Wolfgang Kopp
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/motifcounter |
| git_branch: RELEASE_3_20 |
| git_last_commit: b49cf20 |
| git_last_commit_date: 2024-10-29 10:18:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1316/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifcounter 1.30.0 (landing page) Wolfgang Kopp
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.30.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifcounter.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings motifcounter_1.30.0.tar.gz |
| StartedAt: 2024-12-20 03:41:42 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 03:50:50 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 548.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifcounter.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifcounter.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings motifcounter_1.30.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.30.0'
* 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) 13.3.0'
* 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 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 'F:/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 9.4 0.42 9.83
* 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
'F:/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck/00check.log'
for details.
motifcounter.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL motifcounter
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'motifcounter' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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 -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/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)
motifcounter.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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
311.15 111.37 423.43
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.25 | 0.08 | 0.33 | |
| combinatorialDist | 0.28 | 0.10 | 0.38 | |
| compoundPoissonDist | 0.36 | 0.17 | 0.54 | |
| computeClumpStartProb | 0.19 | 0.06 | 0.25 | |
| generateDNAString | 0.06 | 0.00 | 0.06 | |
| generateDNAStringSet | 0.13 | 0.00 | 0.12 | |
| hitStrand | 0.12 | 0.00 | 0.13 | |
| lenSequences | 0.10 | 0.02 | 0.11 | |
| markovModel | 0.11 | 0.09 | 0.20 | |
| motifAndBackgroundValid | 0.07 | 0.00 | 0.08 | |
| motifEnrichment | 2.47 | 0.16 | 2.62 | |
| motifHitProfile | 0.07 | 0.01 | 0.08 | |
| motifHits | 0.07 | 0.00 | 0.08 | |
| motifValid | 0 | 0 | 0 | |
| motifcounter-package | 1.08 | 0.19 | 1.27 | |
| motifcounterOptions | 0 | 0 | 0 | |
| normalizeMotif | 0.02 | 0.00 | 0.01 | |
| numMotifHits | 0.58 | 0.03 | 0.61 | |
| probOverlapHit | 0.28 | 0.06 | 0.34 | |
| readBackground | 0.08 | 0.00 | 0.08 | |
| revcompMotif | 0 | 0 | 0 | |
| scoreDist | 0.06 | 0.00 | 0.07 | |
| scoreDistBf | 0.08 | 0.00 | 0.08 | |
| scoreDistEmpirical | 2.86 | 0.04 | 2.89 | |
| scoreHistogram | 0.26 | 0.01 | 0.28 | |
| scoreHistogramSingleSeq | 0.09 | 0.02 | 0.11 | |
| scoreProfile | 0.44 | 0.00 | 0.44 | |
| scoreSequence | 0.06 | 0.00 | 0.06 | |
| scoreStrand | 0.07 | 0.00 | 0.06 | |
| scoreThreshold | 0.08 | 0.00 | 0.08 | |
| sigLevel | 0 | 0 | 0 | |
| simulateClumpSizeDist | 9.40 | 0.42 | 9.83 | |
| simulateNumHitsDist | 2.35 | 0.23 | 2.58 | |