FW: GenomicFeatures::makeTranscriptDbFromBiomart - Error in callSuper(...) : could not find function "initRefFields"
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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 6 days ago
United States
Hi Herve and Marc and Bioc fellow-travellers, I am unhappy to report that.... It now happens that: > txdb<-loadFeatures('dmelanogaster_gene_ensembl.sqlite') Error in callSuper(...) : could not find function "initRefFields" ... just after I updated installed Bioc packages today, using source("http://bioconductor.org/biocLite.R") old.packages(repos=biocinstallRepos()) At first glance it seems to be the same as reported earlier here: http://permalink.gmane.org/gmane.science.biology.informatics. conductor/38404 However, trying the same workaround, namely, re-updating from source > biocLite(c('GenomicFeatures'), type='source') and starting a new session, fails to fix... the error still occurs. As a potential workaround, I tried re-building the txdb from ensembl, but this is now failing (possibly due to new schema/data at Ensembl?), yielding the following error: txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Download and preprocess the 'splicings' data frame ... Error in .extractCdsRangesFromBiomartTable(bm_table) : BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart So, I looked for the hoped-for further workaround, of being able to specify an (archive) 'host' to makeTranscriptDbFromBiomart, (as discussed: https://stat.ethz.ch/pipermail/bioconductor/attachments/201 11108/a5ece78c/attachment.pl)_ which I would expect to call as txdb<-makeTranscriptDbFromBiomart(host=' jun2011.archive.ensembl.org/biomart/martservice',biomart="ensembl", dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) but I found that the `host` option is not (yet?) supported (in released). So, most urgently to me, is to find a workaround to my primary problem, namely, of getting past the missing 'initRefFields' when calling `loadFeatures` . Is there a fix/patch/workaround that can address this? Thanks, Malcolm Cook > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0 [4] GenomicRanges_1.6.6 IRanges_1.12.5 loaded via a namespace (and not attached): [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5 [5] RSQLite_0.11.1 XML_3.9-2 biomaRt_2.10.0 rtracklayer_1.14.4 [9] tools_2.14.0 zlibbioc_1.0.0 >
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.7 years ago
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Hi Malcolm, I cannot say why your older annotation database is not working, but I suspect that it is just out of phase with recent changes introduced when you updated the code. But the error you reported from when you tried to generate a new TxDb package is an unhappy message indeed. It means that the data for cds ranges and total cds length (both from biomaRt) no longer agree with each other. In other words, the data from the current drosophila ranges in biomaRt seems to disagree with itself, and so the code is refusing to make a package out of this data as a result. So to try and get the 1st issue fixed I need more information. I suspect that what has happened to your old DB is that is is missing some metadata that is required by the newer versions of GenomicFeatures. Is there a place where you could put your DB so that I could DL it and have a look at it? To get the 2nd issue fixed probably involves talking to ensembl about their CDS data for fly to see if we can resolve the discrepancy. Marc On 02/02/2012 01:58 PM, Cook, Malcolm wrote: > Hi Herve and Marc and Bioc fellow-travellers, > > I am unhappy to report that.... > > It now happens that: > > > txdb<-loadFeatures('dmelanogaster_gene_ensembl.sqlite') > Error in callSuper(...) : could not find function "initRefFields" > > ... just after I updated installed Bioc packages today, using > > source("http://bioconductor.org/biocLite.R") > old.packages(repos=biocinstallRepos()) > > At first glance it seems to be the same as reported earlier here: > > http://permalink.gmane.org/gmane.science.biology.informatics.c onductor/38404 > > However, trying the same workaround, namely, re-updating from source > > > biocLite(c('GenomicFeatures'), type='source') > > and starting a new session, fails to fix... the error still occurs. > > As a potential workaround, I tried re-building the txdb from ensembl, but this is now failing (possibly due to new schema/data at Ensembl?), yielding the following error: > > txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) > Download and preprocess the 'transcripts' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... OK > Download and preprocess the 'splicings' data frame ... Error in .extractCdsRangesFromBiomartTable(bm_table) : > BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart > > So, I looked for the hoped-for further workaround, of being able to specify an (archive) 'host' to makeTranscriptDbFromBiomart, (as discus sed:https://stat.ethz.ch/pipermail/bioconductor/attachments/20111108/a 5ece78c/attachment.pl)_ which I would expect to call as > > txdb<-makeTranscriptDbFromBiomart(host=' jun2011.archive.ensembl.org/biomart/martservice',biomart="ensembl", dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) > > but I found that the `host` option is not (yet?) supported (in released). > > So, most urgently to me, is to find a workaround to my primary problem, namely, of getting past the missing 'initRefFields' when calling `loadFeatures` . > > Is there a fix/patch/workaround that can address this? > > Thanks, > > Malcolm Cook > > > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0 > [4] GenomicRanges_1.6.6 IRanges_1.12.5 > > loaded via a namespace (and not attached): > [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5 > [5] RSQLite_0.11.1 XML_3.9-2 biomaRt_2.10.0 rtracklayer_1.14.4 > [9] tools_2.14.0 zlibbioc_1.0.0 > _______________________________________________ > 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.info rmatics.conductor
