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BioC 3.2: CHECK report for BBCAnalyzer on linux1.bioconductor.org

This page was generated on 2015-10-27 17:27:23 -0400 (Tue, 27 Oct 2015).

Package 77/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BBCAnalyzer 1.0.0
Sarah Sandmann
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BBCAnalyzer
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  TIMEOUT  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BBCAnalyzer
Version: 1.0.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BBCAnalyzer_1.0.0.tar.gz
StartedAt: 2015-10-27 01:14:53 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:18:27 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 214.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BBCAnalyzer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BBCAnalyzer_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BBCAnalyzer.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BBCAnalyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BBCAnalyzer’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BBCAnalyzer’ can be installed ... [17s/17s] 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 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 ... NOTE
plotCountsPerSampleRelativeVcf_plot: warning in png(file =
  paste(directory2, "/", samples[j, 1], ".png", sep = ""), width =
  1600, height = 800): partial argument match of 'file' to 'filename'
plotCountsPerSampleRelative_plot: warning in png(file =
  paste(directory2, "/", samples[j, 1], ".png", sep = ""), width =
  1600, height = 800): partial argument match of 'file' to 'filename'
plotCountsPerSampleVcf_plot: warning in png(file = paste(directory2,
  "/", samples[j, 1], ".png", sep = ""), width = 1600, height = 800):
  partial argument match of 'file' to 'filename'
plotCountsPerSample_plot: warning in png(file = paste(directory2, "/",
  samples[j, 1], ".png", sep = ""), width = 1600, height = 800):
  partial argument match of 'file' to 'filename'
plotCountsPerTargetRelativeVcf_plot: warning in png(file =
  paste(directory2, "/", calling[[1]][j, 1], ";", calling[[1]][j, 2],
  "_", counter, ".png", sep = ""), width = 1600, height = 600): partial
  argument match of 'file' to 'filename'
plotCountsPerTargetRelativeVcf_plot: warning in png(file =
  paste(directory2, "/", calling[[1]][j, 1], ";", calling[[1]][j, 2],
  ".png", sep = ""), width = 1600, height = 600): partial argument
  match of 'file' to 'filename'
plotCountsPerTargetRelative_plot: warning in png(file =
  paste(directory2, "/", calling[[1]][j, 1], ";", calling[[1]][j, 2],
  "_", counter, ".png", sep = ""), width = 1600, height = 600): partial
  argument match of 'file' to 'filename'
plotCountsPerTargetRelative_plot: warning in png(file =
  paste(directory2, "/", calling[[1]][j, 1], ";", calling[[1]][j, 2],
  ".png", sep = ""), width = 1600, height = 600): partial argument
  match of 'file' to 'filename'
plotCountsPerTargetVcf_plot: warning in png(file = paste(directory2,
  "/", calling[[1]][j, 1], ";", calling[[1]][j, 2], "_", counter,
  ".png", sep = ""), width = 1600, height = 600): partial argument
  match of 'file' to 'filename'
plotCountsPerTargetVcf_plot: warning in png(file = paste(directory2,
  "/", calling[[1]][j, 1], ";", calling[[1]][j, 2], ".png", sep = ""),
  width = 1600, height = 600): partial argument match of 'file' to
  'filename'
plotCountsPerTarget_plot: warning in png(file = paste(directory2, "/",
  calling[[1]][j, 1], ";", calling[[1]][j, 2], "_", counter, ".png",
  sep = ""), width = 1600, height = 600): partial argument match of
  'file' to 'filename'
plotCountsPerTarget_plot: warning in png(file = paste(directory2, "/",
  calling[[1]][j, 1], ";", calling[[1]][j, 2], ".png", sep = ""), width
  = 1600, height = 600): partial argument match of 'file' to 'filename'
analyzeReads: no visible global function definition for ‘GRanges’
analyzeReads: no visible global function definition for ‘IRanges’
analyzeReads: no visible global function definition for ‘PhredQuality’
analyzeReads: no visible global function definition for ‘vcountPattern’
analyzeReads: no visible global function definition for ‘encoding’
frequencyAnalysis: no visible global function definition for
  ‘vcountPattern’
frequencyAnalysisVcf: no visible global function definition for
  ‘vcountPattern’
plotCountsPerSample: no visible global function definition for
  ‘GRanges’
plotCountsPerSample: no visible global function definition for
  ‘IRanges’
plotCountsPerSampleRelative: no visible global function definition for
  ‘GRanges’
plotCountsPerSampleRelative: no visible global function definition for
  ‘IRanges’
plotCountsPerSampleRelativeVcf: no visible global function definition
  for ‘GRanges’
plotCountsPerSampleRelativeVcf: no visible global function definition
  for ‘IRanges’
plotCountsPerSampleVcf: no visible global function definition for
  ‘GRanges’
plotCountsPerSampleVcf: no visible global function definition for
  ‘IRanges’
plotCountsPerSample_ref: no visible global function definition for
  ‘rowRanges’
plotCountsPerTarget: no visible global function definition for
  ‘GRanges’
plotCountsPerTarget: no visible global function definition for
  ‘IRanges’
plotCountsPerTargetRelative: no visible global function definition for
  ‘GRanges’
plotCountsPerTargetRelative: no visible global function definition for
  ‘IRanges’
plotCountsPerTargetRelativeVcf: no visible global function definition
  for ‘GRanges’
plotCountsPerTargetRelativeVcf: no visible global function definition
  for ‘IRanges’
plotCountsPerTargetVcf: no visible global function definition for
  ‘GRanges’
plotCountsPerTargetVcf: no visible global function definition for
  ‘IRanges’
plotCountsPerTarget_ref: no visible global function definition for
  ‘rowRanges’
* 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 ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
analyzeBasesPlotOnly 32.208  0.436  32.653
* 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-3.2-bioc/meat/BBCAnalyzer.Rcheck/00check.log’
for details.

BBCAnalyzer.Rcheck/00install.out:

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

BBCAnalyzer.Rcheck/BBCAnalyzer-Ex.timings:

nameusersystemelapsed
BBCAnalyzer-package0.5390.0000.539
analyzeBases0.1620.0040.167
analyzeBasesPlotOnly32.208 0.43632.653