BioC 3.1: CHECK report for HELP on petty
This page was generated on 2015-10-09 09:33:37 -0700 (Fri, 09 Oct 2015).
HELP 1.26.0 Reid F. Thompson
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/HELP | 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: HELP |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HELP_1.26.0.tar.gz |
StartedAt: 2015-10-08 23:39:06 -0700 (Thu, 08 Oct 2015) |
EndedAt: 2015-10-08 23:40:39 -0700 (Thu, 08 Oct 2015) |
EllapsedTime: 93.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HELP.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 HELP_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/HELP.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HELP/DESCRIPTION’ ... OK
* this is package ‘HELP’ version ‘1.26.0’
* 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 ‘HELP’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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: ‘methods’
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
calcTm,character : .local: no visible binding for global variable
‘base.stacking.thermodynamics’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* 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 ... [3s/4s] 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-3.1-bioc/meat/HELP.Rcheck/00check.log’
for details.
HELP.Rcheck/00install.out:
* installing *source* package ‘HELP’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HELP)
HELP.Rcheck/HELP-Ex.timings:
name | user | system | elapsed
|
base.stacking.thermodynamics | 0.032 | 0.004 | 0.037 |
|
calcGC | 0.001 | 0.001 | 0.001 |
|
calcPrototype | 0.061 | 0.003 | 0.064 |
|
calcTm | 0.007 | 0.001 | 0.008 |
|
combineData | 0.023 | 0.001 | 0.025 |
|
createWiggle | 0.007 | 0.000 | 0.007 |
|
exprs2 | 0.001 | 0.000 | 0.001 |
|
fuzzyMatches | 0.004 | 0.000 | 0.005 |
|
getFeatures | 0.107 | 0.006 | 0.170 |
|
getSamples | 0.051 | 0.005 | 0.058 |
|
plotBins | 0.164 | 0.004 | 0.168 |
|
plotChip | 0.141 | 0.009 | 0.182 |
|
plotFeature | 0.093 | 0.005 | 0.124 |
|
plotPairs | 0.699 | 0.008 | 0.753 |
|
quantileNormalize | 0.071 | 0.004 | 0.078 |
|
readDesign | 0.148 | 0.007 | 0.162 |
|
readPairs | 0.155 | 0.003 | 0.158 |
|
readSampleKey | 0.006 | 0.001 | 0.010 |
|