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 |
* 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
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)