BioC 2.14: CHECK report for RpsiXML on petty

Package: RpsiXML

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_2.6.0.tar.gz

StartedAt: 2014-10-07 23:55:46 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-08 00:01:48 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 362.5 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RpsiXML.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘annotate’ ‘graph’ ‘Biobase’ ‘RBGL’ ‘XML’ ‘hypergraph’
  ‘AnnotationDbi’
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 ‘RpsiXML’ can be installed ... [22s/23s] OK
* checking installed package size ... NOTE
  installed size is 33.7Mb
  sub-directories of 1Mb or more:
    extdata  32.7Mb
* 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:
  ‘annotate’ ‘AnnotationDbi’ ‘RBGL’ ‘XML’
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/67s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
translateID           11.242  0.090  11.942
graphSpeciesConverter  6.498  0.090   6.608
psimi25XML2Graph       6.109  0.044   6.195
buildPCHypergraph      4.967  0.042   5.030
interactors            4.802  0.103   5.027
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’ [62s/64s]
 [63s/64s] 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

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

* installing *source* package ‘RpsiXML’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RpsiXML)

name	user	system	elapsed
availableXrefs	0.366	0.003	0.369
bait	0.121	0.009	0.131
buildPCHypergraph	4.967	0.042	5.030
complexName	4.481	0.046	4.548
complexes	4.918	0.053	4.978
eListHandler	0.021	0.001	0.022
getAbstractByPMID	0.978	0.013	1.291
graphSpeciesConverter	6.498	0.090	6.608
interactionType	0.130	0.003	0.134
interactions	0.153	0.005	0.161
interactorInfo	0.169	0.008	0.176
interactors	4.802	0.103	5.027
null2na	0.001	0.000	0.002
parsePsimi25Interaction	4.035	0.027	4.064
psimi25Complex-class	0.004	0.000	0.004
psimi25ComplexEntry-class	0.002	0.000	0.026
psimi25Experiment-class	0.002	0.001	0.002
psimi25Graph-class	0.003	0.000	0.002
psimi25Hypergraph-class	4.160	0.019	4.216
psimi25Hypergraph2GraphNEL	0.001	0.000	0.001
psimi25Interaction-class	0.003	0.001	0.004
psimi25InteractionEntry-class	0.003	0.000	0.004
psimi25Interactor-class	0.002	0.000	0.002
psimi25Source-class	0.002	0.001	0.002
psimi25XML2Graph	6.109	0.044	6.195
separateXMLDataByExpt	1.163	0.023	1.199
translateID	11.242	0.090	11.942
uniprot	0.001	0.000	0.001
validatePSIMI25	0.115	0.028	0.174