| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:41 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 1255/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifcounter 1.22.0 (landing page) Wolfgang Kopp
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: motifcounter |
| Version: 1.22.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifcounter.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings motifcounter_1.22.0.tar.gz |
| StartedAt: 2023-04-11 03:35:50 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 03:43:03 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 432.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: motifcounter.Rcheck |
| Warnings: NA |
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### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:motifcounter.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings motifcounter_1.22.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/motifcounter.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'motifcounter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'motifcounter' version '1.22.0'
* 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
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/motifcounter/libs/x64/motifcounter.dll':
Found '_assert', possibly from 'assert' (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. 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 7.42 0.31 7.73
* 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")
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/motifcounter.Rcheck/00check.log'
for details.
motifcounter.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL motifcounter
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'motifcounter' ...
** using staged installation
** libs
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rbackground.c -o Rbackground.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rcombinatorial.c -o Rcombinatorial.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rcompoundpoisson.c -o Rcompoundpoisson.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rminmaxscore.c -o Rminmaxscore.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Roption.c -o Roption.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Roverlap.c -o Roverlap.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rscore1d.c -o Rscore1d.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -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-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rsimulate.c -o Rsimulate.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c background.c -o background.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c combinatorial.c -o combinatorial.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c compoundpoisson.c -o compoundpoisson.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c markovchain.c -o markovchain.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c markovchain_single.c -o markovchain_single.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix.c -o matrix.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mdist_register.c -o mdist_register.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c minmaxscore.c -o minmaxscore.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c overlap.c -o overlap.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c score1d.c -o score1d.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c score2d.c -o score2d.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -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-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sequence.c -o sequence.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DIN_R -O2 -Wall -std=gnu99 -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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-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.fail
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.20 | 0.03 | 0.23 | |
| combinatorialDist | 0.25 | 0.08 | 0.33 | |
| compoundPoissonDist | 0.30 | 0.11 | 0.40 | |
| computeClumpStartProb | 0.18 | 0.03 | 0.22 | |
| generateDNAString | 0.07 | 0.00 | 0.06 | |
| generateDNAStringSet | 0.12 | 0.00 | 0.13 | |
| hitStrand | 0.11 | 0.00 | 0.11 | |
| lenSequences | 0.08 | 0.00 | 0.08 | |
| markovModel | 0.19 | 0.03 | 0.22 | |
| motifAndBackgroundValid | 0.06 | 0.00 | 0.06 | |
| motifEnrichment | 2.28 | 0.14 | 2.42 | |
| motifHitProfile | 0.08 | 0.00 | 0.08 | |
| motifHits | 0.12 | 0.00 | 0.12 | |
| motifValid | 0 | 0 | 0 | |
| motifcounter-package | 0.91 | 0.11 | 1.02 | |
| motifcounterOptions | 0 | 0 | 0 | |
| normalizeMotif | 0 | 0 | 0 | |
| numMotifHits | 0.47 | 0.02 | 0.49 | |
| probOverlapHit | 0.22 | 0.11 | 0.33 | |
| readBackground | 0.09 | 0.00 | 0.09 | |
| revcompMotif | 0.02 | 0.00 | 0.02 | |
| scoreDist | 0.10 | 0.00 | 0.11 | |
| scoreDistBf | 0.11 | 0.00 | 0.10 | |
| scoreDistEmpirical | 2.52 | 0.01 | 2.54 | |
| scoreHistogram | 0.19 | 0.00 | 0.18 | |
| scoreHistogramSingleSeq | 0.06 | 0.02 | 0.08 | |
| scoreProfile | 0.44 | 0.00 | 0.44 | |
| scoreSequence | 0.11 | 0.00 | 0.11 | |
| scoreStrand | 0.06 | 0.00 | 0.06 | |
| scoreThreshold | 0.06 | 0.02 | 0.08 | |
| sigLevel | 0 | 0 | 0 | |
| simulateClumpSizeDist | 7.42 | 0.31 | 7.73 | |
| simulateNumHitsDist | 1.69 | 0.22 | 1.91 | |