IMA - IMA(Illumina Methylation Analyzer) is a package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray. - check results
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IMA

About IMA
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Package R docs

Version: 3.1.2
Result: WARNING
Check time: 2018-01-26 15:37
* using log directory ''
* using R Under development (unstable) (2018-01-26 r74168)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'IMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IMA' version '3.1.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'WriteXLS' 'limma' 'MASS' 'bioDist' 'preprocessCore' 'dplR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialized R objects in the sources ... OK
* checking whether package 'IMA' can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.3Mb
sub-directories of 1Mb or more:
extdata 19.1Mb
* checking package 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' calls to packages already attached by Depends:
'MASS' 'WriteXLS' 'bioDist' 'limma' 'preprocessCore'
Please remove these calls from your code.
Packages in Depends field not imported from:
'MASS' 'dplR'
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
summits: no visible global function definition for 'density'
Undefined global functions or variables:
density
Consider adding
importFrom("stats", "density")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'IMA.methy450PP.Rd':
\usage lines wider than 90 characters:
= 0.75,locidiff = c(FALSE, 0.01),locidiffgroup = list("g1","g2"), XYchrom = c(FALSE,"X","Y",
\examples lines wider than 100 characters:
data = IMA.methy450R(file = MethyFileName,columnGrepPattern=list(beta=".AVG_Beta",detectp=".Detection.Pval"),groupfile = PhenoFileName) ... [TRUNCATED]
dataf = IMA.methy450PP(data,na.omit = TRUE,normalization=FALSE,transfm =FALSE,peakcorrection = TRUE, samplefilterdetectP = 1e-5,samplef ... [TRUNCATED]

Rd file 'IMA.methy450R.Rd':
\examples lines wider than 100 characters:
data = IMA.methy450R(fileName = MethyFileName,columnGrepPattern=list(beta=".AVG_Beta",detectp=".Detection.Pval"),groupfile = PhenoFileN ... [TRUNCATED]

Rd file 'regionswrapper.Rd':
\examples lines wider than 100 characters:
data = IMA.methy450R(fileName = MethyFileName,columnGrepPattern=list(beta=".AVG_Beta",detectp=".Detection.Pval"),groupfile = PhenoFileN ... [TRUNCATED]
dataf = IMA.methy450PP(data,na.omit = TRUE,normalization=FALSE,transfm = FALSE,samplefilterdetectP = 1e-5,samplefilterperc = 0.75,sitef ... [TRUNCATED]
regionswrapper(dataf,indexmethod="mean",gcase="g2",gcontrol="g1",testmethod="limma",Padj="BH",concov="OFF",paired=FALSE,list11excel="./ ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 examples ... WARNING
Found the following significant warnings:
Warning: working directory was changed to '/IMA/extdata', resetting
Warning: working directory was changed to '/IMA/extdata', resetting
Warning: working directory was changed to '/IMA/extdata', resetting
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
'/00check.log'
for details.



Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Mac OS X 10.5 (R 2.16.x)

ERROR: dependencies ‘WriteXLS’, ‘limma’, ‘bioDist’, ‘preprocessCore’ are not available for package ‘IMA’
* removing ‘/Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/IMA’

Build log for Windows 7 (R 3.0.x)

(IMA 3.1.2)
* installing to library 'z:/rforge/Rlib/win7-3.0'
ERROR: dependencies 'limma', 'bioDist', 'preprocessCore' are not available for package 'IMA'
* removing 'z:/rforge/Rlib/win7-3.0/IMA'