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BioC 2.13: CHECK report for Mfuzz on perceval

This page was generated on 2014-04-05 09:51:50 -0700 (Sat, 05 Apr 2014).

Package 443/750HostnameOS / ArchBUILDCHECKBUILD BIN
Mfuzz 2.20.0
Matthias Futschik
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/Mfuzz
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: Mfuzz
Version: 2.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Mfuzz_2.20.0.tar.gz
StartedAt: 2014-04-05 02:35:14 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:36:38 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 84.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Mfuzz.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Mfuzz.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 ‘Mfuzz/DESCRIPTION’ ... OK
* this is package ‘Mfuzz’ 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 ‘Mfuzz’ can be installed ... [6s/7s] 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘e1071’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... NOTE
Dmin: warning in mfuzz(eset, c = i, m = m): partial argument match of
  'c' to 'centers'
mfuzz.plot2: warning in rgb(b = fancy.blue/255, g = fancy.green/255, r
  = fancy.red/255): partial argument match of 'r' to 'red'
mfuzz.plot2: warning in rgb(b = fancy.blue/255, g = fancy.green/255, r
  = fancy.red/255): partial argument match of 'g' to 'green'
mfuzz.plot2: warning in rgb(b = fancy.blue/255, g = fancy.green/255, r
  = fancy.red/255): partial argument match of 'b' to 'blue'
mfuzzColorBar: warning in rgb(b = fancy.blue/255, g = fancy.green/255,
  r = fancy.red/255): partial argument match of 'r' to 'red'
mfuzzColorBar: warning in rgb(b = fancy.blue/255, g = fancy.green/255,
  r = fancy.red/255): partial argument match of 'g' to 'green'
mfuzzColorBar: warning in rgb(b = fancy.blue/255, g = fancy.green/255,
  r = fancy.red/255): partial argument match of 'b' to 'blue'
Mfuzzgui : objectBrowser2 : viewEnv: warning in ls(env = env, all =
  TRUE): partial argument match of 'env' to 'envir'
Mfuzzgui : objectBrowser2 : viewEnv: warning in ls(env = env, all =
  TRUE): partial argument match of 'all' to 'all.names'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Mfuzz.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [4s/5s] 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/Mfuzz.Rcheck/00check.log’
for details.

Mfuzz.Rcheck/00install.out:

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

Mfuzz.Rcheck/Mfuzz-Ex.timings:

nameusersystemelapsed
Dmin0.0260.0020.028
acore0.0110.0000.011
cselection0.0170.0010.017
fill.NA0.0080.0000.009
filter.NA0.0070.0000.008
filter.std0.9020.0831.521
kmeans20.0160.0010.016
kmeans2.plot0.0130.0010.013
mestimate0.0160.0010.016
mfuzz0.0150.0010.015
mfuzz.plot0.0160.0010.016
mfuzz.plot20.0380.0010.049
mfuzzColorBar0.0100.0010.010
overlap0.0140.0010.014
overlap.plot0.0220.0010.023
partcoef0.0240.0010.045
randomise0.1150.0150.137
standardise0.0130.0000.014
standardise20.0130.0010.014
top.count0.0130.0010.014