Package: iPAC

Version: 1.1.3

Command: rm -rf iPAC.buildbin-libdir && mkdir iPAC.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iPAC.buildbin-libdir iPAC_1.1.3.tar.gz >iPAC-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=iPAC.buildbin-libdir --install="check:iPAC-install.out" --force-multiarch --no-vignettes --timings iPAC_1.1.3.tar.gz && mv iPAC.buildbin-libdir/* iPAC.Rcheck/ && rmdir iPAC.buildbin-libdir

StartedAt: 2013-03-25 03:08:00 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:26:39 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 1118.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: iPAC.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/iPAC.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPAC' version '1.1.3'
* 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 'iPAC' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'iPAC-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get.Positions
> ### Title: get.Positions
> ### Aliases: get.Positions
> ### Keywords: Amino Acids Positions CIF
> 
> ### ** Examples
> 
> ###################################################
> #Observe that the final result from the code below is "OK". That is because the only
> #mismatched residue at position 61, was documented in the CIF file as well.
> #Thus it is considered a "reconciled" mismatch. It is up to the user to decide if 
> #they want to include it in the position sequence or remove it. 
> 
> CIF<-"http://www.pdb.org/pdb/files/3GFT.cif"
> Fasta<-"http://www.sanger.ac.uk/perl/genetics/CGP/cosmic_sequence?ln=KRAS;format=aa"
> KRAS.extracted.positions<- get.Positions(CIF, Fasta, "A")
> ###################################################
> 
> ###################################################
> #Observe that the final result from the code below is "FAILURE". For PIK3CA there were
> #10 mismatched residues between the CIF file and the canonical sequence. 
> #However, none of these residues are explained within the actual CIF file.
> 
> CIF<- "http://www.pdb.org/pdb/files/2RD0.cif"
> Fasta<-"http://www.sanger.ac.uk/perl/genetics/CGP/cosmic_sequence?ln=PIK3CA;format=aa"
> PIK3CA.extracted.positions<- get.Positions(CIF,Fasta , "A")
> ###################################################
> 
> ###################################################
> #Observe that the final result from the code below is "OK". Here we use a different file
> #location for the canonical sequence -- the UNIPROT database. The canonical sequence is slightly 
> #different and matches up exactly to the extracted positions. As there is only 1 isoform listed
> #on UNIPROT for PIK3CA we suggest that users obtain the mutational data and the canonical 
> #sequence information from the same source. For example, if your mutation data was obtained from 
> #COSMIC, you should use COSMIC to get the canonical protein sequence.
> 
> CIF <- "http://www.pdb.org/pdb/files/2RD0.cif"
> Fasta <- "http://www.uniprot.org/uniprot/P42336.fasta"
> PIK3CA.extracted.positions<- get.Positions(CIF, Fasta, "A")
Warning in file(con, "r") : cannot open: HTTP status was '0 (nil)'
Error in file(con, "r") : cannot open the connection
Calls: get.Positions -> get.AASeq -> readLines -> file
Execution halted
** running examples for arch 'x64' ... [10m] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ClusterFind          242.14   1.43  244.85
get.Positions        222.30   6.89  241.74
nmc                   49.07   0.00   49.08
Plot.Protein.Linear   44.03   0.59   45.44
get.Remapped.Order    10.35   0.24   11.39
get.AlignedPositions   8.42   0.21    9.37

install for i386

* installing *source* package 'iPAC' ...
** R
** data
** inst
** preparing package for lazy loading
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'iPAC.Rnw' 
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")

install for x64

* installing *source* package 'iPAC' ...
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* MD5 sums
packaged installation of 'iPAC' as iPAC_1.1.3.zip
* DONE (iPAC)