Weired error: pdbaln()

[Xinqiu Yao]

I got an error when calling

pdbs <- pdbaln(c("1tag", "1as0"), file="tmp.aln")
#  Note: Accessing online PDB files using 4 letter PDBID
#Error in pdbaln(c("1tag", "1as0"), file = "tmp.aln") : 
#  ** Missing files: check filenames
#tmp.aln

while it is fine when

pdbs <- pdbaln(files=c("1tag", "1as0"), file="tmp.aln")

Note that file="tmp.aln" is an option passed to seqaln() via "..."

[Lars Skjærven]

Strange behavior. So, the files argument gets overwritten by the file argument. i.e. if your first line in pdbaln is print(files), then it will print the content of argument file and not files.

Proposing to change the argument name file to outfile in seqaln()

[Xinqiu Yao]

That's what I thought: "File" overwrites "files". Although the mechanism is still not so clear, it seems that change the arg name "file" in seqaln() to "outfile" works properly. Will do it in the next commit.

[Barry Grant]

I agree with this...