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Marc, > I cannot say why your older annotation database is not working, but I > suspect that it is just out of phase with recent changes introduced when > you updated the code. But the error you reported from when you tried to > generate a new TxDb package is an unhappy message indeed. It means that > the data for cds ranges and total cds length (both from biomaRt) no > longer agree with each other. In other words, the data from the current > drosophila ranges in biomaRt seems to disagree with itself, and so the > code is refusing to make a package out of this data as a result. > > > To get the 2nd issue fixed probably involves talking to ensembl about > their CDS data for fly to see if we can resolve the discrepancy. > > > Marc > > > > On 02/02/2012 01:58 PM, Cook, Malcolm wrote: > > Hi Herve and Marc and Bioc fellow-travellers, > > > > I am unhappy to report that.... > > > > It now happens that: > > > > > txdb<-loadFeatures('dmelanogaster_gene_ensembl.sqlite') > > Error in callSuper(...) : could not find function "initRefFields" > > > > ... just after I updated installed Bioc packages today, using > > > > source("http://bioconductor.org/biocLite.R") > > old.packages(repos=biocinstallRepos()) > > > > At first glance it seems to be the same as reported earlier here: > > > > > http://permalink.gmane.org/gmane.science.biology.informatics.con > ductor/38404 > > > > However, trying the same workaround, namely, re-updating from source > > > > > biocLite(c('GenomicFeatures'), type='source') > > > > and starting a new session, fails to fix... the error still occurs. > > > > As a potential workaround, I tried re-building the txdb from ensembl, but > this is now failing (possibly due to new schema/data at Ensembl?), yielding > the following error: > > > > txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", > dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) > > Download and preprocess the 'transcripts' data frame ... OK > > Download and preprocess the 'chrominfo' data frame ... OK > > Download and preprocess the 'splicings' data frame ... Error in > .extractCdsRangesFromBiomartTable(bm_table) : > > BioMart data anomaly: for some transcripts, the cds cumulative > length inferred from the exon and UTR info doesn't match the "cds_length" > attribute from BioMart > > > > So, I looked for the hoped-for further workaround, of being able to specify > an (archive) 'host' to makeTranscriptDbFromBiomart, (as > discussed:https://stat.ethz.ch/pipermail/bioconductor/attachments/20 1111 > 08/a5ece78c/attachment.pl)_ which I would expect to call as > > > > txdb<-makeTranscriptDbFromBiomart(host=' > jun2011.archive.ensembl.org/biomart/martservice',biomart="ensembl", > dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) > > > > but I found that the `host` option is not (yet?) supported (in released). > > > > So, most urgently to me, is to find a workaround to my primary problem, > namely, of getting past the missing 'initRefFields' when calling `loadFeatures` > . > > > > Is there a fix/patch/workaround that can address this? > > > > Thanks, > > > > Malcolm Cook > > > > > > > >> sessionInfo() > > R version 2.14.0 (2011-10-31) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0 > > [4] GenomicRanges_1.6.6 IRanges_1.12.5 > > > > loaded via a namespace (and not attached): > > [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5 > > [5] RSQLite_0.11.1 XML_3.9-2 biomaRt_2.10.0 rtracklayer_1.14.4 > > [9] tools_2.14.0 zlibbioc_1.0.0 > > _______________________________________________ > > 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.con duct > or > > _______________________________________________ > 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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Hi Marc, > I cannot say why your older annotation database is not working, but I > suspect that it is just out of phase with recent changes introduced when > you updated the code. But the error you reported from when you tried to > generate a new TxDb package is an unhappy message indeed. It means that > the data for cds ranges and total cds length (both from biomaRt) no > longer agree with each other. In other words, the data from the current > drosophila ranges in biomaRt seems to disagree with itself, and so the > code is refusing to make a package out of this data as a result. > > So to try and get the 1st issue fixed I need more information. I > suspect that what has happened to your old DB is that is is missing some > metadata that is required by the newer versions of GenomicFeatures. Is > there a place where you could put your DB so that I could DL it and have > a look