Genominator 1.22.0
James Bullard
| 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/Genominator | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 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 | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Genominator_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Genominator.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Genominator/DESCRIPTION’ ... OK
* this is package ‘Genominator’ version ‘1.22.0’
* 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 ‘Genominator’ can be installed ... [14s/14s] 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
'library' or 'require' calls to packages already attached by Depends:
‘GenomeGraphs’ ‘IRanges’
Please remove these calls from your code.
'library' or 'require' call to ‘ShortRead’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘GenomeGraphs’ ‘RSQLite’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addPrimingWeights: no visible global function definition for
‘varLabels’
addPrimingWeights: no visible global function definition for
‘alignData’
addPrimingWeights: no visible global function definition for ‘subseq’
addPrimingWeights: no visible global function definition for ‘sread’
addPrimingWeights: no visible global function definition for
‘AlignedDataFrame’
addPrimingWeights: no visible global function definition for ‘pData’
addPrimingWeights: no visible global function definition for
‘varMetadata’
computePrimingWeights: no visible global function definition for
‘mkAllStrings’
computePrimingWeights : p.compute: no visible global function
definition for ‘tables’
computePrimingWeights : p.compute: no visible global function
definition for ‘subseq’
computePrimingWeights : p.compute: no visible global function
definition for ‘sread’
importFromAlignedReads : weights.AlignedRead: no visible global
function definition for ‘varLabels’
importFromAlignedReads : weights.AlignedRead: no visible global
function definition for ‘alignData’
importFromAlignedReads : importObject: no visible global function
definition for ‘position’
importFromAlignedReads : importObject: no visible global function
definition for ‘chromosome’
importFromAlignedReads : importObject: no visible global function
definition for ‘varLabels’
importFromAlignedReads : importObject: no visible global function
definition for ‘alignData’
importFromAlignedReads: no visible global function definition for
‘readAligned’
makeAnnoFactory: no visible global function definition for
‘DisplayPars’
makeAnnoFactory : regionAnno.Biomart: no visible global function
definition for ‘geneRegionBiomart’
makeAnnoFactory : regionAnno.AnnoData: no visible global function
definition for ‘makeAnnotationTrack’
makeRegionPlotter : <anonymous>: no visible global function definition
for ‘DisplayPars’
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
function definition for ‘makeBaseTrack’
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
function definition for ‘makeGenericArray’
makeRegionPlotter : <anonymous>: no visible global function definition
for ‘makeGenomeAxis’
makeRegionPlotter : <anonymous>: no visible global function definition
for ‘gdPlot’
* 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 ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
joinExpData 8.382 0.050 8.669
addPrimingWeights 7.526 0.195 7.765
plot.genominator.coverage 5.256 0.081 5.471
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/Genominator.Rcheck/00check.log’
for details.
* installing *source* package ‘Genominator’ ...
** R
** data
** 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 (Genominator)