | 0.045 | 0.024 | 0.070 | |
| markovModel | 0.105 | 0.000 | 0.105 | |
| motifAndBackgroundValid | 0.064 | 0.000 | 0.064 | |
| motifEnrichment | 2.313 | 0.012 | 2.326 | |
| motifHitProfile | 0.069 | 0.000 | 0.069 | |
| motifHits | 0.071 | 0.000 | 0.071 | |
| motifValid | 0.001 | 0.000 | 0.002 | |
| motifcounter-package | 0.913 | 0.012 | 0.925 | |
| motifcounterOptions | 0 | 0 | 0 | |
| normalizeMotif | 0.002 | 0.000 | 0.002 | |
| numMotifHits | 0.487 | 0.004 | 0.491 | |
| probOverlapHit | 0.119 | 0.008 | 0.126 | |
| readBackground | 0.064 | 0.000 | 0.064 | |
| revcompMotif | 0.002 | 0.000 | 0.002 | |
| scoreDist | 0.068 | 0.000 | 0.067 | |
| scoreDistBf | 0.086 | 0.008 | 0.094 | |
| scoreDistEmpirical | 2.036 | 0.012 | 2.048 | |
| scoreHistogram | 0.169 | 0.004 | 0.173 | |
| scoreHistogramSingleSeq | 0.069 | 0.004 | 0.073 | |
| scoreProfile | 0.353 | 0.008 | 0.361 | |
| scoreSequence | 0.065 | 0.004 | 0.070 | |
| scoreStrand | 0.068 | 0.000 | 0.069 | |
| scoreThreshold | 0.066 | 0.000 | 0.067 | |
| sigLevel | 0.000 | 0.000 | 0.001 | |
| simulateClumpSizeDist | 9.939 | 0.408 | 10.346 | |
| simulateNumHitsDist | 1.766 | 0.120 | 1.885 | |