Konstantin Krismer
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/transite |
| Branch: master |
| Last Commit: 2f04324 |
| Last Changed Date: 2019-10-29 13:43:21 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:52:36 -0500 (Thu, 16 Jan 2020).
| Package 1741/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| transite 1.5.0 Konstantin Krismer
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: transite |
| Version: 1.5.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transite_1.5.0.tar.gz |
| StartedAt: 2020-01-16 09:34:51 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 09:41:18 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 387.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: transite.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transite_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/transite.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘transite/DESCRIPTION’ ... OK
* this is package ‘transite’ version ‘1.5.0’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘transite’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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
runKmerTSMA 80.775 0.365 96.613
runKmerSPMA 72.059 2.173 82.275
calculateKmerEnrichment 10.853 0.038 10.891
computeKmerEnrichment 5.344 0.008 5.352
runMatrixSPMA 3.480 0.111 5.865
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/transite.Rcheck/00check.log’
for details.
transite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL transite ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘transite’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c scoring.cpp -o scoring.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o transite.so RcppExports.o scoring.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-transite/00new/transite/libs ** R ** data ** 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 (transite)
transite.Rcheck/transite-Ex.timings
| name | user | system | elapsed | |
| RBPMotif-class | 0.010 | 0.001 | 0.011 | |
| SpectrumScore-class | 0.002 | 0.001 | 0.003 | |
| calculateKmerEnrichment | 10.853 | 0.038 | 10.891 | |
| calculateKmerScores | 0.004 | 0.000 | 0.005 | |
| calculateLocalConsistency | 1.091 | 0.071 | 1.163 | |
| calculateMotifEnrichment | 1.691 | 0.063 | 1.753 | |
| calculateTranscriptMC | 0.011 | 0.001 | 0.012 | |
| checkKmers | 0.001 | 0.000 | 0.001 | |
| computeKmerEnrichment | 5.344 | 0.008 | 5.352 | |
| createKmerMotif | 0.003 | 0.000 | 0.003 | |
| createMatrixMotif | 0.006 | 0.000 | 0.006 | |
| drawVolcanoPlot | 0.560 | 0.015 | 0.574 | |
| empiricalEnrichmentMeanCDF | 0.005 | 0.000 | 0.005 | |
| generateIUPACByKmers | 0.002 | 0.000 | 0.001 | |
| generateIUPACByMatrix | 0.004 | 0.000 | 0.005 | |
| generateKmers | 0.303 | 0.010 | 0.314 | |
| generateKmersFromIUPAC | 0.002 | 0.001 | 0.004 | |
| geometricMean | 0.000 | 0.000 | 0.001 | |
| getMotifById | 0.008 | 0.001 | 0.008 | |
| getMotifByRBP | 0.011 | 0.003 | 0.015 | |
| getMotifs | 0.000 | 0.000 | 0.001 | |
| getPPM | 0.011 | 0.001 | 0.012 | |
| initIUPAClookupTable | 0.005 | 0.000 | 0.005 | |
| motifsMetaInfo | 0.029 | 0.008 | 0.038 | |
| pCombine | 0.001 | 0.000 | 0.001 | |
| runKmerSPMA | 72.059 | 2.173 | 82.275 | |
| runKmerTSMA | 80.775 | 0.365 | 96.613 | |
| runMatrixSPMA | 3.480 | 0.111 | 5.865 | |
| runMatrixTSMA | 0.028 | 0.002 | 0.030 | |
| scoreSequences | 0.012 | 0.002 | 0.014 | |
| scoreSpectrum | 1.904 | 0.055 | 1.959 | |
| scoreTranscripts | 0.009 | 0.001 | 0.009 | |
| setMotifs | 0.004 | 0.000 | 0.004 | |
| spectrumClassifier | 1.921 | 0.099 | 2.020 | |
| subdivideData | 0.006 | 0.001 | 0.006 | |