BioC 3.2: CHECK report for iPAC on perceval

Package: iPAC

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iPAC_1.14.0.tar.gz

StartedAt: 2015-10-27 09:09:35 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:16:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 389.8 seconds

RetCode: 0

Status:  OK

CheckDir: iPAC.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 iPAC_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/iPAC.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iPAC’ version ‘1.14.0’
* 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 ‘iPAC’ can be installed ... [10s/11s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biostrings’ ‘gdata’ ‘multtest’ ‘scatterplot3d’
  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
get.AlignedPositions: no visible global function definition for
  ‘PhredQuality’
get.AlignedPositions: no visible global function definition for
  ‘pairwiseAlignment’
nmc: no visible global function definition for ‘mt.rawp2adjp’
plotLinear: no visible global function definition for ‘scatterplot3d’
plotMDS: no visible global function definition for ‘scatterplot3d’
* 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 ... [276s/288s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ClusterFind         175.420  0.484 183.525
get.Positions        34.970  7.165  44.667
nmc                  37.246  0.106  37.354
Plot.Protein.Linear   8.561  0.281   9.411
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/iPAC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ClusterFind	175.420	0.484	183.525
KRAS.Mutations	0.006	0.006	0.012
PIK3CA.Mutations	0.024	0.031	0.056
Plot.Protein.Linear	8.561	0.281	9.411
get.AASeq	0.002	0.001	0.159
get.AlignedPositions	3.415	0.300	4.301
get.Positions	34.970	7.165	44.667
get.Remapped.Order	2.433	0.393	3.532
get.SingleLetterCode	0.001	0.000	0.001
iPAC-package	0.001	0.000	0.002
nmc	37.246	0.106	37.354