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CHECK report for CAGEfightR on malbec2

This page was generated on 2018-10-17 08:31:42 -0400 (Wed, 17 Oct 2018).

Package 178/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.0.0
Malte Thodberg
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CAGEfightR
Branch: RELEASE_3_7
Last Commit: ff2608f
Last Changed Date: 2018-04-30 10:35:52 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEfightR
Version: 1.0.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CAGEfightR_1.0.0.tar.gz
StartedAt: 2018-10-15 22:56:18 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:00:27 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 248.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CAGEfightR_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 or elapsed time > 5s
              user system elapsed
assignGeneID 4.648  0.028   5.043
* 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


Installation output

CAGEfightR.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CAGEfightR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘CAGEfightR’ ...
** 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
* DONE (CAGEfightR)

Tests output


Example timings

CAGEfightR.Rcheck/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID4.6480.0285.043
assignMissingID1.3320.0121.344
assignTxID0.7320.0080.741
assignTxType0.0040.0000.002
bwCommonGenome0.0520.0000.160
bwGenomeCompatibility0.0280.0000.027
bwValid0.0120.0000.011
calcBidirectionality0.4760.0000.494
calcComposition2.4160.0082.427
calcPooled0.0560.0120.071
calcShape2.1960.0282.227
calcSupport0.1240.0000.123
calcTPM0.1680.0120.177
calcTotalTags0.0920.0000.093
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally1.4720.0081.484
combineClusters0.7440.0120.758
exampleDesign0.0000.0040.006
quantifyCTSSs0.0040.0000.001
quantifyClusters0.3360.0040.342
quantifyGenes1.3720.0081.383
quickEnhancers0.0040.0000.000
quickTSSs000
shapeEntropy0.0000.0000.001
shapeIQR0.0040.0000.001
shapeMultimodality000
subsetByBidirectionality0.3000.0000.297
subsetByComposition1.6280.0001.629
subsetBySupport0.0480.0000.049
swapRanges0.1080.0000.111
swapScores0.0480.0000.050
trackBalance4.2840.0044.324
trackCTSS0.9680.0000.970
trackClusters1.3920.0001.394
trimToPeak0.3960.0000.395
trimToPercentiles1.2440.0041.248
tuneTagClustering2.3200.1642.507