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BioC 3.5: CHECK report for ATACseqQC on tokay2

This page was generated on 2017-08-16 13:26:57 -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: rm -rf ATACseqQC.buildbin-libdir ATACseqQC.Rcheck && mkdir ATACseqQC.buildbin-libdir ATACseqQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ATACseqQC.buildbin-libdir ATACseqQC_1.0.4.tar.gz >ATACseqQC.Rcheck\00install.out 2>&1 && cp ATACseqQC.Rcheck\00install.out ATACseqQC-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ATACseqQC.buildbin-libdir --install="check:ATACseqQC-install.out" --force-multiarch --no-vignettes --timings ATACseqQC_1.0.4.tar.gz
StartedAt: 2017-08-15 22:04:46 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:21:07 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 981.2 seconds
RetCode: 0
Status:  OK  
CheckDir: ATACseqQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ATACseqQC.buildbin-libdir ATACseqQC.Rcheck && mkdir ATACseqQC.buildbin-libdir ATACseqQC.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ATACseqQC.buildbin-libdir ATACseqQC_1.0.4.tar.gz >ATACseqQC.Rcheck\00install.out 2>&1 && cp ATACseqQC.Rcheck\00install.out ATACseqQC-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ATACseqQC.buildbin-libdir --install="check:ATACseqQC-install.out" --force-multiarch --no-vignettes --timings ATACseqQC_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ATACseqQC.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'ATACseqQC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
enrichedFragments     106.53   2.45  109.01
splitBam              106.28   1.59  108.73
shiftGAlignmentsList   23.27   0.34   23.61
factorFootprints       22.08   0.32   25.45
splitGAlignmentsByCut   5.76   0.64    6.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
enrichedFragments     130.33   2.28  132.61
splitBam              113.92   1.59  117.05
shiftGAlignmentsList   27.33   0.22   27.55
factorFootprints       23.39   0.27   24.93
splitGAlignmentsByCut   7.68   0.92    8.59
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ATACseqQC.Rcheck/00check.log'
for details.


ATACseqQC.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'ATACseqQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ATACseqQC' as ATACseqQC_1.0.4.zip
* DONE (ATACseqQC)

ATACseqQC.Rcheck/examples_i386/ATACseqQC-Ex.timings:

nameusersystemelapsed
enrichedFragments106.53 2.45109.01
factorFootprints22.08 0.3225.45
fragSizeDist0.500.010.51
plotFootprints0.860.052.14
readBamFile0.870.050.93
shiftGAlignmentsList23.27 0.3423.61
splitBam106.28 1.59108.73
splitGAlignmentsByCut5.760.646.41
writeListOfGAlignments0.440.020.45

ATACseqQC.Rcheck/examples_x64/ATACseqQC-Ex.timings:

nameusersystemelapsed
enrichedFragments130.33 2.28132.61
factorFootprints23.39 0.2724.93
fragSizeDist0.360.020.37
plotFootprints0.750.032.11
readBamFile1.140.031.17
shiftGAlignmentsList27.33 0.2227.55
splitBam113.92 1.59117.05
splitGAlignmentsByCut7.680.928.59
writeListOfGAlignments0.340.000.40