GUIDEseq 1.2.1
Lihua Julie Zhu
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/GUIDEseq | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && mkdir GUIDEseq.buildbin-libdir GUIDEseq.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GUIDEseq.buildbin-libdir GUIDEseq_1.2.1.tar.gz >GUIDEseq.Rcheck\00install.out 2>&1 && cp GUIDEseq.Rcheck\00install.out GUIDEseq-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GUIDEseq.buildbin-libdir --install="check:GUIDEseq-install.out" --force-multiarch --no-vignettes --timings GUIDEseq_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/GUIDEseq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GUIDEseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GUIDEseq' version '1.2.1'
* 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 'GUIDEseq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.9Mb
sub-directories of 1Mb or more:
extdata 10.4Mb
* 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
GUIDEseqAnalysis : <anonymous>: no visible global function definition
for 'write.table'
GUIDEseqAnalysis: no visible global function definition for
'write.table'
combineOfftargets: no visible global function definition for
'read.table'
combineOfftargets: no visible global function definition for
'write.table'
getPeaks: no visible global function definition for 'ppois'
getPeaks: no visible global function definition for 'pnbinom'
getPeaks: no visible global function definition for 'p.adjust'
getPeaks: no visible binding for global variable 'adjusted.p.value'
getPeaks: no visible binding for global variable 'SNratio'
getPeaks.old: no visible global function definition for 'ppois'
getPeaks.old: no visible global function definition for 'pnbinom'
getPeaks.old: no visible global function definition for 'p.adjust'
getUniqueCleavageEvents: no visible binding for global variable
'qwidth.first'
getUniqueCleavageEvents: no visible binding for global variable
'qwidth.last'
getUniqueCleavageEvents: no visible binding for global variable
'strand.last'
getUniqueCleavageEvents: no visible binding for global variable
'strand.first'
getUniqueCleavageEvents: no visible binding for global variable
'readName'
mergePlusMinusPeaks: no visible global function definition for
'write.table'
offTargetAnalysisOfPeakRegions: no visible global function definition
for 'read.table'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
'gRNAPlusPAM'
offTargetAnalysisOfPeakRegions: no visible binding for global variable
'offTarget'
offTargetAnalysisOfPeakRegions: no visible global function definition
for 'write.table'
rbind_dodge : naDF: no visible global function definition for
'setNames'
Undefined global functions or variables:
SNratio adjusted.p.value gRNAPlusPAM offTarget p.adjust pnbinom ppois
qwidth.first qwidth.last read.table readName setNames strand.first
strand.last write.table
Consider adding
importFrom("stats", "p.adjust", "pnbinom", "ppois", "setNames")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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
** running examples for arch 'x64' ... 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: 2 NOTEs
See
'E:/biocbld/bbs-3.3-bioc/meat/GUIDEseq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GUIDEseq' ...
** 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 'GUIDEseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GUIDEseq' as GUIDEseq_1.2.1.zip
* DONE (GUIDEseq)