ChIPpeakAnno 3.3.3
Lihua Julie Zhu , Jianhong Ou
| Snapshot Date: 2015-08-10 16:24:50 -0700 (Mon, 10 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno | | Last Changed Rev: 107075 / Revision: 107311 | | Last Changed Date: 2015-08-04 07:31:10 -0700 (Tue, 04 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && mkdir ChIPpeakAnno.buildbin-libdir ChIPpeakAnno.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChIPpeakAnno.buildbin-libdir ChIPpeakAnno_3.3.3.tar.gz >ChIPpeakAnno.Rcheck\00install.out 2>&1 && cp ChIPpeakAnno.Rcheck\00install.out ChIPpeakAnno-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ChIPpeakAnno.buildbin-libdir --install="check:ChIPpeakAnno-install.out" --force-multiarch --no-vignettes --timings ChIPpeakAnno_3.3.3.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck'
* using R version 3.2.2 beta (2015-08-04 r68843)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPpeakAnno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPpeakAnno' version '3.3.3'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'grid' 'VennDiagram' 'biomaRt' 'IRanges' 'Biostrings' 'GenomicRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'ChIPpeakAnno' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.6Mb
sub-directories of 1Mb or more:
data 9.7Mb
extdata 2.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotatePeakInBatch: no visible global function definition for
'seqlevels'
assignChromosomeRegion : formatSeqnames: no visible global function
definition for 'seqlevels'
assignChromosomeRegion : formatSeqnames: no visible global function
definition for 'seqlevels<-'
assignChromosomeRegion: no visible global function definition for
'seqlengths'
assignChromosomeRegion: no visible global function definition for
'seqlevels'
assignChromosomeRegion: no visible global function definition for
'keepSeqlevels'
findOverlappingPeaks: no visible global function definition for
'DataFrame'
formatSeqnames: no visible global function definition for 'seqlevels'
formatSeqnames: no visible global function definition for 'seqlevels<-'
getAllPeakSequence: no visible global function definition for
'seqlevels'
getAllPeakSequence: no visible global function definition for
'seqlengths'
getAllPeakSequence: no visible global function definition for
'seqlengths<-'
getEnrichedGO: no visible global function definition for 'mappedkeys'
getEnrichedGO : <anonymous>: no visible global function definition for
'GOID'
getEnrichedGO : <anonymous>: no visible global function definition for
'Term'
getEnrichedGO : <anonymous>: no visible global function definition for
'Definition'
getEnrichedGO : <anonymous>: no visible global function definition for
'Ontology'
getEnrichedPATH: no visible global function definition for 'mappedkeys'
mergePlusMinusPeaks: no visible global function definition for
'rowMins'
mergePlusMinusPeaks: no visible global function definition for
'rowMaxs'
* 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' ... [41s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
addGeneIDs 2.76 0.20 7.58
addAncestors 2.28 0.16 8.41
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ExonPlusUtr.human.GRCh37 5.6 0.06 5.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [74s]
[74s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [77s]
[77s] 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
'D:/biocbld/bbs-3.2-bioc/meat/ChIPpeakAnno.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ChIPpeakAnno' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame
install for x64
* installing *source* package 'ChIPpeakAnno' ...
** testing if installed package can be loaded
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame
* MD5 sums
packaged installation of 'ChIPpeakAnno' as ChIPpeakAnno_3.3.3.zip
* DONE (ChIPpeakAnno)