[Biopython-dev] Errors about installing biopython 1.61

[林行众]

2013/5/13 Peter Cock <p.j.a.cock at googlemail.com>

> On Mon, May 13, 2013 at 2:41 AM, 林行众 <linxzh1989 at gmail.com> wrote:
> >
> >> Where did you get the Biopython 1.61 files from? e.g. The zip file
> >> or tar.gz file on our website? Perhaps I accidentally included an
> >> older copy of the Doc/Tutorial.tex file? Could you look for the
> >> "Late Update" line in your Tutorial.tex file for me - does it say:
> >>
> >> \date{Last Update -- 5 February 2013 (Biopython 1.61)}
> >>
> >> Thanks,
> >>
> >> Peter
> >
> > Hi，Peter！
> > Clustalw I am using is 1.83.
>
> Hi Lin,
>
> I also have clustalw 1.83, so this isn't simply a version
> problem. It could be something subtle about the locale -
> what language is your CentOS running in (that can alter
> error messages etc)?
>
> > I've found the 'Late Update' in Tutorial.tex, it's ' \date{Last Update
> -- 5
> > February 2013 (Biopython 1.61)}'.
>
> That's good - that's what it should say :)
>
> (Sorry late/last was my typing error).
>
> >
> > I downloaded the tar.gz from the biopython website.
> >
>
> Thanks. I could reproduce the test_Tutorial.py problem with that.
> This is easy to explain - I forgot to include the test file my_blast.xml
> when doing the release (and you are the first person to report this
> problem). I should have noticed this myself, sorry :(
>
> I've fixed this ready for the next release - thank you for reporting this:
>
> https://github.com/biopython/biopython/commit/c1b63b88dd5a50fa3f6f2aef840a51fe9092e0c5
>
> If you want to, you can get the missing file from here:
> http://biopython.org/SRC/Doc/examples/my_blast.xml
>
> or:
> https://github.com/biopython/biopython/raw/master/Doc/examples/my_blast.xml
>
> If you save that in the Biopython 1.61 source under Doc/examples
> then the Tutorial test should pass.
>
> --
>
> Did you retry the test_Entrez_online.py example to see if
> this was a temporary problem?
>
> --
>
> The good news is these minor issues should not cause you
> any problems installing and using Biopython 1.61 - so you
> can go ahead and run 'python setup.py install.
>
> Thanks,
>
> Peter
>
Hi Peter
I have run the locale in my serve

$ locale
LANG=en_US.UTF-8
LC_CTYPE=zh_CN.UTF-8
LC_NUMERIC=zh_CN.UTF-8
LC_TIME=zh_CN.UTF-8
LC_COLLATE="en_US.UTF-8"
LC_MONETARY=zh_CN.UTF-8
LC_MESSAGES="en_US.UTF-8"
LC_PAPER=zh_CN.UTF-8
LC_NAME=zh_CN.UTF-8
LC_ADDRESS=zh_CN.UTF-8
LC_TELEPHONE=zh_CN.UTF-8
LC_MEASUREMENT=zh_CN.UTF-8
LC_IDENTIFICATION=zh_CN.UTF-8
LC_ALL=

Is that locale you want?

I retryed the the test_Entrez_online.py, it's all right now. As you said,
it should be a connection problem.

I have put the file in the Doc/examples file, but the error still exists.
And i find there is no my_blat.psl in Doc/examples comparing with the zip
file i downloaded from github. After i put the my_blat.psi in the
Doc/examples, the error did not show up again.

Thanks
Lin