On Sat, Mar 31, 2012 at 5:58 AM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > Hi all, > > I'm having a difficult time using the untar() after I retrieve the > supp files using getGEOSuppFiles(). I tried it with gse15653 and > gse12643. Both times different errors and I'm not quite sure what else > to do. My goal is to retrieve the associated .cel files. Please help. Thanks for the report. This should be fixed now. Give things a day or so to move through the build system. Sean > Thanks. > > -Avoks > >> untar("GSE12643/GSE12643_RAW.tar", files = NULL, list = FALSE, exdir = ".", > + ? ? ? compressed = gzip, extras = NULL, verbose = FALSE, > + ? ? ? tar = Sys.getenv("TAR")) > Error in rawToChar(block[seq_len(ns)]) : > ?embedded nul in string: > '\023?\030?T?\002@?e4-\024?W?&??i0??"XR??CGw?\001\024uA?}]Dw???D\036?' >> >> untar("GSE15653/GSE15653_RAW.tar", files = NULL, list = FALSE, exdir = ".", > + ? ? ? compressed = gzip, extras = NULL, verbose = FALSE, > + ? ? ? tar = Sys.getenv("TAR") > + ) > Error in getOct(block, 100, 8) : invalid octal digit > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_xxx.1252 ?LC_CTYPE=English_xxx.1252 > [3] LC_MONETARY=English_xxx.1252 LC_NUMERIC=C > [5] LC_TIME=English_xxx.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] affy_1.32.1 ? ? GEOquery_2.20.8 Biobase_2.14.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Thanks a bunch, Sean. -Avoks On Mon, Apr 9, 2012 at 4:47 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > You'll need version 2.23.1.? It is the current release version. > > Sean > > On Apr 9, 2012 10:39 AM, "Ovokeraye Achinike-Oduaran" <ovokeraye at="" gmail.com=""> > wrote: >> >> Hi Sean, >> >> I still get thesame errors when I run the code as is. Has the fix gone >> through the build system? >> >> Thanks. >> >> Avoks >> >> sessionInfo() >> >> R version 2.15.0 (2012-03-30) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_.1252 ?LC_CTYPE=English_.1252 >> [3] LC_MONETARY=English_.1252 LC_NUMERIC=C >> [5] LC_TIME=English_.1252 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] GEOquery_2.20.8 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.91-1.1 tools_2.15.0 ? XML_3.9-4.1 >> >> On Sun, Apr 1, 2012 at 3:19 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> > On Sat, Mar 31, 2012 at 5:58 AM, Ovokeraye Achinike-Oduaran >> > <ovokeraye at="" gmail.com=""> wrote: >> >> Hi all, >> >> >> >> I'm having a difficult time using the untar() after I retrieve the >> >> supp files using getGEOSuppFiles(). I tried it with gse15653 and >> >> gse12643. Both times different errors and I'm not quite sure what else >> >> to do. My goal is to retrieve the associated .cel files. Please help. >> > >> > Thanks for the report. ?This should be fixed now. ?Give things a day >> > or so to move through the build system. >> > >> > Sean >> > >> > >> >> Thanks. >> >> >> >> -Avoks >> >> >> >>> untar("GSE12643/GSE12643_RAW.tar", files = NULL, list = FALSE, exdir = >> >>> ".", >> >> + ? ? ? compressed = gzip, extras = NULL, verbose = FALSE, >> >> + ? ? ? tar = Sys.getenv("TAR")) >> >> Error in rawToChar(block[seq_len(ns)]) : >> >> ?embedded nul in string: >> >> >> >> '\023?\030?T?\002@?e4-\024?W?&??i0??"XR??CGw?\001\024uA> >> ??9?? ?????L ?O ????\0>?}]Dw???D\036?' >> >>> >> >>> untar("GSE15653/GSE15653_RAW.tar", files = NULL, list = FALSE, exdir = >> >>> ".", >> >> + ? ? ? compressed = gzip, extras = NULL, verbose = FALSE, >> >> + ? ? ? tar = Sys.getenv("TAR") >> >> + ) >> >> Error in getOct(block, 100, 8) : invalid octal digit >> >> >> >>> sessionInfo() >> >> R version 2.14.1 (2011-12-22) >> >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> >> >> locale: >> >> [1] LC_COLLATE=English_xxx.1252 ?LC_CTYPE=English_xxx.1252 >> >> [3] LC_MONETARY=English_xxx.1252 LC_NUMERIC=C >> >> [5] LC_TIME=English_xxx.1252 >> >> >> >> attached base packages: >> >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> >> >> other attached packages: >> >> [1] affy_1.32.1 ? ? GEOquery_2.20.8 Biobase_2.14.0 >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor