BioC 2.13: CHECK report for RpsiXML on zin1

Package: RpsiXML

Version: 2.4.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.4.0.tar.gz

StartedAt: 2014-04-05 03:42:58 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:45:50 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 172.7 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RpsiXML.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.4.0’
* 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 ‘RpsiXML’ can be installed ... [10s/10s] OK
* checking installed package size ... NOTE
  installed size is 33.8Mb
  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:
  ‘AnnotationDbi’ ‘RBGL’ ‘XML’ ‘annotate’
  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 installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘underscore.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RpsiXML.Rnw’, ‘RpsiXMLApp.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [36s/37s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
translateID 6.937  0.052   7.259
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’ [33s/33s]
 [33s/34s] 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 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.100	0.004	0.102
bait	0.076	0.000	0.078
buildPCHypergraph	2.476	0.024	2.505
complexName	2.436	0.000	2.438
complexes	2.652	0.008	2.664
eListHandler	0.024	0.000	0.021
getAbstractByPMID	0.552	0.004	1.156
graphSpeciesConverter	3.485	0.036	3.536
interactionType	0.236	0.004	0.239
interactions	0.08	0.00	0.08
interactorInfo	0.076	0.000	0.076
interactors	2.540	0.032	2.577
null2na	0.004	0.000	0.006
parsePsimi25Interaction	2.976	0.008	2.989
psimi25Complex-class	0.004	0.000	0.006
psimi25ComplexEntry-class	0.004	0.000	0.004
psimi25Experiment-class	0.032	0.000	0.033
psimi25Graph-class	0.004	0.000	0.004
psimi25Hypergraph-class	2.652	0.008	2.666
psimi25Hypergraph2GraphNEL	0.004	0.000	0.003
psimi25Interaction-class	0.004	0.000	0.004
psimi25InteractionEntry-class	0.004	0.000	0.005
psimi25Interactor-class	0.004	0.000	0.004
psimi25Source-class	0.000	0.000	0.004
psimi25XML2Graph	3.188	0.040	3.303
separateXMLDataByExpt	0.616	0.004	0.669
translateID	6.937	0.052	7.259
uniprot	0.004	0.000	0.003
validatePSIMI25	0.044	0.016	0.110