QuartPAC 1.0.0
Gregory Ryslik
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/QuartPAC | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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###
### Running command:
###
### rm -rf QuartPAC.buildbin-libdir QuartPAC.Rcheck && mkdir QuartPAC.buildbin-libdir QuartPAC.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QuartPAC.buildbin-libdir QuartPAC_1.0.0.tar.gz >QuartPAC.Rcheck\00install.out 2>&1 && cp QuartPAC.Rcheck\00install.out QuartPAC-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=QuartPAC.buildbin-libdir --install="check:QuartPAC-install.out" --force-multiarch --no-vignettes --timings QuartPAC_1.0.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/QuartPAC.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QuartPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuartPAC' version '1.0.0'
* 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 'QuartPAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
alignPositions: no visible global function definition for
'PhredQuality'
alignPositions: no visible global function definition for
'pairwiseAlignment'
constructCanonicalNumbering: no visible global function definition for
'pattern'
constructCanonicalNumbering: no visible global function definition for
'subject'
* 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' ... [131s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
QuartPAC-package 55.45 1.61 64.59
makeAlignedSuperStructure 25.64 1.09 50.54
getMutations 0.05 0.00 10.93
** running examples for arch 'x64' ... ERROR
Running examples in 'QuartPAC-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QuartPAC-package
> ### Title: Identifying mutational clusters while incorporating protein
> ### quaternary structure.
> ### Aliases: QuartPAC-package QuartPAC
> ### Keywords: protein quaternary clustering
>
> ### ** Examples
>
>
> #read the mutational data
> mutation_files <- list(
+ system.file("extdata","HFE_Q30201_MutationOutput.txt", package = "QuartPAC"),
+ system.file("extdata","B2M_P61769_MutationOutput.txt", package = "QuartPAC")
+ )
> uniprots <- list("Q30201","P61769")
> mutation.data <- getMutations(mutation_files = mutation_files, uniprots = uniprots)
>
> #read the pdb file
> pdb.location <- "http://www.rcsb.org/pdb/files/1A6Z.pdb"
> assembly.location <- "http://www.rcsb.org/pdb/files/1A6Z.pdb1"
> structural.data <- makeAlignedSuperStructure(pdb.location, assembly.location)
Warning in file(con, "r") :
InternetOpenUrl failed: 'The operation timed out'
Error in file(con, "r") : cannot open the connection
Calls: makeAlignedSuperStructure ... rbindlist -> lapply -> FUN -> get.AASeq -> readLines -> file
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [74s]
[74s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [76s]
[76s] 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: 1 ERROR, 2 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/QuartPAC.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'QuartPAC' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'QuartPAC' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'QuartPAC' as QuartPAC_1.0.0.zip
* DONE (QuartPAC)