hiReadsProcessor 1.0.0
Nirav V Malani
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/hiReadsProcessor | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ 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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### rm -rf hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && mkdir hiReadsProcessor.buildbin-libdir hiReadsProcessor.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiReadsProcessor.buildbin-libdir hiReadsProcessor_1.0.0.tar.gz >hiReadsProcessor.Rcheck\00install.out 2>&1 && cp hiReadsProcessor.Rcheck\00install.out hiReadsProcessor-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=hiReadsProcessor.buildbin-libdir --install="check:hiReadsProcessor-install.out" --force-multiarch --no-vignettes --timings hiReadsProcessor_1.0.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/hiReadsProcessor.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hiReadsProcessor/DESCRIPTION' ... OK
* this is package 'hiReadsProcessor' version '1.0.0'
* 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 'hiReadsProcessor' 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
** checking loading without being on the library search path ... 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 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
blatListedSet : <anonymous>: no visible binding for global variable
'GRangesList'
chunkize: no visible global function definition for 'breakInChunks'
chunkize: no visible global function definition for 'detectCores'
clusterSites: no visible global function definition for 'mcols'
clusterSites: no visible global function definition for 'strand'
clusterSites: no visible global function definition for 'mcols<-'
clusterSites : <anonymous>: no visible binding for global variable
'queryHits'
crossOverCheck: no visible global function definition for 'strand'
crossOverCheck: no visible global function definition for 'mcols'
crossOverCheck: no visible global function definition for 'mcols<-'
crossOverCheck: no visible binding for global variable 'queryHits'
decodeByBarcode: no visible global function definition for 'metadata<-'
decodeByBarcode: no visible global function definition for 'metadata'
extractSeqs : <anonymous>: no visible global function definition for
'metadata'
extractSeqs : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'IRanges'
extractSeqs : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'end<-'
extractSeqs : <anonymous> : <anonymous>: no visible global function
definition for 'IRanges'
extractSeqs : <anonymous> : <anonymous>: no visible global function
definition for 'end<-'
findAndRemoveVector: no visible global function definition for 'reduce'
findAndRemoveVector : <anonymous>: no visible global function
definition for 'ranges'
findAndRemoveVector: no visible global function definition for
'GRangesList'
findAndRemoveVector: no visible global function definition for 'mcols'
findBarcodes: no visible global function definition for 'metadata<-'
findBarcodes: no visible global function definition for 'metadata'
findIntegrations: no visible global function definition for 'mcols'
findIntegrations: no visible global function definition for 'mcols<-'
findIntegrations : <anonymous>: no visible global function definition
for 'mcols'
findIntegrations : <anonymous>: no visible global function definition
for 'ranges<-'
findIntegrations : <anonymous>: no visible global function definition
for 'IRanges'
findLTRs: no visible global function definition for 'end<-'
findLTRs: no visible global function definition for 'start<-'
findVector : <anonymous>: no visible global function definition for
'IRanges'
findVector : <anonymous>: no visible global function definition for
'ranges'
findVector: no visible global function definition for 'end<-'
findVector: no visible global function definition for 'start<-'
getIntegrationSites: no visible global function definition for 'mcols'
getIntegrationSites: no visible global function definition for
'mcols<-'
getIntegrationSites: no visible global function definition for 'strand'
getIntegrationSites: no visible global function definition for 'flank'
getSonicAbund: no visible global function definition for 'mcols'
getSonicAbund: no visible global function definition for 'strand'
getSonicAbund: no visible global function definition for 'mcols<-'
isuSites: no visible global function definition for 'mcols'
isuSites: no visible global function definition for 'mcols<-'
otuSites: no visible global function definition for 'mcols'
otuSites: no visible global function definition for 'strand'
otuSites: no visible global function definition for 'mcols<-'
otuSites : <anonymous>: no visible global function definition for
'mcols'
otuSites : <anonymous>: no visible global function definition for
'mcols<-'
otuSites: no visible global function definition for 'GRangesList'
pairUpAlignments: no visible global function definition for 'mcols'
pairUpAlignments: no visible global function definition for 'mcols<-'
pairUpAlignments: no visible global function definition for 'GRanges'
pairUpAlignments: no visible global function definition for 'ranges'
pairUpAlignments: no visible global function definition for 'strand'
pairUpAlignments: no visible global function definition for 'reduce'
pairUpAlignments : <anonymous>: no visible global function definition
for 'mcols'
pairUpAlignments : <anonymous>: no visible binding for global variable
'queryHits'
pairUpAlignments : <anonymous>: no visible global function definition
for 'mcols<-'
pairwiseAlignSeqs: no visible global function definition for
'IRangesList'
pairwiseAlignSeqs: no visible global function definition for 'IRanges'
primerIDAlignSeqs: no visible global function definition for 'IRanges'
primerIDAlignSeqs: no visible global function definition for 'resize'
primerIDAlignSeqs: no visible global function definition for
'IRangesList'
pslToRangedObject: no visible global function definition for 'GRanges'
pslToRangedObject: no visible global function definition for 'IRanges'
pslToRangedObject: no visible global function definition for 'mcols'
pslToRangedObject: no visible global function definition for 'mcols<-'
read.BAMasPSL: no visible global function definition for 'ScanBamParam'
read.BAMasPSL: no visible global function definition for 'scanBamFlag'
read.BAMasPSL: no visible global function definition for 'mcols'
read.BAMasPSL: no visible global function definition for 'mcols<-'
read.BAMasPSL: no visible global function definition for 'DataFrame'
read.SeqFolder: no visible global function definition for 'SimpleList'
read.sampleInfo: no visible global function definition for 'SimpleList'
vpairwiseAlignSeqs: no visible global function definition for 'Rle'
vpairwiseAlignSeqs: no visible global function definition for
'runLength'
vpairwiseAlignSeqs: no visible global function definition for 'reduce'
vpairwiseAlignSeqs: no visible global function definition for 'GRanges'
vpairwiseAlignSeqs: no visible global function definition for 'IRanges'
vpairwiseAlignSeqs: no visible global function definition for 'ranges'
vpairwiseAlignSeqs: no visible global function definition for
'runValue'
* 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' ... [44s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
read.SeqFolder 3.18 0.07 8.02
** running examples for arch 'x64' ... [39s] 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
NOTE: There was 1 note.
See
'D:/biocbld/bbs-3.0-bioc/meat/hiReadsProcessor.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'hiReadsProcessor' ...
** 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 'hiReadsProcessor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiReadsProcessor' as hiReadsProcessor_1.0.0.zip
* DONE (hiReadsProcessor)