RE: Installing R for Corra

[Mi-Youn Brusniak]

Dear Christian,

After your report on error in Corra -- "Error: mismatch in sample names,
'080731APHDLAg4_01' does not
>> match 'X080731APHDLAg4_01'"

I found that Linux version of R2.6.1 with XML library package adds extra
space in front of attribute object
and dataframe interpreted with "X" in front of name. Therefore, here we
remove "X". Caution. The file name itself shouldn't contain X.

You can swap the attached CorraStatistics.R with
Corra/CorraStatistics.R/trunk/CorraStatistics.R.
I will also shortly update Corra tar files in sourceforge site as well.

Cheers!

Mi-Youn

[Mi-Youn Brusniak]

Hi Christian,

The error doesn't make sense to me since the change I made is only adding a
line to ignore any X in the sample names.
Did you swap the code and build and redeploy? Did you also invoke copy_bin
as well? Please send me CorraStatistics.log file.

Mi-Youn

Mi-Youn Brusniak, Ph.D.
Computational Biology
Seattle Proteome Center
mbru...@systemsbiology.org
Tel: (206) 732-1327


-----Original Message-----
From: mer...@gmail.com [mailto:mer...@gmail.com] On Behalf Of Christian
Paredes
Sent: Friday, August 07, 2009 11:38 AM
To: Co...@googlegroups.com; Mi-Youn Brusniak
Subject: Re: Installing R for Corra

Hi Mi-Youn,

Thanks for the fix! I've run into another problem, unfortunately.
I've tried running it again and ended up getting an error message,
here's the output from the project/PBS/output/cparedes_test_CSR.oe
file:

[root@oscar_server output]# cat cparedes_test_CSR.oe
/proteomics/analysis/Corra/users/cparedes/test
Queue workq
Job Id 195.oscar_server
R --slave --args project=test corra_bin=/proteomics/analysis/Corra/bin
working_dir=.
sample_file=/proteomics/analysis/Corra/users/cparedes/test/SampleInfo.tsv
contrasts_file=/proteomics/analysis/Corra/users/cparedes/test/ContrastFile.t
sv
data_file=aligned_features.apml run_log=CorraStatistics.log
hits_to_report=2.2 na_replace_method=minimum debug_on=TRUE
</proteomics/analysis/Corra/bin/CorraStatistics.R
Error: unexpected '=' in "="
Execution halted

real 0m0.413s
user 0m0.346s
sys 0m0.034s

-- Christian

[Christian Paredes]

Hi Mi-Youn,

I've moved the other CorraStatistics.R file to CorraStatistics.Rbak in
the /proteomics/analysis/Corra/bin directory and then I moved the new
file to that same directory. I also have changed the permissions and
ownership to mirror the old file's properties. I haven't invoked
copy_bin at all, are you talking about the ant post-installation
command? After running CorraStatistics.R, it doesn't generate a new
CorraStatistics.log file, but I'll attach the one I do have before I
replaced CorraStatistics.R.

-- Christian

On Fri, Aug 7, 2009 at 11:50 AM, Mi-Youn

[Mi-Youn Brusniak]

Dear Christian,

You have done is what ant copy_bin does except copying to
CorraStatistics.Rbak.
I gave you an instruction to swap source code and build rather than updating
directly to bin directory.
However, it will work. The previous log file doesn't help since you gave me
earlier.
Not generating any log file tells me some other things has been changed
since you contact me.
For double check, would you do diff on CorraStatistics.Rbak and
CorraStatistics.R and send to me?
I just ran with test data with the new CorraStatistics.R and worked well.