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BioC 3.5: CHECK report for ATACseqQC on malbec2

This page was generated on 2017-08-16 13:18:25 -0400 (Wed, 16 Aug 2017).

Package 74/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ATACseqQC 1.0.4
Jianhong Ou
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ATACseqQC
Last Changed Rev: 131505 / Revision: 131943
Last Changed Date: 2017-07-22 20:49:36 -0400 (Sat, 22 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ATACseqQC
Version: 1.0.4
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ATACseqQC_1.0.4.tar.gz
StartedAt: 2017-08-15 21:15:43 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:24:26 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 523.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ATACseqQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ATACseqQC_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ATACseqQC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACseqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ATACseqQC’ version ‘1.0.4’
* 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 ‘ATACseqQC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   7.5Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
enrichedFragments     102.264 25.936 128.341
splitBam               99.188  3.652 103.142
shiftGAlignmentsList   19.492  0.648  20.154
factorFootprints       17.972  1.432  23.191
splitGAlignmentsByCut   5.604  2.844   8.457
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/ATACseqQC.Rcheck/00check.log’
for details.


ATACseqQC.Rcheck/00install.out:

* installing *source* package ‘ATACseqQC’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ATACseqQC)

ATACseqQC.Rcheck/ATACseqQC-Ex.timings:

nameusersystemelapsed
enrichedFragments102.264 25.936128.341
factorFootprints17.972 1.43223.191
fragSizeDist0.4640.0040.466
plotFootprints1.1440.4121.597
readBamFile0.8800.0480.926
shiftGAlignmentsList19.492 0.64820.154
splitBam 99.188 3.652103.142
splitGAlignmentsByCut5.6042.8448.457
writeListOfGAlignments0.4160.0040.421