rtracklayer export fails
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@michael-dondrup-3849
Last seen 10.2 years ago
Hi, I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS but already the example fails, see below: Best Michael > example(export) export> track <- import(system.file("tests", "v1.gff", package = "rtracklayer")) export> ## Not run: export(track, "my.gff", version = "3") export> ## equivalently, export> ## Not run: export(track, "my.gff3") export> ## or export> ## Not run: export> ##D con <- file("my.gff3") export> ##D export(track, con, "gff3") export> ##D close(con) export> ##D export> ## End(Not run) export> ## or as a string export> export(track, format = "gff3") Error: evaluation nested too deeply: infinite recursion / options(expressions=)? > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 IRanges_1.8.9 loaded via a namespace (and not attached): [1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0 Biostrings_2.18.2 [5] BSgenome_1.18.0 DBI_0.2-5 DESeq_1.2.1 genefilter_1.32.0 [9] geneplotter_1.28.0 GenomicRanges_1.2.0 grid_2.12.1 RColorBrewer_1.0-2 [13] RSQLite_0.9-2 splines_2.12.1 survival_2.36-2 tools_2.12.1 [17] XML_3.2-0 xtable_1.5-6 >
rtracklayer rtracklayer • 1.4k views
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@vincent-j-carey-jr-4
Last seen 10 weeks ago
United States
I'd like to recommend that you attempt this export with the smallest sessionInfo you can muster -- after just library(rtracklayer) if possible. i have run into this recursion error in connection with symbol collisions related to update() methods and it "goes away" if i get rid of certain packages. a full diagnosis awaits.... On Sat, Feb 19, 2011 at 3:21 PM, Michael Dondrup <michael.dondrup@uni.no>wrote: > Hi, > I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS > but already the example fails, see below: > > Best > Michael > > > example(export) > > export> track <- import(system.file("tests", "v1.gff", package = > "rtracklayer")) > > export> ## Not run: export(track, "my.gff", version = "3") > export> ## equivalently, > export> ## Not run: export(track, "my.gff3") > export> ## or > export> ## Not run: > export> ##D con <- file("my.gff3") > export> ##D export(track, con, "gff3") > export> ##D close(con) > export> ##D > export> ## End(Not run) > export> ## or as a string > export> export(track, format = "gff3") > Error: evaluation nested too deeply: infinite recursion / > options(expressions=)? > > sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 IRanges_1.8.9 > > loaded via a namespace (and not attached): > [1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0 > Biostrings_2.18.2 > [5] BSgenome_1.18.0 DBI_0.2-5 DESeq_1.2.1 > genefilter_1.32.0 > [9] geneplotter_1.28.0 GenomicRanges_1.2.0 grid_2.12.1 > RColorBrewer_1.0-2 > [13] RSQLite_0.9-2 splines_2.12.1 survival_2.36-2 > tools_2.12.1 > [17] XML_3.2-0 xtable_1.5-6 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > 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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I've managed to correct this for certain combinations of packages, don't really remember how. But haven't found a solution to the underlying problem. On Sat, Feb 19, 2011 at 1:49 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > I'd like to recommend that you attempt this export with the smallest > sessionInfo you can muster -- after just library(rtracklayer) if possible. > i have run into this recursion error in connection with symbol collisions > related to update() methods and it "goes away" if i get rid of certain > packages. a full diagnosis awaits.... > > On Sat, Feb 19, 2011 at 3:21 PM, Michael Dondrup <michael.dondrup@uni.no> >wrote: > > > Hi, > > I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS > > but already the example fails, see below: > > > > Best > > Michael > > > > > example(export) > > > > export> track <- import(system.file("tests", "v1.gff", package = > > "rtracklayer")) > > > > export> ## Not run: export(track, "my.gff", version = "3") > > export> ## equivalently, > > export> ## Not run: export(track, "my.gff3") > > export> ## or > > export> ## Not run: > > export> ##D con <- file("my.gff3") > > export> ##D export(track, con, "gff3") > > export> ##D close(con) > > export> ##D > > export> ## End(Not run) > > export> ## or as a string > > export> export(track, format = "gff3") > > Error: evaluation nested too deeply: infinite recursion / > > options(expressions=)? > > > sessionInfo() > > R version 2.12.1 (2010-12-16) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 > IRanges_1.8.9 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0 > > Biostrings_2.18.2 > > [5] BSgenome_1.18.0 DBI_0.2-5 DESeq_1.2.1 > > genefilter_1.32.0 > > [9] geneplotter_1.28.0 GenomicRanges_1.2.0 grid_2.12.1 > > RColorBrewer_1.0-2 > > [13] RSQLite_0.9-2 splines_2.12.1 survival_2.36-2 > > tools_2.12.1 > > [17] XML_3.2-0 xtable_1.5-6 > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > 