Mfuzz 2.28.0
Matthias Futschik
| 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/Mfuzz | | 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 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mfuzz_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Mfuzz.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mfuzz/DESCRIPTION’ ... OK
* this is package ‘Mfuzz’ 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 ‘Mfuzz’ can be installed ... [3s/3s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘marray’ 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’ ‘e1071’
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
Dmin: warning in mfuzz(eset, c = i, m = m): partial argument match of
'c' to 'centers'
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'
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 : browseObject: no visible global function definition for
‘exprs’
Mfuzzgui : browseFile: no visible global function definition for
‘exprs’
Mfuzzgui : filter1: no visible global function definition for ‘exprs’
Mfuzzgui : export.eset: no visible global function definition for
‘write.exprs’
Mfuzzgui : export.eset: no visible global function definition for
‘exprs’
acore: no visible global function definition for ‘exprs’
fill.NA: no visible global function definition for ‘exprs’
fill.NA: no visible global function definition for ‘exprs<-’
filter.NA: no visible global function definition for ‘exprs’
filter.std: no visible global function definition for ‘exprs’
kmeans2: no visible global function definition for ‘exprs’
kmeans2.plot: no visible global function definition for ‘exprs’
mestimate: no visible global function definition for ‘exprs’
mfuzz: no visible global function definition for ‘cmeans’
mfuzz: no visible global function definition for ‘exprs’
mfuzz.plot: no visible global function definition for ‘exprs’
mfuzz.plot2: no visible global function definition for ‘exprs’
mfuzzColorBar: no visible global function definition for ‘maColorBar’
randomise: no visible global function definition for ‘exprs’
randomise: no visible global function definition for ‘exprs<-’
standardise: no visible global function definition for ‘exprs’
standardise: no visible global function definition for ‘exprs<-’
standardise2: no visible global function definition for ‘exprs’
standardise2: 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 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 ... [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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/Mfuzz.Rcheck/00check.log’
for details.