pcaExplorer 2.2.0
Federico Marini
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/pcaExplorer | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### rm -rf pcaExplorer.buildbin-libdir pcaExplorer.Rcheck && mkdir pcaExplorer.buildbin-libdir pcaExplorer.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pcaExplorer.buildbin-libdir pcaExplorer_2.2.0.tar.gz >pcaExplorer.Rcheck\00install.out 2>&1 && cp pcaExplorer.Rcheck\00install.out pcaExplorer-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=pcaExplorer.buildbin-libdir --install="check:pcaExplorer-install.out" --force-multiarch --no-vignettes --timings pcaExplorer_2.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pcaExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pcaExplorer' version '2.2.0'
* 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 'pcaExplorer' 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
* 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 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
pcaExplorer: no visible binding for '<<-' assignment to
'pcaexplorer_env'
pcaExplorer : <anonymous>: no visible binding for global variable
'airway'
pcaExplorer : <anonymous>: no visible binding for global variable
'pcaexplorer_env'
Undefined global functions or variables:
airway pcaexplorer_env
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'pcaExplorer-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcaplot3d
> ### Title: Sample PCA plot for transformed data
> ### Aliases: pcaplot3d
>
> ### ** Examples
>
> dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 1)
> rlt <- DESeq2::rlogTransformation(dds)
> pcaplot3d(rlt, ntop=200)
Error in scatterplot3js(d[, 1:3], color = cols, renderer = "canvas", size = 1.3, :
(list) object cannot be coerced to type 'double'
Calls: pcaplot3d -> scatterplot3js
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'pcaExplorer-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcaplot3d
> ### Title: Sample PCA plot for transformed data
> ### Aliases: pcaplot3d
>
> ### ** Examples
>
> dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 1)
> rlt <- DESeq2::rlogTransformation(dds)
> pcaplot3d(rlt, ntop=200)
Error in scatterplot3js(d[, 1:3], color = cols, renderer = "canvas", size = 1.3, :
(list) object cannot be coerced to type 'double'
Calls: pcaplot3d -> scatterplot3js
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 2 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'pcaExplorer' ...
** R
** 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 'pcaExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaExplorer' as pcaExplorer_2.2.0.zip
* DONE (pcaExplorer)