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@r-project.org > 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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Yes, it's totally strange it seemed to be something in my session. If I start R --vanilla the simple example works, however I am still struggling with exporting real-size data because it yields the same error message. I will post an example later. Thanks for your help On Feb 19, 2011, at 11:02 PM, Michael Lawrence wrote: > I've managed to correct this for certain combinations of packages, don't really remember how. But haven't found a solution to the underlying problem. > > On Sat, Feb 19, 2011 at 1:49 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > I'd like to recommend that you attempt this export with the smallest > sessionInfo you can muster -- after just library(rtracklayer) if possible. > i have run into this recursion error in connection with symbol collisions > related to update() methods and it "goes away" if i get rid of certain > packages. a full diagnosis awaits.... > > On Sat, Feb 19, 2011 at 3:21 PM, Michael Dondrup <michael.dondrup at="" uni.no="">wrote: > > > Hi, > > I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS > > but already the example fails, see below: > > > > Best > > Michael > > > > > example(export) > > > > export> track <- import(system.file("tests", "v1.gff", package = > > "rtracklayer")) > > > > export> ## Not run: export(track, "my.gff", version = "3") > > export> ## equivalently, > > export> ## Not run: export(track, "my.gff3") > > export> ## or > > export> ## Not run: > > export> ##D con <- file("my.gff3") > > export> ##D export(track, con, "gff3") > > export> ##D close(con) > > export> ##D > > export> ## End(Not run) > > export> ## or as a string > > export> export(track, format = "gff3") > > Error: evaluation nested too deeply: infinite recursion / > > options(expressions=)? > > > sessionInfo() > > R version 2.12.1 (2010-12-16) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 IRanges_1.8.9 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0 > > Biostrings_2.18.2 > > [5] BSgenome_1.18.0 DBI_0.2-5 DESeq_1.2.1 > > genefilter_1.32.0 > > [9] geneplotter_1.28.0 GenomicRanges_1.2.0 grid_2.12.1 > > RColorBrewer_1.0-2 > > [13] RSQLite_0.9-2 splines_2.12.1 survival_2.36-2 > > tools_2.12.1 > > [17] XML_3.2-0 xtable_1.5-6 > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > 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 r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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So here is the example where export fails: $ R --vanilla > library(rtracklayer) Loading required package: RCurl Loading required package: bitops > library(IRanges) Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table > example(RangedData) .... > rd2 RangedData with 3 rows and 1 value column across 1 space space ranges | score <character> <iranges> | <integer> 1 1 [1, 4] | 10 2 1 [2, 5] | 2 3 1 [3, 6] | NA > export.gff2(rd2, con=stdout()) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? My best guess is that the RangedData object is missing something, but then the error message and the documentation is wrong, because the documentation says it can handle any RangedData object. Best Michael On Feb 20, 2011, at 5:47 PM, Michael Dondrup wrote: > Yes, it's totally strange > it seemed to be something in my session. If I start R --vanilla the simple example works, > however I am still struggling with exporting real-size data because it yields the same error message. > > I will post an example later. > > Thanks for your help > > On Feb 19, 2011, at 11:02 PM, Michael Lawrence wrote: > >> I've managed to correct this for certain combinations of packages, don't really remember how. But haven't found a solution to the underlying problem. >> >> On Sat, Feb 19, 2011 at 1:49 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: >> I'd like to recommend that you attempt this export with the smallest >> sessionInfo you can muster -- after just library(rtracklayer) if possible. >> i have run into this recursion error in connection with symbol collisions >> related to update() methods and it "goes away" if i get rid of certain >> packages. a full diagnosis awaits.... >> >> On Sat, Feb 19, 2011 at 3:21 PM, Michael Dondrup <michael.dondrup at="" uni.no="">wrote: >> >>> Hi, >>> I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS >>> but already the example fails, see below: >>> >>> Best >>> Michael >>> >>>> example(export) >>> >>> export> track <- import(system.file("tests", "v1.gff", package = >>> "rtracklayer")) >>> >>> export> ## Not run: export(track, "my.gff", version = "3") >>> export> ## equivalently, >>> export> ## Not run: export(track, "my.gff3") >>> export> ## or >>> export> ## Not run: >>> export> ##D con <- file("my.gff3") >>> export> ##D export(track, con, "gff3") >>> export> ##D close(con) >>> export> ##D >>> export> ## End(Not run) >>> export> ## or as a string >>> export> export(track, format = "gff3") >>> Error: evaluation nested too deeply: infinite recursion / >>> options(expressions=)? >>>> sessionInfo() >>> R version 2.12.1 (2010-12-16) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 IRanges_1.8.9 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0 >>> Biostrings_2.18.2 >>> [5] BSgenome_1.18.0 DBI_0.2-5 DESeq_1.2.1 >>> genefilter_1.32.0 >>> [9] geneplotter_1.28.0 GenomicRanges_1.2.0 grid_2.12.1 >>> RColorBrewer_1.0-2 >>> [13] RSQLite_0.9-2 splines_2.12.1 survival_2.36-2 >>> tools_2.12.1 >>> [17] XML_3.2-0 xtable_1.5-6 >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> 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 r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On Sun, Feb 20, 2011 at 8:58 AM, Michael Dondrup <michael.dondrup@uni.no>wrote: > So here is the example where export fails: > > $ R --vanilla > > > library(rtracklayer) > Loading required package: RCurl > Loading required package: bitops > > library(IRanges) > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin, > pmin.int, rbind, rep.int, table > > > example(RangedData) > .... > > rd2 > RangedData with 3 rows and 1 value column across 1 space > space ranges | score > <character> <iranges> | <integer> > 1 1 [1, 4] | 10 > 2 1 [2, 5] | 2 > 3 1 [3, 6] | NA > > export.gff2(rd2, con=stdout()) > Error: evaluation nested too deeply: infinite recursion / > options(expressions=)? > > My best guess is that the RangedData object is missing something, but then > the error message and the documentation is wrong, > because the documentation says it can handle any RangedData object. > > No, as Vince said, this infinite recursion usually results from weird dispatching on the update generic. Thanks for the report and simple example. I'll look into it some more. Michael > Best > Michael > > > > > > > > > On Feb 20, 2011, at 5:47 PM, Michael Dondrup wrote: > > > Yes, it's totally strange > > it seemed to be something in my session. If I start R --vanilla the > simple example works, > > however I am still struggling with exporting real-size data because it > yields the same error message. > > > > I will post an example later. > > > > Thanks for your help > > > > On Feb 19, 2011, at 11:02 PM, Michael Lawrence wrote: > > > >> I've managed to correct this for certain combinations of packages, don't > really remember how. But haven't found a solution to the underlying problem. > >> > >> On Sat, Feb 19, 2011 at 1:49 PM, Vincent Carey < > stvjc@channing.harvard.edu> wrote: > >> I'd like to recommend that you attempt this export with the smallest > >> sessionInfo you can muster -- after just library(rtracklayer) if > possible. > >> i have run into this recursion error in connection with symbol > collisions > >> related to update() methods and it "goes away" if i get rid of certain > >> packages. a full diagnosis awaits.... > >> > >> On Sat, Feb 19, 2011 at 3:21 PM, Michael Dondrup < > michael.dondrup@uni.no>wrote: > >> > >>> Hi, > >>> I am trying to use export in the rtracklayer package on R 2.12.1 on > MacOS > >>> but already the example fails, see below: > >>> > >>> Best > >>> Michael > >>> > >>>> example(export) > >>> > >>> export> track <- import(system.file("tests", "v1.gff", package = > >>> "rtracklayer")) > >>> > >>> export> ## Not run: export(track, "my.gff", version = "3") > >>> export> ## equivalently, > >>> export> ## Not run: export(track, "my.gff3") > >>> export> ## or > >>> export> ## Not run: > >>> export> ##D con <- file("my.gff3") > >>> export> ##D export(track, con, "gff3") > >>> export> ##D close(con) > >>> export> ##D > >>> export> ## End(Not run) > >>> export> ## or as a string > >>> export> export(track, format = "gff3") > >>> Error: evaluation nested too deeply: infinite recursion / > >>> options(expressions=)? > >>>> sessionInfo() > >>> R version 2.12.1 (2010-12-16) > >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > >>> > >>> locale: > >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > >>> > >>> attached base packages: > >>> [1] stats graphics grDevices utils datasets methods base > >>> > >>> other attached packages: > >>> [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 > IRanges_1.8.9 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] annotate_1.28.0 AnnotationDbi_1.12.0 Biobase_2.10.0 > >>> Biostrings_2.18.2 > >>> [5] BSgenome_1.18.0 DBI_0.2-5 DESeq_1.2.1 > >>> genefilter_1.32.0 > >>> [9] geneplotter_1.28.0 GenomicRanges_1.2.0 grid_2.12.1 > >>> RColorBrewer_1.0-2 > >>> [13] RSQLite_0.9-2 splines_2.12.1 survival_2.36-2 > >>> tools_2.12.1 > >>> [17] XML_3.2-0 xtable_1.5-6 > >>>> > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> 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@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > 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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