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BioC 3.2: CHECK report for prot2D on oaxaca

This page was generated on 2016-04-23 10:26:45 -0700 (Sat, 23 Apr 2016).

Package 806/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
prot2D 1.8.0
Sebastien Artigaud
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/prot2D
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: prot2D
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prot2D_1.8.0.tar.gz
StartedAt: 2016-04-23 03:16:21 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:17:38 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 76.9 seconds
RetCode: 0
Status:  OK 
CheckDir: prot2D.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prot2D_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/prot2D.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prot2D/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘prot2D’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘fdrtool’ ‘st’ ‘samr’ ‘Biobase’ ‘limma’ ‘Mulcom’ ‘impute’ ‘MASS’
  ‘qvalue’
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 ‘prot2D’ can be installed ... [6s/8s] 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
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘fdrtool’ ‘limma’ ‘samr’ ‘st’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Mulcom’ ‘impute’
  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
Norm.qt: no visible global function definition for ‘normalizeQuantiles’
Norm.vsn: no visible global function definition for ‘normalizeVSN’
robust.fdr : lts.rank.regr: no visible global function definition for
  ‘ltsreg’
* 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 ... [9s/12s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/prot2D.Rcheck/00check.log’
for details.


prot2D.Rcheck/00install.out:

* installing *source* package ‘prot2D’ ...
** 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 (prot2D)

prot2D.Rcheck/prot2D-Ex.timings:

nameusersystemelapsed
ES.prot0.2460.0070.253
Norm.qt0.1110.0040.116
Norm.vsn0.4560.0160.472
RIplot0.0450.0040.051
Sim.Prot.2D1.8240.0211.981
prot2D-package2.0080.0112.067
variousT1.4660.0093.306