BioC 3.5: CHECK report for graphite on oaxaca
This page was generated on 2017-03-04 16:41:45 -0500 (Sat, 04 Mar 2017).
graphite 1.21.0 Gabriele Sales
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/graphite | Last Changed Rev: 122746 / Revision: 127142 | Last Changed Date: 2016-10-18 07:34:37 -0400 (Tue, 18 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
Summary
Package: graphite |
Version: 1.21.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.21.0.tar.gz |
StartedAt: 2017-03-04 04:01:18 -0800 (Sat, 04 Mar 2017) |
EndedAt: 2017-03-04 04:06:42 -0800 (Sat, 04 Mar 2017) |
EllapsedTime: 324.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: graphite.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings graphite_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/graphite.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
‘DEGraph’ ‘RCytoscape’ ‘RCy3’
* 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 ‘graphite’ 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
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘DEGraph’
* 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 ... NOTE
Note: found 28 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runClipperMulti 130.269 1.784 141.379
runClipper 19.015 0.504 19.934
runSPIA 5.276 0.291 20.599
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/graphite.Rcheck/00check.log’
for details.
graphite.Rcheck/00install.out:
* installing *source* package ‘graphite’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (graphite)
graphite.Rcheck/graphite-Ex.timings:
name | user | system | elapsed
|
as.list.DeprecatedPathwayList | 1.665 | 0.274 | 1.946 |
|
as.list.PathwayList | 0.108 | 0.023 | 0.141 |
|
buildPathway | 0.005 | 0.000 | 0.006 |
|
convertIdentifiers | 1.220 | 0.027 | 1.266 |
|
cytoscapePlot | 0.000 | 0.000 | 0.001 |
|
pathwayDatabases | 0.014 | 0.000 | 0.015 |
|
pathwayGraph | 0.048 | 0.000 | 0.049 |
|
pathways | 0 | 0 | 0 |
|
runClipper | 19.015 | 0.504 | 19.934 |
|
runClipperMulti | 130.269 | 1.784 | 141.379 |
|
runDEGraph | 0.002 | 0.000 | 0.001 |
|
runDEGraphMulti | 0.001 | 0.000 | 0.001 |
|
runSPIA | 5.276 | 0.291 | 20.599 |
|
runTopologyGSA | 1.182 | 0.021 | 1.251 |
|
runTopologyGSAMulti | 1.067 | 0.033 | 1.101 |
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