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Package 210/514HostnameOS / ArchBUILDCHECKBUILD BIN
Genominator 1.8.0
James Bullard
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/Genominator
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: Genominator
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Genominator_1.8.0.tar.gz
StartedAt: 2012-03-24 01:24:25 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:27:34 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 188.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Genominator.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/Genominator.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 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.8.0'
* 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 'Genominator' 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.genominator.coverage':
  'plot.genominator.coverage'

S3 methods shown with full name in documentation object 'plot.genominator.goodness.of.fit':
  'plot.genominator.goodness.of.fit'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
  chr1_yeast.rda           528Kb    253Kb       xz
  yeastAnno.rda             79Kb     58Kb       xz
  yeastAnno.sources.rda    755Kb    219Kb       xz
* 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

Genominator.Rcheck/00install.out:

* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Genominator.Rnw' 
   'plotting.Rnw' 
   'withShortRead.Rnw' 
** testing if installed package can be loaded

* DONE (Genominator)

Genominator.Rcheck/Genominator-Ex.timings:

nameusersystemelapsed
ExpData0.0020.0010.002
addPrimingWeights7.9600.2368.279
aggregateExpData2.1980.0292.258
applyMapped1.9480.1342.091
collapseExpData4.2820.1754.539
computeCoverage1.3910.0601.459
computePrimingWeights0.5870.0450.636
getRegion0.2890.0040.295
importFromAlignedReads0.0000.0010.000
importToExpData0.6650.0150.688
joinExpData5.5100.0735.642
makeGeneRepresentation0.4200.0140.437
mergeWithAnnotation0.6140.0080.660
plot.genominator.coverage4.1930.1534.381
plot.genominator.goodness.of.fit1.0960.0771.180
regionGoodnessOfFit-methods0.9910.0621.056
splitByAnnotation1.1580.0111.191
summarizeByAnnotation0.6200.0090.647
summarizeExpData0.8250.0140.853
validAnnotation0.0270.0020.028
yeastAnno0.3370.0140.352