Wolfgang Kopp
| Snapshot Date: 2024-05-01 14:05:06 -0400 (Wed, 01 May 2024) |
| git_url: https://git.bioconductor.org/packages/motifcounter |
| git_branch: devel |
| git_last_commit: a85abf5 |
| git_last_commit_date: 2024-04-30 10:57:02 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-03 11:38:35 -0400 (Fri, 03 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
| 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 1286/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| motifcounter 1.29.0 (landing page) Wolfgang Kopp
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.29.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.29.0.tar.gz |
| StartedAt: 2024-05-02 07:44:09 -0400 (Thu, 02 May 2024) |
| EndedAt: 2024-05-02 07:52:07 -0400 (Thu, 02 May 2024) |
| EllapsedTime: 477.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: motifcounter.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.29.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simulateClumpSizeDist 18.094 0.499 22.122
scoreDistEmpirical 5.625 0.094 6.455
motifEnrichment 5.200 0.054 6.040
simulateNumHitsDist 4.204 0.076 5.111
* 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
‘/Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.Rcheck/00check.log’
for details.
motifcounter.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifcounter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rbackground.c -o Rbackground.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rcombinatorial.c -o Rcombinatorial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rminmaxscore.c -o Rminmaxscore.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Roption.c -o Roption.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Roverlap.c -o Roverlap.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rscore1d.c -o Rscore1d.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
int mins, maxs, noscores;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rsimulate.c -o Rsimulate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c background.c -o background.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c combinatorial.c -o combinatorial.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c compoundpoisson.c -o compoundpoisson.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c markovchain.c -o markovchain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c markovchain_single.c -o markovchain_single.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c matrix.c -o matrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c mdist_register.c -o mdist_register.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c minmaxscore.c -o minmaxscore.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c overlap.c -o overlap.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c score1d.c -o score1d.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c score2d.c -o score2d.o
score2d.c:597:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
double p, p0 = 0.0, p1 = 0.0, ptmp;
^
score2d.c:597:15: warning: variable 'p0' set but not used [-Wunused-but-set-variable]
double p, p0 = 0.0, p1 = 0.0, ptmp;
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
int j, i, index, cindex, ds;
^
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
int s, index, cindex;
^
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
int s, index, cindex;
^
3 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c sequence.c -o sequence.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c simulate.c -o simulate.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
203.026 3.792 245.607
motifcounter.Rcheck/motifcounter-Ex.timings
| name | user | system | elapsed | |
| clumpSizeDist | 0.351 | 0.016 | 0.452 | |
| combinatorialDist | 0.503 | 0.040 | 0.622 | |
| compoundPoissonDist | 0.354 | 0.040 | 0.442 | |
| computeClumpStartProb | 0.257 | 0.006 | 0.296 | |
| generateDNAString | 0.213 | 0.009 | 0.345 | |
| generateDNAStringSet | 0.308 | 0.005 | 0.355 | |
| hitStrand | 0.208 | 0.024 | 0.258 | |
| lenSequences | 0.201 | 0.031 | 0.268 | |
| markovModel | 0.243 | 0.007 | 0.276 | |
| motifAndBackgroundValid | 0.187 | 0.004 | 0.218 | |
| motifEnrichment | 5.200 | 0.054 | 6.040 | |
| motifHitProfile | 0.194 | 0.009 | 0.241 | |
| motifHits | 0.196 | 0.008 | 0.226 | |
| motifValid | 0.003 | 0.001 | 0.004 | |
| motifcounter-package | 1.651 | 0.047 | 1.931 | |
| motifcounterOptions | 0.000 | 0.000 | 0.001 | |
| normalizeMotif | 0.003 | 0.001 | 0.004 | |
| numMotifHits | 1.446 | 0.023 | 1.690 | |
| probOverlapHit | 0.307 | 0.010 | 0.355 | |
| readBackground | 0.194 | 0.005 | 0.219 | |
| revcompMotif | 0.003 | 0.002 | 0.004 | |
| scoreDist | 0.192 | 0.005 | 0.232 | |
| scoreDistBf | 0.226 | 0.005 | 0.273 | |
| scoreDistEmpirical | 5.625 | 0.094 | 6.455 | |
| scoreHistogram | 0.489 | 0.025 | 0.547 | |
| scoreHistogramSingleSeq | 0.207 | 0.021 | 0.260 | |
| scoreProfile | 1.071 | 0.016 | 1.168 | |
| scoreSequence | 0.196 | 0.008 | 0.217 | |
| scoreStrand | 0.196 | 0.007 | 0.221 | |
| scoreThreshold | 0.184 | 0.004 | 0.208 | |
| sigLevel | 0.000 | 0.000 | 0.001 | |
| simulateClumpSizeDist | 18.094 | 0.499 | 22.122 | |
| simulateNumHitsDist | 4.204 | 0.076 | 5.111 | |