Error in AnnotationDbi 1.7.8
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Simon Anders ▴ 150
@simon-anders-2626
Last seen 7.3 years ago
Hi I've just tried to update my Bioc 2.5 installation (on Ubuntu Intrepid x86_64) to the current packages, and AnnotationDbi 1.7.8 fails to install: ---8<--- * installing *source* package ?AnnotationDbi? ... [...] Creating a new generic function for "mget" in "AnnotationDbi" Creating a new generic function for "eapply" in "AnnotationDbi" Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : arguments after '...' in the generic (all.names) must appear in the method, in the same place at the end of the argument list Error : unable to load R code in package 'AnnotationDbi' ---8<--- Note that the build cluster currently reports the same error message on gewurz and liverpool (the Windows machines), so I suppose you are aware of the problem. However, I wanted to add that I observe the same error on my Linux box too, even though wilson2 seems to see no problem. The error occurred with v1.7.8; v1.7.7 is fine. Cheers Simon > sessionInfo() R version 2.10.0 Under development (unstable) (2009-06-26 r48838) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.0 +--- | Dr. Simon Anders, Dipl.-Phys. | European Molecular Biology Laboratory (EMBL), Heidelberg | preferred (permanent) e-mail: sanders at fs.tum.de
AnnotationDbi AnnotationDbi • 1.1k views
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Tony Chiang ▴ 570
@tony-chiang-1769
Last seen 7.3 years ago
Hi Simon, I guess so as to avoid confusion, maybe this should go to the Bioc- Devel list? I think that AnnotationDbi works for the current release version of Bioc. But I am sure that Marc will appreciate the update anyhow. Cheers, --tony On Thu, Aug 6, 2009 at 7:42 AM, Simon Anders <anders@ebi.ac.uk> wrote: > Hi > > I've just tried to update my Bioc 2.5 installation (on Ubuntu Intrepid > x86_64) to the current packages, and AnnotationDbi 1.7.8 fails to install: > > ---8<--- > * installing *source* package ¬ĎAnnotationDbi¬í ... > [...] > Creating a new generic function for "mget" in "AnnotationDbi" > Creating a new generic function for "eapply" in "AnnotationDbi" > Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : > arguments after '...' in the generic (all.names) must appear in the > method, in the same place at the end of the argument list > Error : unable to load R code in package 'AnnotationDbi' > ---8<--- > > Note that the build cluster currently reports the same error message on > gewurz and liverpool (the Windows machines), so I suppose you are aware of > the problem. However, I wanted to add that I observe the same error on my > Linux box too, even though wilson2 seems to see no problem. > > The error occurred with v1.7.8; v1.7.7 is fine. > > Cheers > Simon > > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-06-26 r48838) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > > > +--- > | Dr. Simon Anders, Dipl.-Phys. > | European Molecular Biology Laboratory (EMBL), Heidelberg > | preferred (permanent) e-mail: sanders@fs.tum.de > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Simon, The issue you are experiencing is to do a change in base R in the R-devel code line. The signature of base::eapply changed and so AnnotationDbi in BioC 2.5 changed accordingly. If you update your R-devel installation, this issue will be resolved. Patrick Tony Chiang wrote: > Hi Simon, > > I guess so as to avoid confusion, maybe this should go to the Bioc- Devel > list? I think that AnnotationDbi works for the current release version of > Bioc. But I am sure that Marc will appreciate the update anyhow. > > Cheers, > --tony > > On Thu, Aug 6, 2009 at 7:42 AM, Simon Anders <anders at="" ebi.ac.uk=""> wrote: > > >> Hi >> >> I've just tried to update my Bioc 2.5 installation (on Ubuntu Intrepid >> x86_64) to the current packages, and AnnotationDbi 1.7.8 fails to install: >> >> ---8<--- >> * installing *source* package ?AnnotationDbi? ... >> [...] >> Creating a new generic function for "mget" in "AnnotationDbi" >> Creating a new generic function for "eapply" in "AnnotationDbi" >> Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : >> arguments after '...' in the generic (all.names) must appear in the >> method, in the same place at the end of the argument list >> Error : unable to load R code in package 'AnnotationDbi' >> ---8<--- >> >> Note that the build cluster currently reports the same error message on >> gewurz and liverpool (the Windows machines), so I suppose you are aware of >> the problem. However, I wanted to add that I observe the same error on my >> Linux box too, even though wilson2 seems to see no problem. >> >> The error occurred with v1.7.8; v1.7.7 is fine. >> >> Cheers >> Simon >> >> >>> sessionInfo() >>> >> R version 2.10.0 Under development (unstable) (2009-06-26 r48838) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tools_2.10.0 >> >> >> >> +--- >> | Dr. Simon Anders, Dipl.-Phys. >> | European Molecular Biology Laboratory (EMBL), Heidelberg >> | preferred (permanent) e-mail: sanders at fs.tum.de >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > [[alternative HTML version deleted]] > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Yes thanks for the heads up, but Patrick's answers is correct. There was a change in R, and so to clear things up you will have to update that. Just to be clear, this stuff should only affect people using the development branch of R. Marc Patrick Aboyoun wrote: > Simon, > The issue you are experiencing is to do a change in base R in the > R-devel code line. The signature of base::eapply changed and so > AnnotationDbi in BioC 2.5 changed accordingly. If you update your > R-devel installation, this issue will be resolved. > > > Patrick > > > Tony Chiang wrote: >> Hi Simon, >> >> I guess so as to avoid confusion, maybe this should go to the Bioc- Devel >> list? I think that AnnotationDbi works for the current release >> version of >> Bioc. But I am sure that Marc will appreciate the update anyhow. >> >> Cheers, >> --tony >> >> On Thu, Aug 6, 2009 at 7:42 AM, Simon Anders <anders at="" ebi.ac.uk=""> wrote: >> >> >>> Hi >>> >>> I've just tried to update my Bioc 2.5 installation (on Ubuntu Intrepid >>> x86_64) to the current packages, and AnnotationDbi 1.7.8 fails to >>> install: >>> >>> ---8<--- >>> * installing *source* package ?AnnotationDbi? ... >>> [...] >>> Creating a new generic function for "mget" in "AnnotationDbi" >>> Creating a new generic function for "eapply" in "AnnotationDbi" >>> Error in rematchDefinition(definition, fdef, mnames, fnames, >>> signature) : >>> arguments after '...' in the generic (all.names) must appear in the >>> method, in the same place at the end of the argument list >>> Error : unable to load R code in package 'AnnotationDbi' >>> ---8<--- >>> >>> Note that the build cluster currently reports the same error message on >>> gewurz and liverpool (the Windows machines), so I suppose you are >>> aware of >>> the problem. However, I wanted to add that I observe the same error >>> on my >>> Linux box too, even though wilson2 seems to see no problem. >>> >>> The error occurred with v1.7.8; v1.7.7 is fine. >>> >>> Cheers >>> Simon >>> >>> >>>> sessionInfo() >>>> >>> R version 2.10.0 Under development (unstable) (2009-06-26 r48838) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.10.0 >>> >>> >>> >>> +--- >>> | Dr. Simon Anders, Dipl.-Phys. >>> | European Molecular Biology Laboratory (EMBL), Heidelberg >>> | preferred (permanent) e-mail: sanders at fs.tum.de >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> [[alternative HTML version deleted]] >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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