Package: apComplex

Version: 2.19.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch apComplex_2.19.0.tar.gz

StartedAt: 2011-07-07 01:26:16 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:29:35 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 198.7 seconds

RetCode: 0

Status:  OK

CheckDir: apComplex.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/apComplex.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'apComplex/DESCRIPTION' ... OK
* this is package 'apComplex' version '2.19.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'apComplex' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                                old_size new_size compress
  HMSPCI.rda                        21Kb     10Kb    bzip2
  HMSPCIgraph.rda                   36Kb     19Kb       xz
  SBMHcHMSPCI.rda                   21Kb     10Kb    bzip2
  SBMHcTAP.rda                      15Kb      8Kb    bzip2
  TAP.rda                           19Kb      9Kb    bzip2
  TAPgraph.rda                      17Kb      9Kb       xz
  UnRBBcHMSPCI.rda                  11Kb      6Kb    bzip2
  gavin06FilteredEstimates.rda      43Kb     26Kb    bzip2
  gavinBP2006.rda                   83Kb     28Kb    bzip2
  krogan06FilteredEstimates.rda     89Kb     56Kb    bzip2
  kroganBPMat2006.rda              253Kb     84Kb    bzip2
  yNameTAP.rda                      13Kb      7Kb    bzip2
  yTAP.rda                          10Kb      7Kb    bzip2
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'apComplex' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: DBI

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'apComplex.Rnw' 
** testing if installed package can be loaded

* DONE (apComplex)

name	user	system	elapsed
FilteredEstimates	0.059	0.003	0.063
HMSPCI	0.310	0.010	0.319
Krogan	0.022	0.001	0.024
LCjoin	0.202	0.010	0.234
MBMEcHMSPCI	0.027	0.002	0.029
MBMEcKrogan	0.007	0.001	0.008
MBMEcTAP	0.046	0.003	0.050
TAP	0.175	0.008	0.185
apEX	0.005	0.001	0.007
bhmaxSubgraph	0.100	0.008	0.108
findComplexes	0.100	0.005	0.105
gavinBP2006	1.124	0.043	1.168
kroganBPMat2006	3.046	0.127	3.177
mergeComplexes	0.098	0.021	0.119
plotComplex	0.119	0.015	0.345
sortComplexes	0.045	0.007	0.051
yNameTAP	0.094	0.005	0.099
yTAP	0.007	0.001	0.008