Re: [aroma.affymetrix] Re: OSX 10.6 10.7 users: Workaround for faulty BioC build of affxparser v1.26.2
It worked!!! :) Thank you very much! Martina Il giorno mercoledì 26 settembre 2012 22:09:28 UTC+2, Henrik Bengtsson ha scritto: Hi, sorry about the affxparser mess. See if the following source(http://aroma-project.org/affxparser.R;); installAffxparser(); solves your problems. The above will run tests to make sure everything works fine and if it says that is the case, you're read to rock'n'roll. Please report back and let me know if it works, because then I'll include the above as part of the default installation. /Henrik On Wed, Sep 26, 2012 at 7:12 AM, Martina Dori martin...@gmail.comjavascript: wrote: Hi Henrik, I'm working on OS X 10.8.2 and sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-apple-darwin9.8.0/i386 (32-bit) I followed the instruction you gave and uninstalled the affxparser I had and re-installed the previous version. It gave me this warning: Warning messages: 1: In packageDescription(pkg) : no package 'affxparser' was found 2: package ‘R.utils’ was built under R version 2.15.1 3: package ‘R.oo’ was built under R version 2.15.1 4: package ‘R.methodsS3’ was built under R version 2.15.1 So I checked if it was installed packageDescription(affxparser)$Packaged [1] 2011-11-20 16:44:36 UTC; khansen Because it seemed to be installed, I tried to check my CDF file (GenomeWideSNP_6,Full.cdf) as you mentioned as test but it returned me as follows *** caught segfault *** address 0xfffc, cause 'memory not mapped' Traceback: 1: .Call(R_affx_get_cdf_file_header, filename, PACKAGE = affxparser) 2: readCdfHeader(annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace R(2155,0xacadaa28) malloc: *** error for object 0xbfffe730: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug I loaded the aroma.affymetrix library and because it didn't find the affxparser R automatically installed the latest version. What should I do? Thank you very much for any help Martina Il giorno sabato 31 marzo 2012 02:31:50 UTC+2, Jorge Melendez ha scritto: Hi Henrik worked ok library(affxparser); readCdfHeader(annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf); $ncols [1] 2560 $nrows [1] 2560 $nunits [1] 262338 $nqcunits [1] 6 $refseq [1] $chiptype [1] Mapping250K_Nsp $filename [1] annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf $rows [1] 2560 $cols [1] 2560 $probesets [1] 262338 $qcprobesets [1] 6 $reference [1] sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) Thank you! :: (*) If you have access to OSX 10.7 (Lion), could you please check whether the patched version of affxparser on OSX or not, and report back? Try the following: library(affxparser); readCdfHeader(annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf); It should not crash R, but return a list of CDF attributes. The above CDF can be downloaded from: http://www.aroma-project.org/data/annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf.gz -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-af...@googlegroups.comjavascript: To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Re: OSX 10.6 10.7 users: Workaround for faulty BioC build of affxparser v1.26.2
Hi, sorry about the affxparser mess. See if the following source(http://aroma-project.org/affxparser.R;); installAffxparser(); solves your problems. The above will run tests to make sure everything works fine and if it says that is the case, you're read to rock'n'roll. Please report back and let me know if it works, because then I'll include the above as part of the default installation. /Henrik On Wed, Sep 26, 2012 at 7:12 AM, Martina Dori martina.d...@gmail.com wrote: Hi Henrik, I'm working on OS X 10.8.2 and sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-apple-darwin9.8.0/i386 (32-bit) I followed the instruction you gave and uninstalled the affxparser I had and re-installed the previous version. It gave me this warning: Warning messages: 1: In packageDescription(pkg) : no package 'affxparser' was found 2: package ‘R.utils’ was built under R version 2.15.1 3: package ‘R.oo’ was built under R version 2.15.1 4: package ‘R.methodsS3’ was built under R version 2.15.1 So I checked if it was installed packageDescription(affxparser)$Packaged [1] 2011-11-20 16:44:36 UTC; khansen Because it seemed to be installed, I tried to check my CDF file (GenomeWideSNP_6,Full.cdf) as you mentioned as test but it returned me as follows *** caught segfault *** address 0xfffc, cause 'memory not mapped' Traceback: 1: .Call(R_affx_get_cdf_file_header, filename, PACKAGE = affxparser) 2: readCdfHeader(annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace R(2155,0xacadaa28) malloc: *** error for object 0xbfffe730: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug I loaded the aroma.affymetrix library and because it didn't find the affxparser R automatically installed the latest version. What should I do? Thank you very much for any help Martina Il giorno sabato 31 marzo 2012 02:31:50 UTC+2, Jorge Melendez ha scritto: Hi Henrik worked ok library(affxparser); readCdfHeader(annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf); $ncols [1] 2560 $nrows [1] 2560 $nunits [1] 262338 $nqcunits [1] 6 $refseq [1] $chiptype [1] Mapping250K_Nsp $filename [1] annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf $rows [1] 2560 $cols [1] 2560 $probesets [1] 262338 $qcprobesets [1] 6 $reference [1] sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) Thank you! :: (*) If you have access to OSX 10.7 (Lion), could you please check whether the patched version of affxparser on OSX or not, and report back? Try the following: library(affxparser); readCdfHeader(annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf); It should not crash R, but return a list of CDF attributes. The above CDF can be downloaded from: http://www.aroma-project.org/data/annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf.gz -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
