exomePeak 2.2.2
Lin Zhang , Lian Liu , Jia Meng
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/exomePeak | | Last Changed Rev: 111938 / Revision: 116712 | | Last Changed Date: 2015-12-27 22:31:29 -0800 (Sun, 27 Dec 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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 exomePeak.buildbin-libdir exomePeak.Rcheck && mkdir exomePeak.buildbin-libdir exomePeak.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=exomePeak.buildbin-libdir exomePeak_2.2.2.tar.gz >exomePeak.Rcheck\00install.out 2>&1 && cp exomePeak.Rcheck\00install.out exomePeak-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=exomePeak.buildbin-libdir --install="check:exomePeak-install.out" --force-multiarch --no-vignettes --timings exomePeak_2.2.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/exomePeak.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'exomePeak/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'exomePeak' version '2.2.2'
* 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 'exomePeak' 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 ... NOTE
Packages in Depends field not imported from:
'GenomicAlignments' 'GenomicFeatures' 'Rsamtools' 'rtracklayer'
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
.bed2grangeslist: no visible global function definition for 'makeTxDb'
.bed2grangeslist: no visible global function definition for 'exonsBy'
.exomepeak_notification: no visible global function definition for
'mcols<-'
.get.bam.chrs: no visible global function definition for 'indexBam'
.get.bam.chrs: no visible global function definition for 'ScanBamParam'
.get.bam.chrs: no visible global function definition for 'scanBam'
.get.bam.read.length: no visible global function definition for
'indexBam'
.get.bam.read.length: no visible global function definition for
'ScanBamParam'
.get.bam.read.length: no visible global function definition for
'scanBam'
.get.check.points.reads.count: no visible global function definition
for 'RangesList'
.get.check.points.reads.count: no visible global function definition
for 'IRanges'
.get.check.points.reads.count: no visible global function definition
for 'ScanBamParam'
.get.check.points.reads.count: no visible global function definition
for 'scanBam'
.read.gtf: no visible global function definition for 'makeTxDbFromUCSC'
.read.gtf: no visible global function definition for 'makeTxDbFromGFF'
.read.gtf: no visible global function definition for 'keys'
.read.gtf: no visible global function definition for 'select'
.read.gtf: no visible global function definition for 'columns'
.readTxDb2: no visible global function definition for
'makeTxDbFromUCSC'
.readTxDb2: no visible global function definition for 'makeTxDbFromGFF'
.xls2Grangeslist: no visible global function definition for 'makeTxDb'
.xls2Grangeslist: no visible global function definition for 'exonsBy'
.xls2Grangeslist: no visible global function definition for 'mcols<-'
RMT: no visible global function definition for 'findOverlaps'
RMT: no visible global function definition for 'ranges'
RMT: no visible global function definition for 'exonsBy'
RMT: no visible global function definition for 'readGAlignments'
RMT: no visible global function definition for 'ScanBamParam'
RMT: no visible global function definition for 'scanBam'
RMT: no visible global function definition for 'countOverlaps'
RMT: no visible global function definition for 'width'
exomepeak: no visible global function definition for 'indexBam'
* checking Rd files ... NOTE
prepare_Rd: RMT.Rd:60-62: Dropping empty section \details
prepare_Rd: RMT.Rd:74-76: Dropping empty section \note
prepare_Rd: RMT.Rd:80-82: Dropping empty section \seealso
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [48s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RMT 23.23 0.34 25.52
exomepeak 8.13 0.08 8.38
** running examples for arch 'x64' ... [52s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
RMT 28.08 0.26 31.28
exomepeak 9.44 0.06 9.64
* 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: 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/exomePeak.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'exomePeak' ...
** R
** 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 'exomePeak' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'exomePeak' as exomePeak_2.2.2.zip
* DONE (exomePeak)