Hi, I have just noticed that my package AnnotationFuncs does pass build and check for the next release on the Windows hosts. On the Linux and Max OS X hosts there are no problems. The error logs are these: - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/liverpool-buildsrc.html - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/moscato1-checksrc.html My personal workstation is also running Windows (7), and I have checked and built the package using the latest R release (R version 2.14.0 alpha (2011-10-04 r57169)), but I am not able to reproduce the errors displayed on the log at BioConductor. I have also been looking through my code, and I cannot trace the error giving problems in the build and check above: Error in function (x) : no function to return from, jumping to top level Execution halted Error in function (x) : attempt to apply non-function Execution halted Any suggestions? Kind regards, Stefan McKinnon H?j-Edwards Dept. of Molecular Biology and Genetics Ph.D. Fellow Aarhus University Blichers All? 20, Postboks 50 DK-8830 Tjele Tel.: +45 8715 7969 Tel.: +45 8715 6000 Email: Stefan.Hoj-Edwards at agrsci.dk Web: www.agrsci.dk
[Bioc-devel] Reproducing erros on build and check
5 messages · Stefan McKinnon Høj-Edwards, Benilton Carvalho, Martin Morgan +1 more
liverpool and moscato1 are running r57266 and r57224 respectively. that may help you tracking down the problem. b 2011/10/18 Stefan McKinnon H?j-Edwards <Stefan.Hoj-Edwards at agrsci.dk>:
Hi, I have just noticed that my package AnnotationFuncs does pass build and check for the next release on the Windows hosts. On the Linux and Max OS X hosts there are no problems. The error logs are these: - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/liverpool-buildsrc.html - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/moscato1-checksrc.html My personal workstation is also running Windows (7), and I have checked and built the package using the latest R release (R version 2.14.0 alpha (2011-10-04 r57169)), but I am not able to reproduce the errors displayed on the log at BioConductor. I have also been looking through my code, and I cannot trace the error giving problems in the build and check above: Error in function (x) ?: no function to return from, jumping to top level Execution halted Error in function (x) ?: attempt to apply non-function Execution halted Any suggestions? Kind regards, Stefan McKinnon H?j-Edwards ? ? ? ? ? ? ?Dept. of Molecular Biology and Genetics Ph.D. Fellow ? ? ? ? ? ? ? ? ? ? ? ? ? ? Aarhus University ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Blichers All? 20, Postboks 50 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? DK-8830 Tjele Tel.: +45 8715 7969 ? ? ? ? ? ? ? ? ? ? ?Tel.: +45 8715 6000 Email: Stefan.Hoj-Edwards at agrsci.dk ? ? ?Web: www.agrsci.dk
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Hi, Nope. I downloaded the latest build, r57258 (the link for the beta is broken), and still nothing. I can however see, that the problem occurs during checking examples on the x64 architecture, while i386 arc performs OK. /Stefan -----Oprindelig meddelelse----- Fra: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] Sendt: 18. oktober 2011 10:22 Til: Stefan McKinnon H?j-Edwards Cc: bioc-devel at r-project.org Emne: Re: [Bioc-devel] Reproducing erros on build and check liverpool and moscato1 are running r57266 and r57224 respectively. that may help you tracking down the problem. b
On 10/17/2011 11:59 PM, Stefan McKinnon H?j-Edwards wrote:
Hi, I have just noticed that my package AnnotationFuncs does pass build and check for the next release on the Windows hosts. On the Linux and Max OS X hosts there are no problems. The error logs are these: - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/liverpool-buildsrc.html - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/moscato1-checksrc.html My personal workstation is also running Windows (7), and I have checked and built the package using the latest R release (R version 2.14.0 alpha (2011-10-04 r57169)), but I am not able to reproduce the errors displayed on the log at BioConductor. I have also been looking through my code, and I cannot trace the error giving problems in the build and check above: Error in function (x) : no function to return from, jumping to top level Execution halted Error in function (x) : attempt to apply non-function Execution halted
These errors seem to be an issue with the build system / R. They show up intermitently on all platforms, but much more commonly on our windows build machines. We don't know what the precise issue is (maybe contention of multiple installation threads for some R-wide resource? a memory allocation bug in R?) but these seem to be on our side of the fence and not yours. Actually, though, we are quite stumped about the root cause so any insights from the broader community would be great... While on the topic, it can also be disconcerting to see your package fail, but tracing to some dependency -- all authors should check carefully, especially at this point in the release cycle, that their changes work. The recommended strategy for PkgA is to make a local svn export cd /tmp svn export /home/mtmorgan/mypkgs/PkgA then in the /tmp directory build R CMD build PkgA then check R CMD check PkgA_0.99.0.tar.gz The local svn export makes sure that everything you think is in svn actually is. R CMD build creates the vignette; the --no-vignette flag can be useful to speed things up for other-than-final checks. Martin
Any suggestions?
Kind regards,
Stefan McKinnon H?j-Edwards Dept. of Molecular Biology and Genetics
Ph.D. Fellow Aarhus University
Blichers All? 20, Postboks 50
DK-8830 Tjele
Tel.: +45 8715 7969 Tel.: +45 8715 6000
Email: Stefan.Hoj-Edwards at agrsci.dk Web: www.agrsci.dk
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Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
2011/10/18 Martin Morgan <mtmorgan at fhcrc.org>:
On 10/17/2011 11:59 PM, Stefan McKinnon H?j-Edwards wrote:
Hi, I have just noticed that my package AnnotationFuncs does pass build and check for the next release on the Windows hosts. On the Linux and Max OS X hosts there are no problems. The error logs are these: - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/liverpool-buildsrc.html - http://bioconductor.org/checkResults/devel/bioc-LATEST/AnnotationFuncs/moscato1-checksrc.html My personal workstation is also running Windows (7), and I have checked and built the package using the latest R release (R version 2.14.0 alpha (2011-10-04 r57169)), but I am not able to reproduce the errors displayed on the log at BioConductor. I have also been looking through my code, and I cannot trace the error giving problems in the build and check above: Error in function (x) ?: no function to return from, jumping to top level Execution halted Error in function (x) ?: attempt to apply non-function Execution halted
These errors seem to be an issue with the build system ?/ R. They show up intermitently on all platforms, but much more commonly on our windows build machines. We don't know what the precise issue is (maybe contention of multiple installation threads for some R-wide resource? a memory allocation bug in R?) but these seem to be on our side of the fence and not yours. Actually, though, we are quite stumped about the root cause so any insights from the broader community would be great...
Yesterday I installed on moscato1 an R build without byte-compilation, and in today's build report all of these errors have disappeared. Further investigation is required to figure out exactly what is going on, but I think we can reasonably say that byte-compilation has something to do with it. Dan
While on the topic, it can also be disconcerting to see your package fail, but tracing to some dependency -- all authors should check carefully, especially at this point in the release cycle, that their changes work. The recommended strategy for PkgA is to make a local svn export ?cd /tmp ?svn export /home/mtmorgan/mypkgs/PkgA then in the /tmp directory build ?R CMD build PkgA then check ?R CMD check PkgA_0.99.0.tar.gz The local svn export makes sure that everything you think is in svn actually is. R CMD build creates the vignette; the --no-vignette flag can be useful to speed things up for other-than-final checks. Martin
Any suggestions? Kind regards, Stefan McKinnon H?j-Edwards ? ? ? ? ? ? ?Dept. of Molecular Biology and Genetics Ph.D. Fellow ? ? ? ? ? ? ? ? ? ? ? ? ? ? Aarhus University ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Blichers All? 20, Postboks 50 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?DK-8830 Tjele Tel.: +45 8715 7969 ? ? ? ? ? ? ? ? ? ? ?Tel.: +45 8715 6000 Email: Stefan.Hoj-Edwards at agrsci.dk ? ? ?Web: www.agrsci.dk
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-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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