Malte Thodberg
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CAGEfightR |
| Branch: master |
| Last Commit: 1318c4f |
| Last Changed Date: 2019-10-29 13:43:09 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:51:18 -0500 (Thu, 16 Jan 2020).
| Package 212/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CAGEfightR 1.7.0 Malte Thodberg
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CAGEfightR |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEfightR_1.7.0.tar.gz |
| StartedAt: 2020-01-16 02:25:03 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:34:51 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 587.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CAGEfightR.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:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEfightR_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CAGEfightR.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 ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.7.0’
* 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 ‘CAGEfightR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findLinks 6.205 1.309 6.892
calcShape 6.741 0.188 6.930
assignGeneID 6.225 0.328 6.559
trimToPercentiles 5.145 0.302 5.452
trackCTSS 4.821 0.508 5.330
* 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: OK
CAGEfightR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEfightR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘CAGEfightR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (CAGEfightR)
CAGEfightR.Rcheck/CAGEfightR-Ex.timings
| name | user | system | elapsed | |
| assignGeneID | 6.225 | 0.328 | 6.559 | |
| assignMissingID | 1.827 | 0.148 | 1.975 | |
| assignTxID | 1.696 | 0.106 | 1.802 | |
| assignTxType | 0.001 | 0.002 | 0.002 | |
| balanceBC | 0.001 | 0.000 | 0.002 | |
| balanceD | 0.001 | 0.000 | 0.002 | |
| bwCommonGenome | 0.085 | 0.010 | 0.140 | |
| bwGenomeCompatibility | 0.030 | 0.006 | 0.036 | |
| bwValid | 0.012 | 0.003 | 0.015 | |
| calcBidirectionality | 1.317 | 0.132 | 1.641 | |
| calcComposition | 2.912 | 0.151 | 3.064 | |
| calcPooled | 0.26 | 0.02 | 0.28 | |
| calcShape | 6.741 | 0.188 | 6.930 | |
| calcSupport | 0.194 | 0.020 | 0.213 | |
| calcTPM | 0.227 | 0.021 | 0.248 | |
| calcTotalTags | 0.089 | 0.016 | 0.106 | |
| checkPeaked | 0.120 | 0.016 | 0.136 | |
| checkPooled | 0.119 | 0.019 | 0.138 | |
| clusterBidirectionally | 0.000 | 0.001 | 0.001 | |
| clusterUnidirectionally | 2.796 | 0.120 | 2.916 | |
| combineClusters | 1.632 | 0.050 | 1.838 | |
| exampleDesign | 0.013 | 0.016 | 0.029 | |
| findLinks | 6.205 | 1.309 | 6.892 | |
| findStretches | 1.092 | 0.226 | 1.318 | |
| quantifyCTSSs | 0.001 | 0.001 | 0.002 | |
| quantifyClusters | 1.127 | 0.276 | 1.404 | |
| quantifyGenes | 2.463 | 0.321 | 2.843 | |
| quickEnhancers | 0.000 | 0.000 | 0.001 | |
| quickTSSs | 0.000 | 0.000 | 0.001 | |
| shapeEntropy | 0.001 | 0.001 | 0.002 | |
| shapeIQR | 0.001 | 0.001 | 0.002 | |
| shapeMultimodality | 0.000 | 0.001 | 0.000 | |
| subsetByBidirectionality | 1.048 | 0.143 | 1.191 | |
| subsetByComposition | 2.457 | 0.150 | 2.607 | |
| subsetBySupport | 0.233 | 0.033 | 0.266 | |
| swapRanges | 0.361 | 0.021 | 0.383 | |
| swapScores | 0.331 | 0.014 | 0.346 | |
| trackBalance | 0.000 | 0.001 | 0.002 | |
| trackCTSS | 4.821 | 0.508 | 5.330 | |
| trackClusters | 3.091 | 0.103 | 3.196 | |
| trackLinks | 2.151 | 0.625 | 2.476 | |
| trimToPeak | 2.072 | 0.366 | 2.467 | |
| trimToPercentiles | 5.145 | 0.302 | 5.452 | |
| tuneTagClustering | 0.000 | 0.000 | 0.001 | |