Genominator 1.25.0
James Bullard
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Genominator | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf Genominator.buildbin-libdir Genominator.Rcheck && mkdir Genominator.buildbin-libdir Genominator.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Genominator.buildbin-libdir Genominator_1.25.0.tar.gz >Genominator.Rcheck\00install.out 2>&1 && cp Genominator.Rcheck\00install.out Genominator-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Genominator.buildbin-libdir --install="check:Genominator-install.out" --force-multiarch --no-vignettes --timings Genominator_1.25.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/Genominator.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.25.0'
* 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 whether package 'Genominator' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
Undefined global functions or variables:
AlignedDataFrame DisplayPars alignData chromosome gdPlot
geneRegionBiomart makeAnnotationTrack makeBaseTrack makeGenericArray
makeGenomeAxis mkAllStrings pData position readAligned sread subseq
tables varLabels varMetadata
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [26s] OK
** running examples for arch 'x64' ... [30s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
joinExpData 5.92 0.02 5.94
* 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
'c:/biocbld/bbs-3.3-bioc/meat/Genominator.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'Genominator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Genominator' as Genominator_1.25.0.zip
* DONE (Genominator)