systemPipeR 1.5.3
Thomas Girke
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/systemPipeR | | Last Changed Rev: 109910 / Revision: 109948 | | Last Changed Date: 2015-10-25 15:38:03 -0400 (Sun, 25 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings systemPipeR_1.5.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/systemPipeR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.5.3’
* 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 ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 2.9Mb
extdata 1.8Mb
* 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'
.resizeFeature: no visible global function definition for ‘DataFrame’
.subsetReadsByMappingRegion: no visible global function definition for
‘IRanges’
.subsetReadsByMappingRegion: no visible global function definition for
‘seqlengths’
.subsetReadsByMappingRegion: no visible global function definition for
‘readGAlignments’
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’
countRangeset: no visible global function definition for
‘summarizeOverlaps’
featureCoverage: no visible global function definition for
‘readGAlignments’
featureCoverage: no visible global function definition for ‘qwidth’
featureCoverage: no visible global function definition for ‘Rle’
featuretypeCounts: no visible global function definition for
‘readGAlignments’
featuretypeCounts: no visible global function definition for
‘readGAlignmentPairs’
featuretypeCounts: no visible global function definition for ‘qwidth’
featuretypeCounts: no visible global function definition for ‘last’
featuretypeCounts: no visible global function definition for ‘first’
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’
genFeatures: no visible global function definition for ‘DataFrame’
genFeatures: no visible global function definition for ‘seqlengths<-’
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’
plotfeatureCoverage: no visible binding for global variable ‘extendmax’
plotfeatureCoverage: no visible binding for global variable ‘Coverage’
plotfeatureCoverage: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible binding for global variable ‘Feature’
plotfeaturetypeCounts: no visible binding for global variable ‘Counts’
plotfeaturetypeCounts: no visible binding for global variable ‘Strand’
plotfeaturetypeCounts: no visible binding for global variable ‘Length’
predORF : .predORF: no visible global function definition for ‘IRanges’
scaleRanges : .scaleRanges: no visible global function definition for
‘IRanges’
scaleRanges: no visible global function definition for ‘DataFrame’
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’
Undefined global functions or variables:
AllVariants Base Comparisons Counts Coverage Cycle DataFrame Feature
Frequency IRanges Intersect_Sets Length Level Method Outliers Percent
Quality RelDiv Rle Sample SampleMatch Strand Type alt altDepth<-
asVCF chunk extendmax first import.bed last locateVariants low mid
minQuality predictCoding qwidth readGAlignmentPairs readGAlignments
readVcf ref refDepth<- seqlengths seqlengths<- summarizeOverlaps
test_sample top tophatargs totalDepth<- vennset writeVcf
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/43s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
genFeatures 12.662 0.327 13.694
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [13s/14s]
[13s/14s] 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/systemPipeR.Rcheck/00check.log’
for details.