RNAither 2.19.0
Lars Kaderali
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RNAither | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
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### Running command:
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### rm -rf RNAither.buildbin-libdir RNAither.Rcheck && mkdir RNAither.buildbin-libdir RNAither.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.19.0.tar.gz >RNAither.Rcheck\00install.out 2>&1 && cp RNAither.Rcheck\00install.out RNAither-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.19.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/RNAither.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.19.0'
* 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 'RNAither' 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 ... NOTE
Found the following CITATION file in a non-standard place:
inst/extdata/CITATION
Most likely 'inst/CITATION' should be used instead.
* 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 ... NOTE
Namespace in Imports field not imported from: 'methods'
All declared Imports should be used.
Package in Depends field not imported from: 'RankProd'
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
PlotSpatialDistrib: no visible global function definition for
'brewer.pal'
RankProduct: no visible global function definition for 'RP'
compareReplicateSD: no visible global function definition for
'brewer.pal'
compareReplicateSDPerScreen: no visible global function definition for
'brewer.pal'
spatialDistrib: no visible global function definition for 'brewer.pal'
Undefined global functions or variables:
RP brewer.pal
* 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 'RNAither-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compareReplicateSD
> ### Title: Plot the standard deviation of replicates
> ### Aliases: compareReplicateSD
> ### Keywords: arith device
>
> ### ** Examples
>
> data(exampleHeader, package="RNAither")
> data(exampleDataset, package="RNAither")
>
> compareReplicateSD(header, dataset, "Replicate standard intensity deviation",
+ "SigIntensity", "GeneName", 1)
Error in if (!is.vector(char) || length(char) != length(ind) || !all(nchar(char) <= :
missing value where TRUE/FALSE needed
Calls: compareReplicateSD -> plotPlate
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RNAither-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compareReplicateSD
> ### Title: Plot the standard deviation of replicates
> ### Aliases: compareReplicateSD
> ### Keywords: arith device
>
> ### ** Examples
>
> data(exampleHeader, package="RNAither")
> data(exampleDataset, package="RNAither")
>
> compareReplicateSD(header, dataset, "Replicate standard intensity deviation",
+ "SigIntensity", "GeneName", 1)
Error in if (!is.vector(char) || length(char) != length(ind) || !all(nchar(char) <= :
missing value where TRUE/FALSE needed
Calls: compareReplicateSD -> plotPlate
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, 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/RNAither.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'RNAither' ...
** R
** data
** inst
** preparing package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
install for x64
* installing *source* package 'RNAither' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'RNAither' as RNAither_2.19.0.zip
* DONE (RNAither)