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BioC 3.2: CHECK report for KCsmart on perceval

This page was generated on 2015-11-10 14:46:14 -0800 (Tue, 10 Nov 2015).

Package 551/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KCsmart 2.28.0
Jorma de Ronde
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/KCsmart
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: KCsmart
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KCsmart_2.28.0.tar.gz
StartedAt: 2015-11-10 06:19:17 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 06:21:14 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 117.3 seconds
RetCode: 0
Status:  OK 
CheckDir: KCsmart.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KCsmart_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/KCsmart.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.28.0’
* 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 ‘KCsmart’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... 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’
  ‘.findfdrcutoff’ ‘.findPeaks’ ‘.getRegions’ ‘.getSigRegions’
  ‘.makePermutations’ ‘.mirrorData’ ‘.permutedSpm’ ‘.samplePointMatrix’
  ‘.samplePointMatrixOld’ ‘.snr’ ‘.spm2spmc’ ‘.varr’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.comparativeKcSiggenes: no visible binding for global variable ‘sam’
.samplePointMatrix: no visible global function definition for ‘locpoly’
.samplePointMatrix: no visible global function definition for ‘bkde’
getSigRegionsCompKC: no visible global function definition for
  ‘findDelta’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/68s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      16.833  0.803  17.652
getSigRegionsCompKC   9.383  0.725  10.109
calcSpmCollection     8.779  0.885   9.667
compareSpmCollection  8.859  0.787   9.646
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-package16.833 0.80317.652
calcSpm1.4390.0421.499
calcSpmCollection8.7790.8859.667
compKc-class0.0010.0000.002
compKcSigRegions-class0.0010.0000.001
compareSpmCollection8.8590.7879.646
findSigLevelFdr2.9340.1783.126
findSigLevelTrad2.4890.1872.685
getSigRegionsCompKC 9.383 0.72510.109
getSigSegments1.9540.1832.138
idPoints0.0130.0010.014
plot2.8790.1943.092
plotScaleSpace4.4560.3244.781
samplePointMatrix-class0.0010.0000.001
sigSegments-class0.0010.0000.001
spmCollection-class0.0010.0000.002
write.table2.0510.1772.227