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 [[alternative HTML version deleted]]

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 Tel: +86-20-85222677 Email: guangchuangyu@gmail.com guangchuangyu@jnu.edu.cn Blog: http://ygc.name Scholar Profile: http://bit.ly/IpzxpH -~----------~----~----~----~------~----~------~--~--- 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 > ** > ** > ** > [[alternative HTML version deleted]]