(resending the message as my initial attempts were refused) Hi, I'm looking for some insight on the source of the problem reported by 'wilson2' when building oligo: http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html This machine has R-devel r49067... The other machines have r49060 and r49021. So, because the pkg builds just fine on other machines but wilson2, I thought that the source of the problem would be on changes between r49060 and r49067. Looking at the log of R-devel for all these revisions, I don't see any change that would cause the error "'dimnames' applied to non-array" to come up. I just installed the latest R-devel and I can't reproduce the problem. So, is it just a matter of waiting until R-devel is updated on the machines used to build the packages? Thanks a lot, b
[Bioc-devel] problem when building oligo on wilson2
5 messages · Robert Gentleman, Patrick Aboyoun, Benilton Carvalho
Hi Benilton,
It could be any one of a number of things, not necessarily the build
of R (although that could be a factor). Someone here will likely need
to try to run this and see if it is reproducible from the command line
and if so, to try and find the problem. Alternatively you could check
out that version of R and see if the problem is reproducible on a
computer near you.
best wishes
Robert
Benilton Carvalho wrote:
(resending the message as my initial attempts were refused) Hi, I'm looking for some insight on the source of the problem reported by 'wilson2' when building oligo: http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html This machine has R-devel r49067... The other machines have r49060 and r49021. So, because the pkg builds just fine on other machines but wilson2, I thought that the source of the problem would be on changes between r49060 and r49067. Looking at the log of R-devel for all these revisions, I don't see any change that would cause the error "'dimnames' applied to non-array" to come up. I just installed the latest R-devel and I can't reproduce the problem. So, is it just a matter of waiting until R-devel is updated on the machines used to build the packages? Thanks a lot, b
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Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
Benilton, I pushed an early report of the builds today that don't include Windows because those machines haven't completed the build process yet. For today's report oligo isn't building on wilson2 (Linux), pitt (Mac OS X Tiger), pelham (Mac OSX Leopard). http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pitt-buildsrc.html http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pelham-buildsrc.html because of the error Error: processing vignette 'oligo.Rnw' failed with diagnostics: chunk 3 (label=crlmm) Error in crlmm(fullFilenames, outputDir, verbose = FALSE) : could not find function "requireAnnotation" Execution halted This missing symbol could be masking the more subtler problem you mentioned, but at least the current error should be easy to correct. Patrick
Robert Gentleman wrote:
Hi Benilton,
It could be any one of a number of things, not necessarily the build
of R (although that could be a factor). Someone here will likely need
to try to run this and see if it is reproducible from the command line
and if so, to try and find the problem. Alternatively you could check
out that version of R and see if the problem is reproducible on a
computer near you.
best wishes
Robert
Benilton Carvalho wrote:
(resending the message as my initial attempts were refused) Hi, I'm looking for some insight on the source of the problem reported by 'wilson2' when building oligo: http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html This machine has R-devel r49067... The other machines have r49060 and r49021. So, because the pkg builds just fine on other machines but wilson2, I thought that the source of the problem would be on changes between r49060 and r49067. Looking at the log of R-devel for all these revisions, I don't see any change that would cause the error "'dimnames' applied to non-array" to come up. I just installed the latest R-devel and I can't reproduce the problem. So, is it just a matter of waiting until R-devel is updated on the machines used to build the packages? Thanks a lot, b
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Dear Robert and Patrick, Thank you very much for your time. Patrick, I just exposed the function, thanks for the heads up. Robert, thanks for the hint. I'll get r49067 and try to reproduce the problem. b
On Aug 7, 2009, at 2:17 PM, Patrick Aboyoun wrote:
Benilton, I pushed an early report of the builds today that don't include Windows because those machines haven't completed the build process yet. For today's report oligo isn't building on wilson2 (Linux), pitt (Mac OS X Tiger), pelham (Mac OSX Leopard). http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pitt-buildsrc.html http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pelham-buildsrc.html because of the error Error: processing vignette 'oligo.Rnw' failed with diagnostics: chunk 3 (label=crlmm) Error in crlmm(fullFilenames, outputDir, verbose = FALSE) : could not find function "requireAnnotation" Execution halted This missing symbol could be masking the more subtler problem you mentioned, but at least the current error should be easy to correct. Patrick Robert Gentleman wrote:
Hi Benilton, It could be any one of a number of things, not necessarily the build of R (although that could be a factor). Someone here will likely need to try to run this and see if it is reproducible from the command line and if so, to try and find the problem. Alternatively you could check out that version of R and see if the problem is reproducible on a computer near you. best wishes Robert Benilton Carvalho wrote:
(resending the message as my initial attempts were refused) Hi, I'm looking for some insight on the source of the problem reported by 'wilson2' when building oligo: http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html This machine has R-devel r49067... The other machines have r49060 and r49021. So, because the pkg builds just fine on other machines but wilson2, I thought that the source of the problem would be on changes between r49060 and r49067. Looking at the log of R-devel for all these revisions, I don't see any change that would cause the error "'dimnames' applied to non-array" to come up. I just installed the latest R-devel and I can't reproduce the problem. So, is it just a matter of waiting until R-devel is updated on the machines used to build the packages? Thanks a lot, b
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
I got the revision 49067, but wasn't able to reproduce the problem on the machine I have access to... so I'll just wait for the next build and see what comes up. Thank you very much, b
On Aug 7, 2009, at 2:27 PM, Benilton Carvalho wrote:
Dear Robert and Patrick, Thank you very much for your time. Patrick, I just exposed the function, thanks for the heads up. Robert, thanks for the hint. I'll get r49067 and try to reproduce the problem. b On Aug 7, 2009, at 2:17 PM, Patrick Aboyoun wrote:
Benilton, I pushed an early report of the builds today that don't include Windows because those machines haven't completed the build process yet. For today's report oligo isn't building on wilson2 (Linux), pitt (Mac OS X Tiger), pelham (Mac OSX Leopard). http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pitt-buildsrc.html http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pelham-buildsrc.html because of the error Error: processing vignette 'oligo.Rnw' failed with diagnostics: chunk 3 (label=crlmm) Error in crlmm(fullFilenames, outputDir, verbose = FALSE) : could not find function "requireAnnotation" Execution halted This missing symbol could be masking the more subtler problem you mentioned, but at least the current error should be easy to correct. Patrick Robert Gentleman wrote:
Hi Benilton, It could be any one of a number of things, not necessarily the build of R (although that could be a factor). Someone here will likely need to try to run this and see if it is reproducible from the command line and if so, to try and find the problem. Alternatively you could check out that version of R and see if the problem is reproducible on a computer near you. best wishes Robert Benilton Carvalho wrote:
(resending the message as my initial attempts were refused) Hi, I'm looking for some insight on the source of the problem reported by 'wilson2' when building oligo: http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html This machine has R-devel r49067... The other machines have r49060 and r49021. So, because the pkg builds just fine on other machines but wilson2, I thought that the source of the problem would be on changes between r49060 and r49067. Looking at the log of R-devel for all these revisions, I don't see any change that would cause the error "'dimnames' applied to non-array" to come up. I just installed the latest R-devel and I can't reproduce the problem. So, is it just a matter of waiting until R-devel is updated on the machines used to build the packages? Thanks a lot, b
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel