Hi, With the help from Herve, we found out that the devel version of biomaRt is broken with the new Rcurl version 095-1. This is confirmed by the build system: http://bioconductor.org/checkResults/2.5/bioc-LATEST/biomaRt/wilson2-buildsr c.html As you can see, it's broken on Linux and Mac OS. It looks OK on the Window build machine because this machine is using an older version of RCurl (0.94-1). I am in the process of submitting a contributed package that relies on biomaRt and my package won't be passed to the reviewers until biomaRt is fixed. Could someone please fix the devel version of biomaRt? Thanks a lot for your kind help! Best regards, Julie ******************************************* Julie Zhu, Ph.D Research Assistant Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 http://www.umassmed.edu/pgfe/faculty/zhu.cfm
[Bioc-devel] Need help on biomaRt
4 messages · Julie Zhu, Tony Chiang, Florian Hahne
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The problem was fixed by Duncan Temple Lang in the latest RCurl version 0.97-3 which is available from Omegahat (http://www.omegahat.org/RCurl/ ) The automatic updates on our build systems should pick this up any time now, so all you need is patience for one or two more days :) Florian
On 28.05.2009, at 11:32, Julie Zhu wrote:
Hi, With the help from Herve, we found out that the devel version of biomaRt is broken with the new Rcurl version 095-1. This is confirmed by the build system: http://bioconductor.org/checkResults/2.5/bioc-LATEST/biomaRt/wilson2-buildsr c.html As you can see, it's broken on Linux and Mac OS. It looks OK on the Window build machine because this machine is using an older version of RCurl (0.94-1). I am in the process of submitting a contributed package that relies on biomaRt and my package won't be passed to the reviewers until biomaRt is fixed. Could someone please fix the devel version of biomaRt? Thanks a lot for your kind help! Best regards, Julie ******************************************* Julie Zhu, Ph.D Research Assistant Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 http://www.umassmed.edu/pgfe/faculty/zhu.cfm
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Florian, Thank you very much for the great news! Best regards, Julie
On 5/29/09 11:33 AM, "Florian Hahne" <fhahne at fhcrc.org> wrote:
The problem was fixed by Duncan Temple Lang in the latest RCurl version 0.97-3 which is available from Omegahat (http://www.omegahat.org/RCurl/ ) The automatic updates on our build systems should pick this up any time now, so all you need is patience for one or two more days :) Florian On 28.05.2009, at 11:32, Julie Zhu wrote:
Hi, With the help from Herve, we found out that the devel version of biomaRt is broken with the new Rcurl version 095-1. This is confirmed by the build system: http://bioconductor.org/checkResults/2.5/bioc-LATEST/biomaRt/wilson2-buildsr c.html As you can see, it's broken on Linux and Mac OS. It looks OK on the Window build machine because this machine is using an older version of RCurl (0.94-1). I am in the process of submitting a contributed package that relies on biomaRt and my package won't be passed to the reviewers until biomaRt is fixed. Could someone please fix the devel version of biomaRt? Thanks a lot for your kind help! Best regards, Julie ******************************************* Julie Zhu, Ph.D Research Assistant Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 http://www.umassmed.edu/pgfe/faculty/zhu.cfm
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