Package: apComplex

Version: 2.20.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch apComplex_2.20.0.tar.gz

StartedAt: 2012-03-23 23:19:18 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:23:09 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 231.6 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 2.14.2 (2012-02-29)
* 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 '2.20.0'
* 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 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'IRanges' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'IRanges' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
** 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	0.062	0.003	0.065
HMSPCI	0.394	0.013	0.408
Krogan	0.022	0.002	0.023
LCjoin	0.404	0.012	0.416
MBMEcHMSPCI	0.027	0.001	0.028
MBMEcKrogan	0.006	0.001	0.007
MBMEcTAP	0.048	0.003	0.051
TAP	0.302	0.010	0.314
apEX	0.005	0.002	0.006
bhmaxSubgraph	0.177	0.006	0.184
findComplexes	0.176	0.005	0.182
gavinBP2006	1.281	0.051	1.335
kroganBPMat2006	3.230	0.134	3.374
mergeComplexes	0.172	0.023	0.196
plotComplex	0.097	0.017	0.199
sortComplexes	0.041	0.006	0.048
yNameTAP	0.093	0.004	0.097
yTAP	0.006	0.001	0.007