GenVisR 1.4.1
Zachary Skidmore
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GenVisR | | Last Changed Rev: 125041 / Revision: 128728 | | Last Changed Date: 2016-12-12 14:22:09 -0500 (Mon, 12 Dec 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / 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 GenVisR.buildbin-libdir GenVisR.Rcheck && mkdir GenVisR.buildbin-libdir GenVisR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenVisR.buildbin-libdir GenVisR_1.4.1.tar.gz >GenVisR.Rcheck\00install.out 2>&1 && cp GenVisR.Rcheck\00install.out GenVisR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GenVisR.buildbin-libdir --install="check:GenVisR-install.out" --force-multiarch --no-vignettes --timings GenVisR_1.4.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/GenVisR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.4.1'
* 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 'GenVisR' 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 ... OK
* 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 'GenVisR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lolliplot
> ### Title: Construct a lolliplot
> ### Aliases: lolliplot
>
> ### ** Examples
>
> # Create input data
> data <- brcaMAF[brcaMAF$Hugo_Symbol == 'TP53',c('Hugo_Symbol', 'amino_acid_change_WU')]
> data <- as.data.frame(cbind(data, 'ENST00000269305'))
> colnames(data) <- c('gene', 'amino_acid_change', 'transcript_name')
>
> # Call lolliplot
> lolliplot(data)
Using the following host: www.ensembl.org for biomaRt queries to change the ensembl annotation version alter this parameter!
Querying biomaRt for transcript sequence
Error in if (nchar(x)%%3 != 0) { : argument is of length zero
Calls: lolliplot -> lolliplot_DNAconv
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GenVisR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lolliplot
> ### Title: Construct a lolliplot
> ### Aliases: lolliplot
>
> ### ** Examples
>
> # Create input data
> data <- brcaMAF[brcaMAF$Hugo_Symbol == 'TP53',c('Hugo_Symbol', 'amino_acid_change_WU')]
> data <- as.data.frame(cbind(data, 'ENST00000269305'))
> colnames(data) <- c('gene', 'amino_acid_change', 'transcript_name')
>
> # Call lolliplot
> lolliplot(data)
Using the following host: www.ensembl.org for biomaRt queries to change the ensembl annotation version alter this parameter!
Querying biomaRt for transcript sequence
Error in if (nchar(x)%%3 != 0) { : argument is of length zero
Calls: lolliplot -> lolliplot_DNAconv
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
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/GenVisR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GenVisR' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'GenVisR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenVisR' as GenVisR_1.4.1.zip
* DONE (GenVisR)