##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:iPAC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings iPAC_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/iPAC.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘iPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iPAC’ version ‘1.48.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘iPAC’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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<-"https://files.rcsb.org/view/3GFT.cif"
> Fasta<-"https://www.uniprot.org/uniprot/P01116-2.fasta"
> 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<- "https://files.rcsb.org/view/2RD0.cif"
> Fasta<-"https://cancer.sanger.ac.uk/cosmic/sequence?width=700&ln=PIK3CA&type=protein&height=500"
> PIK3CA.extracted.positions<- get.Positions(CIF,Fasta , "A")
Warning in file(con, "r") :
  cannot open URL 'https://cancer.sanger.ac.uk/cosmic/sequence?width=700&ln=PIK3CA&type=protein&height=500': HTTP status was '403 Forbidden'
Error in file(con, "r") : 
  cannot open the connection to 'https://cancer.sanger.ac.uk/cosmic/sequence?width=700&ln=PIK3CA&type=protein&height=500'
Calls: get.Positions -> get.AASeq -> readLines -> file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/iPAC.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL iPAC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘iPAC’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iPAC)