at it? Sure - great - thanks - here it is: ftp://ftp.stowers- institute.org/pub/MEC/dmelanogaster_gene_ensembl.sqlite > To get the 2nd issue fixed probably involves talking to ensembl about > their CDS data for fly to see if we can resolve the discrepancy. I would be happy to take this to them. Can you recommend a best way to get a more diagnostic trace from the attempt at txdb creation so we can correctly report to ensembl team the errant transcript(s) ? Finally, do you have any information on the progress of adding a 'host' option to makeTranscriptDbFromBiomart ? If I install Bioc-dev should I expect to find this implemented? And if I do, will a txdb so-created be backward compatible with current released GenomicFeatures (i.e. should I be able to load it)? Thanks so much for you help, Cheers, Malcolm > > txdb<-makeTranscriptDbFromBiomart(host=' > jun2011.archive.ensembl.org/biomart/martservice',biomart="ensembl", > dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) > > > > but I found that the `host` option is not (yet?) supported (in released). > > > > So, most urgently to me, is to find a workaround to my primary problem, > namely, of getting past the missing 'initRefFields' when calling `loadFeatures` > . > > > > Is there a fix/patch/workaround that can address this? > > > > Thanks, > > > > Malcolm Cook > > > > > > > >> sessionInfo() > > R version 2.14.0 (2011-10-31) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0 > > [4] GenomicRanges_1.6.6 IRanges_1.12.5 > > > > loaded via a namespace (and not attached): > > [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5 > > [5] RSQLite_0.11.1 XML_3.9-2 biomaRt_2.10.0 rtracklayer_1.14.4 > > [9] tools_2.14.0 zlibbioc_1.0.0 > > _______________________________________________ > > 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.con duct > or > > _______________________________________________ > 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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Hi Malcolm, A host argument has indeed been added to the devel branch. But more pertinent to your current issue is the fact that I am able to easily load your database using loadFeatures() or loadDB(). So I don't see anything wrong with the DB on this end. We tested it in both Linux and Mac and are unable to recreate the problem. This makes me think that there is something wrong with your current setup. Your version of R could be a little more current, I don't really anticipate that this would cause a problem like this, but it might be worth updating to 2.14.1 anyhow. And the only package I have that is more current than yours is XML, which should not matter here. Are you sure that you have read permissions for your copy of this DB? Marc On 02/03/2012 07:43 AM, Cook, Malcolm wrote: > Hi Marc, > >> I cannot say why your older annotation database is not working, but I >> suspect that it is just out of phase with recent changes introduced when >> you updated the code. But the error you reported from when you tried to >> generate a new TxDb package is an unhappy message indeed. It means that >> the data for cds ranges and total cds length (both from biomaRt) no >> longer agree with each other. In other words, the data from the current >> drosophila ranges in biomaRt seems to disagree with itself, and so the >> code is refusing to make a package out of this data as a result. >> >> So to try and get the 1st issue fixed I need more information. I >> suspect that what has happened to your old DB is that is is missing some >> metadata that is required by the newer versions of GenomicFeatures. Is >> there a place where you could put your DB so that I could DL it and have >> a look at it? > Sure - great - thanks - here it is: > > ftp://ftp.stowers- institute.org/pub/MEC/dmelanogaster_gene_ensembl.sqlite > >> To get the 2nd issue fixed probably involves talking to ensembl about >> their CDS data for fly to see if we can resolve the discrepancy. > I would be happy to take this to them. > > Can you recommend a best way to get a more diagnostic trace from the attempt at txdb creation so we can correctly report to ensembl team the errant transcript(s) ? > > Finally, do you have any information on the progress of adding a 'host' option to makeTranscriptDbFromBiomart ? > If I install Bioc-dev should I expect to find this implemented? > And if I do, will a txdb so-created be backward compatible with current released GenomicFeatures (i.e. should I be able to load it)? > > Thanks so much for you help, > > Cheers, > > Malcolm > > > >>> txdb<-makeTranscriptDbFromBiomart(host=' >> jun2011.archive.ensembl.org/biomart/martservice',biomart="ensembl", >> dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) >>> but I found that the `host` option is not (yet?) supported (in released). >>> >>> So, most urgently to me, is to find a workaround to my primary problem, >> namely, of getting past the missing 'initRefFields' when calling `loadFeatures` >> . >>> Is there a fix/patch/workaround that can address this? >>> >>> Thanks, >>> >>> Malcolm Cook >>> >>> >>> >>>> sessionInfo() >>> R version 2.14.0 (2011-10-31) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0 >>> [4] GenomicRanges_1.6.6 IRanges_1.12.5 >>> >>> loaded via a namespace (and not attached): >>> [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5 >>> [5] RSQLite_0.11.1 XML_3.9-2 biomaRt_2.10.0 rtracklayer_1.14.4 >>> [9] tools_2.14.0 zlibbioc_1.0.0 >>> _______________________________________________ >>> 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.co nduct >> or >> >> _______________________________________________ >> 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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Hi Marc, > A host argument has indeed been added to the devel branch. Great > But more > pertinent to your current issue is the fact that I am able to easily > load your database using loadFeatures() or loadDB(). So I don't see > anything wrong with the DB on this end. We tested it in both Linux and > Mac and are unable to recreate the problem. Hmmm... > This makes me think that there is something wrong with your current > setup. Your version of R could be a little more current, I don't really > anticipate that this would cause a problem like this, but it might be > worth updating to 2.14.1 anyhow. And the only package I have that is > more current than yours is XML, which should not matter here. Are you > sure that you have read permissions for your copy of this DB? Yes. I am sure. FWIW: google finds a few others similarly afflicted , but only in very the recent past: 5 days ago - http://lists.hexdump.org/pipermail/twitter-users- hexdump.org/2012-January/000027.html 5 days ago - same problem in ggplot- https://groups.google.com/forum/?fromgroups#!topic/ggplot2/FciMhMfDZp4 But wait. SUCCESS: I just tried rebuilding from source, and, after the following I was able to load the database biocLite(c('RCurl','rtracklayer','GenomicFeatures','Annotation Dbi','Biobase','GenomicRanges','IRanges'), type='source') HOORAY! I guess we're not going to find the root cause this time. Like last time: http://permalink.gmane.org/gmane.science.biology.infor matics.conductor/38404 That's OK. If you have any suggestions for me to try something, fire away. Other than that.... Thanks for your help sleuthing with me. !!! Cheers, Malcolm > > > Marc > > > On 02/03/2012 07:43 AM, Cook, Malcolm wrote: > > Hi Marc, > > > >> I cannot say why your older annotation database is not working, but I > >> suspect that it is just out of phase with recent changes introduced when > >> you updated the code. But the error you reported from when you tried > to > >> generate a new TxDb package is an unhappy message indeed. It means > that > >> the data for cds ranges and total cds length (both from biomaRt) no > >> longer agree with each other. In other words, the data from the current > >> drosophila ranges in biomaRt seems to disagree with itself, and so the > >> code is refusing to make a package out of this data as a result. > >> > >> So to try and get the 1st issue fixed I need more information. I > >> suspect that what has happened to your old DB is that is is missing some > >> metadata that is required by the newer versions of GenomicFeatures. Is > >> there a place where you could put your DB so that I could DL it and have > >> a look at it? > > Sure - great - thanks - here it is: > > > > ftp://ftp.stowers- > institute.org/pub/MEC/dmelanogaster_gene_ensembl.sqlite > > > >> To get the 2nd issue fixed probably involves talking to ensembl about > >> their CDS data for fly to see if we can resolve the discrepancy. > > I would be happy to take this to them. > > > > Can you recommend a best way to get a more diagnostic trace from the > attempt at txdb creation so we can correctly report to ensembl team the > errant transcript(s) ? > > > > Finally, do you have any information on the progress of adding a 'host' > option to makeTranscriptDbFromBiomart ? > > If I install Bioc-dev should I expect to find this implemented? > > And if I do, will a txdb so-created be backward compatible with current > released GenomicFeatures (i.e. should I be able to load it)? > > > > Thanks so much for you help, > > > > Cheers, > > > > Malcolm > > > > > > > >>> txdb<-makeTranscriptDbFromBiomart(host=' > >> jun2011.archive.ensembl.org/biomart/martservice',biomart="ensembl", > >> dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL) > >>> but I found that the `host` option is not (yet?) supported (in released). > >>> > >>> So, most urgently to me, is to find a workaround to my primary problem, > >> namely, of getting past the missing 'initRefFields' when calling > `loadFeatures` > >> . > >>> Is there a fix/patch/workaround that can address this? > >>> > >>> Thanks, > >>> > >>> Malcolm Cook > >>> > >>> > >>> > >>>> sessionInfo() > >>> R version 2.14.0 (2011-10-31) > >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > >>> > >>> locale: > >>> [1] C > >>> > >>> attached base packages: > >>> [1] stats graphics grDevices utils datasets methods base > >>> > >>> other attached packages: > >>> [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0 > >>> [4] GenomicRanges_1.6.6 IRanges_1.12.5 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5 > >>> [5] RSQLite_0.11.1 XML_3.9-2 biomaRt_2.10.0 > rtracklayer_1.14.4 > >>> [9] tools_2.14.0 zlibbioc_1.0.0 > >>> _______________________________________________ > >>> 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.con duct > >> or > >> > >> _______________________________________________ > >> 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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