recoup 1.5.0
Panagiotis Moulos
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/recoup | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf recoup.buildbin-libdir recoup.Rcheck && mkdir recoup.buildbin-libdir recoup.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=recoup.buildbin-libdir recoup_1.5.0.tar.gz >recoup.Rcheck\00install.out 2>&1 && cp recoup.Rcheck\00install.out recoup-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=recoup.buildbin-libdir --install="check:recoup-install.out" --force-multiarch --no-vignettes --timings recoup_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/recoup.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'recoup/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'recoup' version '1.5.0'
* package encoding: UTF-8
* 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 'recoup' 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
baseCoverageMatrix: no visible global function definition for
'runValue'
baseCoverageMatrix : <anonymous>: no visible global function definition
for 'runValue'
binCoverageMatrix : <anonymous>: no visible global function definition
for 'runValue'
buildAnnotationStore: no visible global function definition for
'Seqinfo'
calcCoverage: no visible global function definition for 'runValue'
cleanRanges: no visible global function definition for 'seqlevels'
cleanRanges: no visible global function definition for 'seqlevels<-'
cmclapply: no visible global function definition for 'mclapply'
cmcmapply: no visible global function definition for 'mcmapply'
coverageFromBam: no visible global function definition for
'ScanBamParam'
coverageFromBam: no visible global function definition for
'seqlevels<-'
coverageFromBigWig : <anonymous> : <anonymous>: no visible global
function definition for 'Rle'
coverageFromBigWig: no visible global function definition for 'Rle'
coverageFromBigWig : <anonymous>: no visible global function definition
for 'Rle'
coverageFromRanges: no visible global function definition for
'subjectHits'
coverageFromRanges : <anonymous> : <anonymous>: no visible global
function definition for 'Rle'
coverageFromRanges: no visible global function definition for 'Rle'
coverageFromRangesOld: no visible global function definition for
'subjectHits'
getGcContent: no visible global function definition for 'Rle'
getGcContent: no visible global function definition for 'IRanges'
getGcContent: no visible global function definition for
'alphabetFrequency'
getMainRnaRangesOnTheFly: no visible binding for global variable
'genomeRanges'
getUcscAnnotation: no visible global function definition for 'dbDriver'
getUcscAnnotation: no visible global function definition for
'dbConnect'
getUcscAnnotation: no visible global function definition for
'dbGetQuery'
getUcscAnnotation: no visible global function definition for
'dbDisconnect'
getUcscDbl: no visible global function definition for 'dbDriver'
getUcscDbl: no visible global function definition for 'dbConnect'
getUcscDbl: no visible global function definition for 'dbWriteTable'
getUcscDbl: no visible global function definition for 'dbDisconnect'
loadBsGenome: no visible global function definition for
'installed.genomes'
loadBsGenome: no visible global function definition for 'getBSgenome'
loadBsGenome: no visible global function definition for 'biocLite'
prepareBam: no visible global function definition for 'indexBam'
prepareBam : <anonymous>: no visible global function definition for
'sortBam'
prepareBam : <anonymous>: no visible global function definition for
'indexBam'
preprocessRanges: no visible global function definition for
'ScanBamParam'
preprocessRanges: no visible global function definition for
'bamWhich<-'
readBed: no visible global function definition for 'seqlevels'
readBed: no visible global function definition for 'Seqinfo'
recoup: no visible binding for global variable 'gene'
recoup: no visible binding for global variable 'sexon'
recoup: no visible binding for global variable 'flankedSexon'
recoup : <anonymous>: no visible global function definition for
'runValue'
recoupCorrelation: no visible binding for global variable 'Index'
recoupCorrelation: no visible binding for global variable 'Coverage'
recoupCorrelation: no visible binding for global variable 'Condition'
recoupCorrelation: no visible binding for global variable 'Design'
recoupHeatmap : <anonymous>: no visible global function definition for
'grid.text'
recoupProfile: no visible binding for global variable 'Signal'
recoupProfile: no visible binding for global variable 'Condition'
recoupProfile: no visible binding for global variable 'Design'
reduceExons : <anonymous>: no visible global function definition for
'DataFrame'
splitVector: no visible global function definition for 'Rle'
Undefined global functions or variables:
Condition Coverage DataFrame Design IRanges Index Rle ScanBamParam
Seqinfo Signal alphabetFrequency bamWhich<- biocLite dbConnect
dbDisconnect dbDriver dbGetQuery dbWriteTable flankedSexon gene
genomeRanges getBSgenome grid.text indexBam installed.genomes
mclapply mcmapply runValue seqlevels seqlevels<- sexon sortBam
subjectHits
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mergeRuns 15.25 0.30 15.54
profileMatrix 13.91 0.44 14.34
kmeansDesign 5.51 0.04 5.56
getAnnotation 1.43 0.43 6.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
profileMatrix 14.80 0.56 15.36
mergeRuns 14.23 0.05 14.34
recoup 6.98 0.05 7.03
kmeansDesign 6.08 0.03 6.11
recoupPlot 5.05 0.06 5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/recoup.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'recoup' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'recoup' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recoup' as recoup_1.5.0.zip
* DONE (recoup)