BioC 3.3: CHECK report for IdeoViz on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:44 -0400 (Tue, 27 Oct 2015).
IdeoViz 1.5.0 Shraddha Pai
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IdeoViz | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
Summary
Package: IdeoViz |
Version: 1.5.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IdeoViz_1.5.0.tar.gz |
StartedAt: 2015-10-27 04:56:19 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 04:59:13 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 174.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IdeoViz.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IdeoViz_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/IdeoViz.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IdeoViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdeoViz’ version ‘1.5.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘IdeoViz’ can be installed ... [10s/10s] 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
* 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
.plot_values: no visible binding for global variable ‘span’
Undefined global functions or variables:
span
* 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 ... [10s/65s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
avgByBin 1.801 0.040 23.244
getBins 0.815 0.009 17.613
getIdeo 0.471 0.012 17.306
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/IdeoViz.Rcheck/00check.log’
for details.
IdeoViz.Rcheck/00install.out:
* 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
* DONE (IdeoViz)
IdeoViz.Rcheck/IdeoViz-Ex.timings:
name | user | system | elapsed
|
GSM733664_broadPeaks | 0.088 | 0.000 | 0.088 |
|
avgByBin | 1.801 | 0.040 | 23.244 |
|
binned_fullGenome | 0.017 | 0.000 | 0.017 |
|
binned_multiSeries | 0.012 | 0.000 | 0.012 |
|
binned_singleSeries | 0.011 | 0.000 | 0.011 |
|
getBins | 0.815 | 0.009 | 17.613 |
|
getIdeo | 0.471 | 0.012 | 17.306 |
|
hg18_ideo | 0.011 | 0.000 | 0.011 |
|
plotChromValuePair | 0.407 | 0.000 | 0.407 |
|
plotOnIdeo | 0.269 | 0.000 | 0.269 |
|
wins | 0.011 | 0.004 | 0.015 |
|
wins_discrete | 0.018 | 0.000 | 0.018 |
|
wins_entiregenome | 0.014 | 0.000 | 0.014 |
|