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BioC 3.1: CHECK report for clusterStab on petty

This page was generated on 2015-10-09 09:32:51 -0700 (Fri, 09 Oct 2015).

Package 180/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterStab 1.40.0
James W. MacDonald
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/clusterStab
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterStab
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterStab_1.40.0.tar.gz
StartedAt: 2015-10-08 22:09:13 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:09:57 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 43.8 seconds
RetCode: 0
Status:  OK 
CheckDir: clusterStab.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterStab_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/clusterStab.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterStab/DESCRIPTION’ ... OK
* this is package ‘clusterStab’ version ‘1.40.0’
* 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 ‘clusterStab’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘clusterStab/R/zzz.R’:
  .First.lib calls:
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim): partial
  argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim): partial
  argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim): partial
  argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim): partial
  argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
show,ClusterComp: warning in matrix(paste(round(object@percent, 0),
  "%", sep = ""), nr = 1): partial argument match of 'nr' to 'nrow'
.First.lib: no visible global function definition for ‘addVigs2WinMenu’
benhur,ExpressionSet : .local: no visible global function definition
  for ‘exprs’
clusterComp,ExpressionSet : .local: no visible global function
  definition for ‘exprs’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/clusterStab.Rcheck/00check.log’
for details.


clusterStab.Rcheck/00install.out:

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

clusterStab.Rcheck/clusterStab-Ex.timings:

nameusersystemelapsed
benhur0.4040.0140.420
clusterComp0.2810.0090.291