BioC 2.14: CHECK report for PCpheno on zin2

Package: PCpheno

Version: 1.26.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings PCpheno_1.26.0.tar.gz

StartedAt: 2014-10-08 01:43:37 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:47:04 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 207.1 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings PCpheno_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/PCpheno.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.26.0’
* 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 ... [17s/18s] 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
Packages in Depends field not imported from:
  ‘SLGI’ ‘annotate’ ‘ppiData’ ‘ppiStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/33s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
graphTheory    6.393  0.088   6.496
gtResult-class 5.892  0.352   6.256
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/PCpheno.Rcheck/00check.log’
for details.

* installing *source* package ‘PCpheno’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	0.616	0.024	0.643
Dudley	0.004	0.000	0.007
Giaever	0.356	0.004	0.361
HI	0.004	0.000	0.002
KEGG2SCISI	0.492	0.012	0.507
Kastenmayer	0.016	0.000	0.013
Lesage	0.004	0.000	0.006
Osterberg	0.02	0.00	0.02
SGDphenoL	0.028	0.000	0.026
YEASTOHNOLOG	0.008	0.000	0.007
buildFDMat	0.392	0.004	0.395
categoryToEntrezBuilder	0.340	0.000	0.351
complexStatus	1.384	0.016	1.405
deResult-class	0.084	0.008	0.093
densityEstimate	1.432	0.008	1.487
getDescr	0.640	0.004	0.645
getFDgene	0.112	0.008	0.124
graphTheory	6.393	0.088	6.496
gtResult-class	5.892	0.352	6.256
overlap	0.004	0.000	0.002
plot	1.284	0.024	1.311
ppiInteraction	3.881	0.048	3.936
reduceM	0.000	0.000	0.001
truncName	0.000	0.000	0.001