LowMACA 1.2.0
Stefano de Pretis , Giorgio Melloni
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/LowMACA | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf LowMACA.buildbin-libdir LowMACA.Rcheck && mkdir LowMACA.buildbin-libdir LowMACA.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LowMACA.buildbin-libdir LowMACA_1.2.0.tar.gz >LowMACA.Rcheck\00install.out 2>&1 && cp LowMACA.Rcheck\00install.out LowMACA-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=LowMACA.buildbin-libdir --install="check:LowMACA-install.out" --force-multiarch --no-vignettes --timings LowMACA_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/LowMACA.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LowMACA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LowMACA' version '1.2.0'
* 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 'LowMACA' 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' ... [12m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
allPfamAnalysis 221.63 2.37 242.33
lfmSingleSequence 133.41 1.69 141.59
setup 31.06 5.55 106.92
LowMACA-class 22.12 3.24 68.08
LowMACA-package 12.78 1.58 37.88
newLowMACA 5.58 0.04 5.63
alignSequences 5.36 0.03 18.36
lmPlotSingleSequence 4.65 0.28 11.65
lmPlot 4.33 0.12 13.58
getMutations 2.37 0.33 11.92
** running examples for arch 'x64' ... ERROR
Running examples in 'LowMACA-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alignSequences
> ### Title: Align sequences via clustalo
> ### Aliases: alignSequences
>
> ### ** Examples
>
> #Create an object of class LowMACA for RAS domain family
> lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
All Gene Symbols correct!
> #Align sequences using local installation of clustalo
> lm <- alignSequences(lm)
Aligning sequences...
> #Web service clustalomega aligner
> lm <- alignSequences(lm , mail="lowmaca@gmail.com")
Aligning sequences...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
http status: 400 Bad Request Invalid parameters:
Sequence -> Error in reading input sequence. Please check your input. at D:/biocbld/bbs-3.2-bioc/meat/LowMACA.buildbin-libdir/LowMACA/clustalo_lwp.pl line 262.
Warning: running command '"C:\Perl\bin\perl.exe" "D:/biocbld/bbs-3.2-bioc/meat/LowMACA.buildbin-libdir/LowMACA/clustalo_lwp.pl" --noguidetreeout --stype protein --dismatout --outfmt clustal --email lowmaca@gmail.com --outfile "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpKK1w7d/webClustal" "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpKK1w7d\file1890275a5a3"' had status 255
Error in .clustalOAlign(genesData, clustal_cmd, clustalo_filename, mail, :
Alignment with ClustalOmega had non 0 exit status:
Calls: alignSequences -> alignSequences -> .clustalOAlign
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: 1 ERROR
See
'D:/biocbld/bbs-3.2-bioc/meat/LowMACA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'LowMACA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
install for x64
* installing *source* package 'LowMACA' ...
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* MD5 sums
packaged installation of 'LowMACA' as LowMACA_1.2.0.zip
* DONE (LowMACA)