ChromHeatMap 1.27.0
Tim F. Rayner
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChromHeatMap | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
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### Running command:
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### rm -rf ChromHeatMap.buildbin-libdir ChromHeatMap.Rcheck && mkdir ChromHeatMap.buildbin-libdir ChromHeatMap.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChromHeatMap.buildbin-libdir ChromHeatMap_1.27.0.tar.gz >ChromHeatMap.Rcheck\00install.out 2>&1 && cp ChromHeatMap.Rcheck\00install.out ChromHeatMap-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ChromHeatMap.buildbin-libdir --install="check:ChromHeatMap-install.out" --force-multiarch --no-vignettes --timings ChromHeatMap_1.27.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/ChromHeatMap.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChromHeatMap/DESCRIPTION' ... OK
* this is package 'ChromHeatMap' version '1.27.0'
* 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 whether package 'ChromHeatMap' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculateCytoband: no visible global function definition for 'data'
createChrMatrix: no visible global function definition for 'new'
makeRangedDataList : makeRangedData: no visible global function
definition for 'as'
paintCytobands: no visible global function definition for 'data'
plotChrMap: no visible global function definition for 'new'
makeChrStrandData,matrix: no visible global function definition for
'new'
Undefined global functions or variables:
as data new
Consider adding
importFrom("methods", "as", "new")
importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'ChromHeatMap-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeRangedDataList
> ### Title: Plot expression data as tracks in the UCSC genome browser
> ### Aliases: makeRangedDataList
>
> ### ** Examples
>
> data('demo')
> r <- makeRangedDataList( data=chrdata, chr=22, cytoband='q11.23', genome='hg18' )
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Error: RangedDataList objects are defunct in favor of GRangesList objects (the
GRangesList class is defined in the GenomicRanges package).
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'ChromHeatMap-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeRangedDataList
> ### Title: Plot expression data as tracks in the UCSC genome browser
> ### Aliases: makeRangedDataList
>
> ### ** Examples
>
> data('demo')
> r <- makeRangedDataList( data=chrdata, chr=22, cytoband='q11.23', genome='hg18' )
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Error: RangedDataList objects are defunct in favor of GRangesList objects (the
GRangesList class is defined in the GenomicRanges package).
Execution halted
* 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: 2 ERRORs, 1 NOTE
See
'D:/biocbld/bbs-3.4-bioc/meat/ChromHeatMap.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ChromHeatMap' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'ChromHeatMap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChromHeatMap' as ChromHeatMap_1.27.0.zip
* DONE (ChromHeatMap)