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BioC 2.13: CHECK report for Category on perceval

This page was generated on 2014-04-05 09:51:46 -0700 (Sat, 05 Apr 2014).

Package 112/750HostnameOS / ArchBUILDCHECKBUILD BIN
Category 2.28.0
Bioconductor Package Maintainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Category
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: Category
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Category_2.28.0.tar.gz
StartedAt: 2014-04-05 00:01:24 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:08:43 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 438.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Category.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Category.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.28.0’
* 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 ‘Category’ can be installed ... [28s/28s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘methods’ ‘Biobase’ ‘AnnotationDbi’ ‘graph’ ‘genefilter’
A package should be listed in only one of these fields.
* 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:
  ‘GO.db’ ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘DatPkgFactory’
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Category.Rnw’, ‘ChromBand.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [72s/72s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChrBandTree-class 23.479  0.387  23.887
MAPAmat           13.573  0.470  14.072
makeChrBandGraph  13.498  0.274  13.827
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [87s/87s]
 [87s/88s] 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-2.13-bioc/meat/Category.Rcheck/00check.log’
for details.

Category.Rcheck/00install.out:

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

Category.Rcheck/Category-Ex.timings:

nameusersystemelapsed
ChrBandTree-class23.479 0.38723.887
ChrMapHyperGParams-class0.0040.0040.007
ChrMapHyperGResult-class0.0040.0040.009
ChrMapLinearMParams-class0.0150.0050.019
ChrMapLinearMResult-class0.0040.0040.008
DatPkg-class0.1290.0120.141
HyperGResult-accessors1.0180.0671.085
LinearMResult-class0.0040.0040.007
MAPAmat13.573 0.47014.072
applyByCategory0.0090.0050.014
cateGOryMatrix0.3910.0590.450
cb_parse_band_Hs0.0330.0040.037
cb_parse_band_Mm0.0140.0030.018
findAMstats0.5430.0280.572
getPathNames0.1220.0110.134
gseattperm1.3490.1391.491
hyperg1.0890.1671.271
makeChrBandGraph13.498 0.27413.827
makeEBcontr0.3870.0140.400
probes2MAP0.4190.0200.439
probes2Path0.1740.0120.187
ttperm0.0400.0080.048