IMA
About IMA
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Version: 3.1.2
Result: WARNING Check time: 2018-01-26 21:37 * 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
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' |