BioC 3.1: CHECK report for PCpheno on petty

Package: PCpheno

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PCpheno_1.30.0.tar.gz

StartedAt: 2015-10-09 01:02:46 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:07:49 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 302.5 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.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 PCpheno_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/PCpheno.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 ‘PCpheno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCpheno’ version ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Category’ ‘ScISI’ ‘SLGI’ ‘ppiStats’ ‘ppiData’ ‘annotate’
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 ‘PCpheno’ can be installed ... [26s/27s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Category’ ‘ScISI’ ‘KEGG.db’ ‘GO.db’
A package should be listed in only one of these fields.
* 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 in package code:
  ‘GO.db’ ‘KEGG.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘annotate’ ‘ppiData’ ‘ppiStats’ ‘SLGI’
  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 ... OK
* 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 ... [51s/51s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
graphTheory    10.599  0.301  10.908
gtResult-class  8.684  1.040   9.724
ppiInteraction  6.417  0.227   6.691
* 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/PCpheno.Rcheck/00check.log’
for details.

* installing *source* package ‘PCpheno’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	0.696	0.034	0.762
Dudley	0.011	0.010	0.021
Giaever	0.242	0.021	0.263
HI	0.003	0.001	0.004
KEGG2SCISI	0.796	0.031	0.882
Kastenmayer	0.022	0.002	0.025
Lesage	0.013	0.001	0.014
Osterberg	0.036	0.010	0.046
SGDphenoL	0.043	0.008	0.053
YEASTOHNOLOG	0.031	0.004	0.036
buildFDMat	0.319	0.040	0.359
categoryToEntrezBuilder	0.613	0.021	0.646
complexStatus	0.980	0.050	1.051
deResult-class	0.128	0.019	0.147
densityEstimate	2.771	0.089	2.869
getDescr	1.240	0.029	1.320
getFDgene	0.240	0.018	0.258
graphTheory	10.599	0.301	10.908
gtResult-class	8.684	1.040	9.724
overlap	0.004	0.001	0.003
plot	2.530	0.229	2.767
ppiInteraction	6.417	0.227	6.691
reduceM	0.001	0.001	0.002
truncName	0.001	0.000	0.002