Hi GC,
Thanks so much. buildGOmap is OK when I add the parameter: compress=FALSE.
But, Gff2GeneTable()  is still not work well and report the same error.
<I'm so confused that buildGOmap and Gff2GeneTable work well once or twice without anychanges on parameters.>

BTW, how about KEGG enrichment for unsupported organisms using your packages?

2013-03-19



Room 8612,
The Centre for Structural and Molecular Biology,
Institute of Biophysics, Chinese Academy of Sciences
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Email: wangm08@yeah.net
Tel: 86-10-64888299



发件人：Guangchuang Yu
发送时间：2013-03-19 14:59
主题：Re: xzfile() cannot open the connection, lzma encoder error 5.
收件人："Wang Ming"<wangm08@yeah.net>
抄送："bioconductor"<bioconductor@r-project.org>

Hi,

It's due to some of the windows version of R does not support rda file compression.  Someone had reported this issue before, and I add a parameter compress in buildGOmap function. Please set it to FALSE, and it will works fine.

Best Regards!

Guangchuang Yu
--~--~---------~--~----~------------~-------~--~----~
Department of Biochemistry & Molecular Biology
College of Life Science and Technology
Jinan University, 601 Huangpu Ave. W.
Guangzhou 510632,  P.R. China
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Email: guangchuangyu@gmail.com
           guangchuangyu@jnu.edu.cn
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On Tue, Mar 19, 2013 at 2:27 PM, Wang Ming <wangm08@yeah.net> wrote:

Dear all,
I was stopped by the following error when using Package: clusterProfiler on R 2.15.3 on windows 7.
Error in xzfile(file, “wb”, compression = 9) : Cannot open the connection
In addition: warning message:
  cannot initialize lzma encoder, error 5
The too functions: Gff2GeneTable() and buildGOmap() are not working because of this error.

Could you please let me know how to fix these error.
 [source of the package: http://bioconductor.org/packages/2.11/bioc/html/clusterProfiler.html]

Here are what I typed in R:
---------------------------------------------------------------
R version 2.15.3 (2013-03-01) -- "Security Blanket"
Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-w64-mingw32/i386 (32-bit)

> suppressPackageStartupMessages(require(clusterProfiler))
> Gff2GeneTable(“NC_007297.gff”)
Reading NC_007297.gff: found 3989 rows with classes:...
Error in xzfile(file, "wb", compression = 9) : cannot open the connection
In addition: Warning message:
In xzfile(file, "wb", compression = 9) :
  cannot initialize lzma encoder, error 5

> buildGOmap(gomap)
Error in xzfile(file, "wb", compression = 9) : cannot open the connection
In addition: Warning message:
In xzfile(file, "wb", compression = 9) :
  cannot initialize lzma encoder, error 5
-----------------------------------------------------------------

2013-03-19



Ming Wang, PhD
Room 8612,
The Centre for Structural and Molecular Biology,
Institute of Biophysics, Chinese Academy of Sciences
15 Datun Road, Chaoyang District, Beijing 100101, China
Email: wangm08@yeah.net
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