Guitar 1.11.9
Jia Meng
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Guitar | | Last Changed Rev: 119412 / Revision: 121152 | | Last Changed Date: 2016-07-17 03:05:22 -0700 (Sun, 17 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | 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 Guitar.buildbin-libdir Guitar.Rcheck && mkdir Guitar.buildbin-libdir Guitar.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Guitar.buildbin-libdir Guitar_1.11.9.tar.gz >Guitar.Rcheck\00install.out 2>&1 && cp Guitar.Rcheck\00install.out Guitar-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Guitar.buildbin-libdir --install="check:Guitar-install.out" --force-multiarch --no-vignettes --timings Guitar_1.11.9.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Guitar.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 'Guitar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Guitar' version '1.11.9'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Rsamtools' 'GenomicFeatures' 'rtracklayer' 'GenomicAlignments'
'GenomicRanges' 'ggplot2' 'grid' 'IRanges'
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 'Guitar' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
extdata 4.7Mb
* 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
.makeFigure_fill: no visible global function definition for 'pdf'
.makeFigure_fill: no visible global function definition for 'dev.off'
.makeFigure_nofill: no visible global function definition for 'pdf'
.makeFigure_nofill: no visible global function definition for 'dev.off'
BED12toGRangesList: no visible global function definition for
'read.table'
BED12toGRangesList: no visible global function definition for 'head'
narrowPeaktoGRanges: no visible global function definition for
'read.table'
Undefined global functions or variables:
dev.off head pdf read.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("utils", "head", "read.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 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
combinedGuitarPlot 12.67 0.02 12.68
GuitarPlot 11.21 0.03 11.25
Guitar-package 11.19 0.00 11.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
combinedGuitarPlot 15.48 0.00 15.47
GuitarPlot 12.76 0.05 12.81
Guitar-package 12.76 0.03 12.81
* 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-3.4-bioc/meat/Guitar.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Guitar' ...
** 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 'Guitar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Guitar' as Guitar_1.11.9.zip
* DONE (Guitar)