BBCAnalyzer 0.99.4
Sarah Sandmann
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BBCAnalyzer | | Last Changed Rev: 107391 / Revision: 107696 | | Last Changed Date: 2015-08-13 14:21:16 -0700 (Thu, 13 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BBCAnalyzer_0.99.4.tar.gz
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* 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 ‘0.99.4’
* 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 ‘BBCAnalyzer’ can be installed ... [15s/15s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [41s/43s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyzeBasesPlotOnly 32.342 0.26 34.602
* 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.