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Package 29/251HostnameOS / ArchBUILDCHECKBUILD BIN
bgafun 1.1.0
Iain Wallace
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bgafun
Last Changed Rev: 27716 / Revision: 29143
Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  ERROR 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  ERROR 
wellington Linux (openSUSE 10.3) / i686  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
lemming Windows Server 2003 (32-bit) / x64  OK [ ERROR ] OK 
Package: bgafun
Version: 1.1.0
Command: D:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check bgafun_1.1.0.tar.gz
StartedAt: 2007-12-11 05:23:40 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 05:25:26 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 105.8 seconds
RetCode: 1
Status: ERROR
CheckDir: bgafun.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.2-bioc/meat/bgafun.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'bgafun/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bgafun' version '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'bgafun' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating bgafun-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'bgafun-Ex.R' failed.
The error most likely occurred in:

> ### * bgafun
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: BGAfun
> ### Title: BGAfun A method to identify specifity determining residues in
> ###   protein families
> ### Aliases: bgafun
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> library(bgafun)
> #read in alignment
> LDH <- read.alignment(File = system.file("sequences/LDH-MDH-PF00056.fasta", package = "bgafun"), format = "fasta")
Warning in read.alignment(File = system.file("sequences/LDH-MDH-PF00056.fasta",  :
  argument File is deprecated, use file instead
> 
> #Assign into groups
> LDH.amino=convert_aln_amino(LDH)
Error in strsplit(Alignment$seq[i], split = NULL) : 
  non-character argument
Calls: convert_aln_amino -> unlist -> strsplit
Execution halted

bgafun.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.2-bioc/meat/bgafun.Rcheck


---------- Making package bgafun ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
Note: unmatched right brace in 'add_pseudo_counts' on or after line 9
Note: unmatched right brace in 'add_pseudo_counts.Rd' on or after line 9
Note: unmatched right brace in 'run_between_pca' on or after line 8
Note: unmatched right brace in 'run_between_pca.Rd' on or after line 8
 >>> Building/Updating help pages for package 'bgafun'
     Formats: text html latex example chm 
  Calculate_Row_Weights             text    html    latex   example chm
  Henikoff_weights                  text    html    latex           chm
  LDH                               text    html    latex           chm
  LDH.aap                           text    html    latex           chm
  LDH.aap.ave                       text    html    latex           chm
  LDH.amino                         text    html    latex           chm
  LDH.amino.gapless                 text    html    latex           chm
  LDH.amino.pseudo                  text    html    latex           chm
  LDH.groups                        text    html    latex           chm
  Weight_Amino                      text    html    latex           chm
  add_pseudo_counts                 text    html    latex   example chm
  amino_counts                      text    html    latex           chm
  average_cols_aap                  text    html    latex   example chm
  bgafun                            text    html    latex   example chm
  calculate_pseudo                  text    html    latex           chm
  convertAAP.package                text    html    latex           chm
  convert_aln_AAP                   text    html    latex   example chm
  convert_aln_amino                 text    html    latex   example chm
  convert_amino.package             text    html    latex           chm
  convert_seq_AAP                   text    html    latex           chm
  convert_seq_amino                 text    html    latex           chm
  create_colnames_AAP               text    html    latex           chm
  create_colnames_amino             text    html    latex           chm
  create_probab                     text    html    latex           chm
  create_profile                    text    html    latex           chm
  create_profile_strings            text    html    latex   example chm
  pseudo_counts                     text    html    latex           chm
  remove_gaps                       text    html    latex           chm
  remove_gaps_groups                text    html    latex   example chm
  run_between_pca                   text    html    latex   example chm
  sum_20_aln                        text    html    latex           chm
  sum_20_cols                       text    html    latex           chm
  sum_aln                           text    html    latex           chm
  top_residues_2_groups             text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.2-bioc\meat\bgafun.Rcheck\00_pkg_src\bgafun\chm\bgafun.chm


Compile time: 0 minutes, 0 seconds
35	Topics
67	Local links
0	Internet links
1	Graphic


Created d:\biocbld\bbs-2.2-bioc\meat\bgafun.Rcheck\00_pkg_src\bgafun\chm\bgafun.chm, 32,591 bytes
Compression decreased file by 30,743 bytes.
  adding MD5 sums

* DONE (bgafun)