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BioC 2.13: CHECK report for KCsmart on zin1

This page was generated on 2014-04-05 09:47:40 -0700 (Sat, 05 Apr 2014).

Package 387/750HostnameOS / ArchBUILDCHECKBUILD BIN
KCsmart 2.20.0
Jorma de Ronde
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/KCsmart
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: KCsmart
Version: 2.20.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings KCsmart_2.20.0.tar.gz
StartedAt: 2014-04-05 02:05:12 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:06:55 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 103.2 seconds
RetCode: 0
Status:  OK 
CheckDir: KCsmart.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/KCsmart.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KCsmart/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KCsmart’ 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘KCsmart’ can be installed ... [3s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘siggenes’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘siggenes’
  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:
  ‘.add2spmc’ ‘.checkMirrorLocs’ ‘.comparativeKcPerms’
  ‘.comparativeKcSiggenes’ ‘.convertCGHbase’ ‘.findCutoffByFdr’
  ‘.findPeaks’ ‘.findfdrcutoff’ ‘.getRegions’ ‘.getSigRegions’
  ‘.makePermutations’ ‘.mirrorData’ ‘.permutedSpm’ ‘.samplePointMatrix’
  ‘.samplePointMatrixOld’ ‘.snr’ ‘.spm2spmc’ ‘.varr’
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘KCS.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [63s/63s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      17.825  0.176  18.048
getSigRegionsCompKC   9.557  0.044   9.646
compareSpmCollection  8.569  0.028   8.635
calcSpmCollection     8.128  0.032   8.175
* 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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 ‘write.table’ from package ‘utils’ in package ‘KCsmart’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KCsmart)

KCsmart.Rcheck/KCsmart-Ex.timings:

nameusersystemelapsed
KCsmart-package17.825 0.17618.048
calcSpm1.2240.0041.231
calcSpmCollection8.1280.0328.175
compKc-class0.0000.0000.002
compKcSigRegions-class0.0040.0000.003
compareSpmCollection8.5690.0288.635
findSigLevelFdr2.7200.0202.743
findSigLevelTrad2.2920.0002.294
getSigRegionsCompKC9.5570.0449.646
getSigSegments1.8560.0241.889
idPoints0.0160.0000.017
plot2.8920.0122.934
plotScaleSpace4.1800.0084.194
samplePointMatrix-class0.0000.0000.002
sigSegments-class0.0000.0000.001
spmCollection-class0.0040.0000.005
write.table2.0560.0002.072