IdeoViz 1.8.0
Shraddha Pai
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/IdeoViz | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / 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 IdeoViz.buildbin-libdir IdeoViz.Rcheck && mkdir IdeoViz.buildbin-libdir IdeoViz.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IdeoViz.buildbin-libdir IdeoViz_1.8.0.tar.gz >IdeoViz.Rcheck\00install.out 2>&1 && cp IdeoViz.Rcheck\00install.out IdeoViz-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=IdeoViz.buildbin-libdir --install="check:IdeoViz-install.out" --force-multiarch --no-vignettes --timings IdeoViz_1.8.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/IdeoViz.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IdeoViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdeoViz' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase' 'IRanges' 'GenomicRanges' 'RColorBrewer' 'rtracklayer'
'GenomeInfoDb'
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 'IdeoViz' 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
.plotChromosome: no visible global function definition for 'modifyList'
.plot_values: no visible global function definition for 'modifyList'
.plot_values: no visible global function definition for 'loess'
.plot_values: no visible binding for global variable 'span'
.plot_values: no visible global function definition for 'predict'
avgByBin: no visible global function definition for 'ave'
plotChromValuePair: no visible global function definition for
'modifyList'
Undefined global functions or variables:
ave loess modifyList predict span
Consider adding
importFrom("stats", "ave", "loess", "predict")
importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GSM733664_broadPeaks.Rd:11-12: Dropping empty section \format
prepare_Rd: GSM733664_broadPeaks.Rd:16-18: Dropping empty section \source
prepare_Rd: binned_fullGenome.Rd:12-13: Dropping empty section \format
prepare_Rd: binned_fullGenome.Rd:14-16: Dropping empty section \details
prepare_Rd: binned_fullGenome.Rd:20-22: Dropping empty section \references
prepare_Rd: binned_multiSeries.Rd:12-13: Dropping empty section \format
prepare_Rd: binned_multiSeries.Rd:14-15: Dropping empty section \details
prepare_Rd: binned_multiSeries.Rd:19-20: Dropping empty section \references
prepare_Rd: binned_singleSeries.Rd:11-12: Dropping empty section \format
prepare_Rd: binned_singleSeries.Rd:13-15: Dropping empty section \details
prepare_Rd: binned_singleSeries.Rd:19-21: Dropping empty section \references
prepare_Rd: hg18_ideo.Rd:11-12: Dropping empty section \format
prepare_Rd: hg18_ideo.Rd:13-14: Dropping empty section \details
prepare_Rd: hg18_ideo.Rd:18-19: Dropping empty section \references
prepare_Rd: wins.Rd:12-13: Dropping empty section \format
prepare_Rd: wins.Rd:14-15: Dropping empty section \details
prepare_Rd: wins.Rd:19-20: Dropping empty section \references
prepare_Rd: wins_discrete.Rd:11-12: Dropping empty section \format
prepare_Rd: wins_discrete.Rd:13-15: Dropping empty section \details
prepare_Rd: wins_discrete.Rd:19-21: Dropping empty section \references
prepare_Rd: wins_entiregenome.Rd:11-12: Dropping empty section \format
prepare_Rd: wins_entiregenome.Rd:13-15: Dropping empty section \details
prepare_Rd: wins_entiregenome.Rd:19-21: Dropping empty section \references
* 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
avgByBin 3.31 0.25 26.32
getBins 0.53 0.01 23.64
getIdeo 0.36 0.00 20.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
avgByBin 3.58 0.39 26.66
getBins 0.71 0.01 23.75
getIdeo 0.58 0.02 20.07
* 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
'C:/Users/biocbuild/bbs-3.4-bioc/meat/IdeoViz.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'IdeoViz' ...
** 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 'IdeoViz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IdeoViz' as IdeoViz_1.8.0.zip
* DONE (IdeoViz)