BioC 3.1: CHECK report for OCplus on zin2
This page was generated on 2015-10-09 09:23:06 -0700 (Fri, 09 Oct 2015).
OCplus 1.42.0 Alexander Ploner
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/OCplus | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| 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 | |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: OCplus |
Version: 1.42.0 |
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings OCplus_1.42.0.tar.gz |
StartedAt: 2015-10-09 04:02:09 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 04:02:56 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 46.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OCplus.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings OCplus_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/OCplus.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OCplus/DESCRIPTION’ ... OK
* this is package ‘OCplus’ version ‘1.42.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OCplus’ can be installed ... [2s/2s] 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 ... NOTE
Package in Depends field not imported from: ‘akima’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Tornadoplot: no visible global function definition for ‘interp’
Volcanoplot: no visible global function definition for ‘interp’
plot.fdr2d.result: no visible global function definition for ‘interp’
* checking Rd files ... NOTE
prepare_Rd: tstatistics.Rd:38-39: Dropping empty section \examples
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.FDR.result':
‘plot.FDR.result’
S3 methods shown with full name in documentation object 'plot.fdr1d.result':
‘plot.fdr1d.result’
S3 methods shown with full name in documentation object 'plot.fdr2d.result':
‘plot.fdr2d.result’
S3 methods shown with full name in documentation object 'summary.fdr.result':
‘summary.fdr.result’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/18s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
samplesize 5.874 0.228 6.105
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/OCplus.Rcheck/00check.log’
for details.
OCplus.Rcheck/00install.out:
* installing *source* package ‘OCplus’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OCplus)
OCplus.Rcheck/OCplus-Ex.timings:
name | user | system | elapsed
|
EOC | 0.585 | 0.000 | 0.585 |
|
FDR | 0.003 | 0.000 | 0.003 |
|
MAsim.smyth | 0.271 | 0.000 | 0.270 |
|
OCshow | 1.399 | 0.008 | 1.406 |
|
TOC | 0.365 | 0.024 | 0.388 |
|
average.fdr | 1.067 | 0.016 | 1.091 |
|
fdr1d | 0.464 | 0.000 | 0.464 |
|
fdr2d | 0.676 | 0.000 | 0.676 |
|
plot.FDR.result | 0.123 | 0.000 | 0.122 |
|
plot.fdr1d.result | 0.500 | 0.008 | 0.799 |
|
plot.fdr2d.result | 0.711 | 0.004 | 0.714 |
|
samplesize | 5.874 | 0.228 | 6.105 |
|
smooth1d | 0.027 | 0.008 | 0.035 |
|
summary.fdr.result | 0.495 | 0.008 | 0.503 |
|
tMixture | 3.400 | 0.184 | 3.582 |
|