BioC 3.1: CHECK report for prot2D on petty

Package: prot2D

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prot2D_1.6.0.tar.gz

StartedAt: 2015-10-09 01:14:13 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:16:04 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 111.4 seconds

RetCode: 0

Status:  OK

CheckDir: prot2D.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prot2D_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/prot2D.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 ‘prot2D/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘prot2D’ version ‘1.6.0’
* 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 ... [10s/10s] 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:
  ‘fdrtool’ ‘limma’ ‘MASS’ ‘samr’ ‘st’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘impute’ ‘MASS’ ‘Mulcom’
  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 ... [13s/13s] 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-3.1-bioc/meat/prot2D.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
ES.prot	0.296	0.009	0.304
Norm.qt	0.121	0.003	0.124
Norm.vsn	0.749	0.021	0.771
RIplot	0.076	0.003	0.079
Sim.Prot.2D	2.505	0.023	2.580
prot2D-package	2.554	0.010	2.567
variousT	2.549	0.010	2.563