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Package 326/609HostnameOS / ArchBUILDCHECKBUILD BIN
KCsmart 2.16.0
Jorma de Ronde
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/KCsmart
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: KCsmart
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KCsmart_2.16.0.tar.gz
StartedAt: 2013-03-25 00:10:48 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:14:30 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 221.7 seconds
RetCode: 0
Status:  OK 
CheckDir: KCsmart.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/KCsmart.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'KCsmart/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KCsmart' version '2.16.0'
* 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 'KCsmart' 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 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 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 ... NOTE
prepare_Rd: calcSpm.Rd:52-53: Dropping empty section \note
prepare_Rd: calcSpm.Rd:50: Dropping empty section \references
prepare_Rd: calcSpmCollection.Rd:54-55: Dropping empty section \note
prepare_Rd: calcSpmCollection.Rd:52: Dropping empty section \references
prepare_Rd: compareSpmCollection.Rd:28-29: Dropping empty section \note
prepare_Rd: compareSpmCollection.Rd:26: Dropping empty section \references
prepare_Rd: getSigRegionsCompKC.Rd:30-31: Dropping empty section \note
prepare_Rd: getSigRegionsCompKC.Rd:28: Dropping empty section \references
prepare_Rd: getSigSegments.Rd:29-30: Dropping empty section \note
prepare_Rd: hsSampleData.Rd:12-13: Dropping empty section \references
prepare_Rd: idPoints.Rd:29-30: Dropping empty section \note
prepare_Rd: plot.Rd:39-40: Dropping empty section \details
prepare_Rd: plot.Rd:51-52: Dropping empty section \note
prepare_Rd: plotScaleSpace.Rd:25-26: Dropping empty section \note
prepare_Rd: write.table.Rd:79-81: Dropping empty section \value
prepare_Rd: write.table.Rd:83-84: Dropping empty section \note
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      28.302 11.276  40.920
getSigRegionsCompKC  15.592  8.903  27.481
compareSpmCollection 15.071  8.905  25.580
calcSpmCollection    15.007  8.538  25.422
plotScaleSpace        7.063  3.891  11.516
plot                  4.122  1.798   6.224
findSigLevelFdr       3.992  1.797   6.203
write.table           3.205  1.764   5.237
findSigLevelTrad      3.284  1.635   5.987
getSigSegments        2.919  1.870   5.323
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/KCsmart.Rcheck/00check.log'
for details.

KCsmart.Rcheck/00install.out:

* installing *source* package 'KCsmart' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'sort' from package 'base' in package 'KCsmart'
Creating a generic function for 'unlist' from package 'base' in package 'KCsmart'
Creating a generic function for 'write.table' from package 'utils' in package 'KCsmart'
** help
*** installing help indices
** building package indices
** installing vignettes
   'KCS.Rnw' 
** testing if installed package can be loaded

* DONE (KCsmart)

KCsmart.Rcheck/KCsmart-Ex.timings:

nameusersystemelapsed
KCsmart-package28.30211.27640.920
calcSpm2.0990.8373.070
calcSpmCollection15.007 8.53825.422
compKc-class0.0010.0010.001
compKcSigRegions-class0.0000.0000.001
compareSpmCollection15.071 8.90525.580
findSigLevelFdr3.9921.7976.203
findSigLevelTrad3.2841.6355.987
getSigRegionsCompKC15.592 8.90327.481
getSigSegments2.9191.8705.323
idPoints0.0150.0030.023
plot4.1221.7986.224
plotScaleSpace 7.063 3.89111.516
samplePointMatrix-class0.0010.0000.001
sigSegments-class0.0000.0000.002
spmCollection-class0.0010.0010.001
write.table3.2051.7645.237