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BioC 3.1: CHECK report for sRAP on morelia

This page was generated on 2015-10-09 09:41:21 -0700 (Fri, 09 Oct 2015).

Package 944/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sRAP 1.8.0
Charles Warden
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/sRAP
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  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: sRAP
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sRAP_1.8.0.tar.gz
StartedAt: 2015-10-09 06:39:01 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:41:40 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 159.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: sRAP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sRAP_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/sRAP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sRAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRAP’ version ‘1.8.0’
* 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 ‘sRAP’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                              old_size new_size compress
  bdfunc.enrichment.human.rda    1.3Mb    951Kb    bzip2
  bdfunc.enrichment.mouse.rda     31Kb     26Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘sRAP.bbl’
Please remove them from your package.
* checking examples ... [127s/127s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
RNA.bdfunc.signal 83.229  4.393  87.709
RNA.bdfunc.fc     16.032  0.960  17.409
RNA.deg           13.980  0.901  14.991
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/sRAP.Rcheck/00check.log’
for details.


sRAP.Rcheck/00install.out:

* installing *source* package ‘sRAP’ ...
** 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 (sRAP)

sRAP.Rcheck/sRAP-Ex.timings:

nameusersystemelapsed
RNA.bdfunc.fc16.032 0.96017.409
RNA.bdfunc.signal83.229 4.39387.709
RNA.deg13.980 0.90114.991
RNA.norm2.7280.1412.872
RNA.prepare.input0.0200.0060.030
RNA.qc3.1120.2453.384