BioC 2.14: CHECK report for Mfuzz on petty

Package: Mfuzz

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Mfuzz_2.22.0.tar.gz

StartedAt: 2014-10-07 22:52:27 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:53:58 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 90.8 seconds

RetCode: 0

Status:  OK

CheckDir: Mfuzz.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Mfuzz_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Mfuzz.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.22.0’
* 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 ... [7s/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 files in ‘vignettes’ ... OK
* checking examples ... [5s/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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/Mfuzz.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
Dmin	0.005	0.001	0.006
acore	0.003	0.000	0.004
cselection	0.006	0.000	0.008
fill.NA	0.001	0.000	0.002
filter.NA	0.001	0.001	0.001
filter.std	1.167	0.082	1.269
kmeans2	0.003	0.000	0.003
kmeans2.plot	0.003	0.000	0.003
mestimate	0.005	0.001	0.005
mfuzz	0.006	0.001	0.006
mfuzz.plot	0.005	0.000	0.005
mfuzz.plot2	0.020	0.000	0.021
mfuzzColorBar	0.001	0.000	0.002
overlap	0.004	0.001	0.004
overlap.plot	0.008	0.000	0.008
partcoef	0.008	0.000	0.009
randomise	0.129	0.014	0.144
standardise	0.003	0.000	0.004
standardise2	0.002	0.000	0.003
top.count	0.003	0.000	0.003