BioC 3.1: CHECK report for systemPipeR on zin2
This page was generated on 2015-10-09 09:26:24 -0700 (Fri, 09 Oct 2015).
systemPipeR 1.2.23 Thomas Girke
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/systemPipeR | Last Changed Rev: 108397 / Revision: 109384 | Last Changed Date: 2015-09-09 22:24:58 -0700 (Wed, 09 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
Package: systemPipeR |
Version: 1.2.23 |
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings systemPipeR_1.2.23.tar.gz |
StartedAt: 2015-10-09 05:56:29 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 06:00:13 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 224.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: systemPipeR.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings systemPipeR_1.2.23.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/systemPipeR.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 ‘systemPipeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘systemPipeR’ version ‘1.2.23’
* 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:
inst/extdata/.BatchJobs.R
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 ‘systemPipeR’ can be installed ... [21s/21s] 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘BiocGenerics’ ‘VariantAnnotation’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
countRangeset: warning in read.delim(infile1(args)[i], comment = "#"):
partial argument match of 'comment' to 'comment.char'
vennPlot : ellipseVenn: warning in close.screen(all = TRUE): partial
argument match of 'all' to 'all.screens'
writeTargetsRef: warning in read.delim(infile, comment = "#"): partial
argument match of 'comment' to 'comment.char'
.codingReport: no visible global function definition for ‘transcripts’
.subsetReadsByMappingRegion: no visible global function definition for
‘IRanges’
.subsetReadsByMappingRegion: no visible global function definition for
‘seqlengths’
GOHyperGAll_Subset: no visible binding for global variable
‘test_sample’
clusterRun: no visible global function definition for ‘chunk’
countRangeset: no visible global function definition for ‘import.bed’
filterDEGs: no visible binding for global variable ‘Comparisons’
filterDEGs: no visible binding for global variable ‘Counts’
filterDEGs: no visible binding for global variable ‘Type’
filterVars: no visible global function definition for ‘readVcf’
filterVars: no visible global function definition for ‘totalDepth<-’
filterVars: no visible global function definition for ‘refDepth<-’
filterVars: no visible global function definition for ‘altDepth<-’
filterVars: no visible global function definition for ‘asVCF’
filterVars: no visible global function definition for ‘writeVcf’
getQsubargs: no visible binding for global variable ‘tophatargs’
goBarplot: no visible binding for global variable ‘SampleMatch’
goBarplot: no visible binding for global variable ‘Sample’
olBarplot: no visible binding for global variable ‘Intersect_Sets’
olBarplot: no visible binding for global variable ‘Counts’
olBarplot: no visible binding for global variable ‘Level’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘Cycle’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘low’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘mid’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘top’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘Frequency’
seeFastqPlot : fastqPlot: no visible binding for global variable ‘Base’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘Quality’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘RelDiv’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘Method’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘minQuality’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘Percent’
seeFastqPlot : fastqPlot: no visible binding for global variable
‘Outliers’
variantReport: no visible global function definition for ‘readVcf’
variantReport: no visible global function definition for
‘locateVariants’
variantReport: no visible global function definition for ‘AllVariants’
variantReport: no visible global function definition for
‘predictCoding’
variantReport: no visible global function definition for ‘ref’
variantReport: no visible global function definition for ‘alt’
show,INTERSECTset: no visible binding for global variable ‘vennset’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [10s/10s]
[11s/11s] 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.
systemPipeR.Rcheck/00install.out:
* installing *source* package ‘systemPipeR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (systemPipeR)
systemPipeR.Rcheck/systemPipeR-Ex.timings:
name | user | system | elapsed
|
GOHyperGAll | 0.001 | 0.000 | 0.001 |
|
INTERSECTset-class | 0.008 | 0.004 | 0.012 |
|
SYSargs-class | 0.025 | 0.007 | 0.033 |
|
VENNset-class | 0.006 | 0.004 | 0.009 |
|
alignStats | 0.014 | 0.000 | 0.014 |
|
catDB-class | 0.000 | 0.003 | 0.001 |
|
catmap | 0.000 | 0.000 | 0.001 |
|
clusterRun | 0.014 | 0.001 | 0.014 |
|
countRangeset | 0.057 | 0.000 | 0.057 |
|
filterDEGs | 3.576 | 0.012 | 3.585 |
|
filterVars | 0.010 | 0.004 | 0.013 |
|
getQsubargs | 0.014 | 0.000 | 0.014 |
|
mergeBamByFactor | 0.011 | 0.000 | 0.012 |
|
moduleload | 0 | 0 | 0 |
|
olBarplot | 0.342 | 0.012 | 0.354 |
|
overLapper | 0.343 | 0.020 | 0.363 |
|
preprocessReads | 0.025 | 0.000 | 0.026 |
|
qsubRun | 0.015 | 0.000 | 0.014 |
|
readComp | 0.019 | 0.000 | 0.019 |
|
returnRPKM | 0 | 0 | 0 |
|
runCommandline | 0.014 | 0.000 | 0.014 |
|
runDiff | 0.047 | 0.000 | 0.046 |
|
run_DESeq2 | 2.735 | 0.004 | 2.850 |
|
run_edgeR | 3.222 | 0.004 | 3.222 |
|
seeFastq | 0 | 0 | 0 |
|
symLink2bam | 0.012 | 0.000 | 0.011 |
|
sysargs | 0.013 | 0.000 | 0.014 |
|
systemArgs | 0.015 | 0.000 | 0.014 |
|
variantReport | 0.014 | 0.000 | 0.013 |
|
vennPlot | 0.352 | 0.008 | 0.360 |
|
writeTargetsRef | 0.002 | 0.000 | 0.001 |
|
writeTargetsout | 0.005 | 0.008 | 0.013 |
|