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BioC 3.2: CHECK report for CoverageView on zin1

This page was generated on 2016-04-23 10:13:45 -0700 (Sat, 23 Apr 2016).

Package 232/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoverageView 1.6.0
Ernesto Lowy
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CoverageView
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoverageView
Version: 1.6.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CoverageView_1.6.0.tar.gz
StartedAt: 2016-04-22 23:40:06 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:42:19 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 132.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CoverageView.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CoverageView_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CoverageView.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoverageView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoverageView’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoverageView’ can be installed ... [12s/12s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘parallel::parLapplyLB’ by ‘BiocGenerics::parLapplyLB’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::parApply’ by ‘BiocGenerics::parApply’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::clusterApplyLB’ by ‘BiocGenerics::clusterApplyLB’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::clusterExport’ by ‘BiocGenerics::clusterExport’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::parSapply’ by ‘BiocGenerics::parSapply’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::clusterCall’ by ‘BiocGenerics::clusterCall’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::clusterApply’ by ‘BiocGenerics::clusterApply’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::parSapplyLB’ by ‘BiocGenerics::parSapplyLB’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::parCapply’ by ‘BiocGenerics::parCapply’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::parLapply’ by ‘BiocGenerics::parLapply’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::clusterMap’ by ‘BiocGenerics::clusterMap’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::clusterEvalQ’ by ‘BiocGenerics::clusterEvalQ’ when loading ‘CoverageView’
  Warning: replacing previous import ‘parallel::parRapply’ by ‘BiocGenerics::parRapply’ when loading ‘CoverageView’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/CoverageView.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/12s] OK
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/CoverageView.Rcheck/00check.log’
for details.


CoverageView.Rcheck/00install.out:

* installing *source* package ‘CoverageView’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘parallel::parLapplyLB’ by ‘BiocGenerics::parLapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parApply’ by ‘BiocGenerics::parApply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterApplyLB’ by ‘BiocGenerics::clusterApplyLB’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterExport’ by ‘BiocGenerics::clusterExport’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parSapply’ by ‘BiocGenerics::parSapply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterCall’ by ‘BiocGenerics::clusterCall’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterApply’ by ‘BiocGenerics::clusterApply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parSapplyLB’ by ‘BiocGenerics::parSapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parCapply’ by ‘BiocGenerics::parCapply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parLapply’ by ‘BiocGenerics::parLapply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterMap’ by ‘BiocGenerics::clusterMap’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterEvalQ’ by ‘BiocGenerics::clusterEvalQ’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parRapply’ by ‘BiocGenerics::parRapply’ when loading ‘CoverageView’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘parallel::parLapplyLB’ by ‘BiocGenerics::parLapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parApply’ by ‘BiocGenerics::parApply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterApplyLB’ by ‘BiocGenerics::clusterApplyLB’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterExport’ by ‘BiocGenerics::clusterExport’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parSapply’ by ‘BiocGenerics::parSapply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterCall’ by ‘BiocGenerics::clusterCall’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterApply’ by ‘BiocGenerics::clusterApply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parSapplyLB’ by ‘BiocGenerics::parSapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parCapply’ by ‘BiocGenerics::parCapply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parLapply’ by ‘BiocGenerics::parLapply’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterMap’ by ‘BiocGenerics::clusterMap’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::clusterEvalQ’ by ‘BiocGenerics::clusterEvalQ’ when loading ‘CoverageView’
Warning: replacing previous import ‘parallel::parRapply’ by ‘BiocGenerics::parRapply’ when loading ‘CoverageView’
* DONE (CoverageView)

CoverageView.Rcheck/CoverageView-Ex.timings:

nameusersystemelapsed
CoverageBamFile-class0.0180.0040.022
CoverageBigWigFile-class0.010.000.01
cov.interval0.4780.0120.490
cov.matrix2.4940.8151.850
draw.heatmap2.1220.0682.188
draw.profile0.1840.0000.184
export.wig0.1290.0000.130
genome.covplot.cumdepth0.3870.0040.390
genome.covplot.depth0.3490.0000.349
write.profile0.1090.0690.218