BioC 3.2: CHECK report for PCpheno on oaxaca

Package: PCpheno

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PCpheno_1.32.0.tar.gz

StartedAt: 2016-04-23 02:56:45 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:59:55 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 190.0 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_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PCpheno.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 ‘PCpheno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCpheno’ version ‘1.32.0’
* 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 ... [16s/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
'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:
  ‘SLGI’ ‘annotate’ ‘ppiData’ ‘ppiStats’
  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 ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
graphTheory    5.535  0.173   5.712
gtResult-class 4.628  0.604   5.237
* 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-3.2-bioc/meat/PCpheno.Rcheck/00check.log’
for details.

* installing *source* package ‘PCpheno’ ...
** R
** data
** inst
** preparing package for lazy loading
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
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	0.408	0.030	0.955
Dudley	0.008	0.009	0.017
Giaever	0.149	0.017	0.165
HI	0.003	0.002	0.004
KEGG2SCISI	0.459	0.023	0.524
Kastenmayer	0.017	0.003	0.019
Lesage	0.006	0.002	0.009
Osterberg	0.024	0.009	0.033
SGDphenoL	0.030	0.007	0.037
YEASTOHNOLOG	0.008	0.002	0.009
buildFDMat	0.222	0.027	0.248
categoryToEntrezBuilder	0.357	0.018	0.382
complexStatus	0.576	0.042	0.619
deResult-class	0.089	0.016	0.106
densityEstimate	1.565	0.064	1.628
getDescr	0.778	0.039	0.858
getFDgene	0.163	0.014	0.177
graphTheory	5.535	0.173	5.712
gtResult-class	4.628	0.604	5.237
overlap	0.002	0.001	0.003
plot	1.340	0.135	1.476
ppiInteraction	4.314	0.415	4.780
reduceM	0.001	0.000	0.001
truncName	0.000	0.000	0.001