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Question: 'version' is missing error when running makeTxDbPackageFromUCSC
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gravatar for Michael Steeves
4.3 years ago by
Michael Steeves40 wrote:
On OS X (10.8.4) with R 3.0.1, I'm getting an error when running the following three lines of code: library(GenomicRanges) library(GenomicFeatures) txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename = 'refGene') Download the refGene table ... OK Download the refLink table ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TranscriptDb object ... OK Error in list(PKGTITLE = paste("Annotation package for", dbType, "object(s)"), : 'version' is missing In addition: There were 50 or more warnings (use warnings() to see the first 50) If I run this on RHEL5, the same code fails in the same place, though with a slightly different error message: > txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename = 'refGene') Download the refGene table ... OK Download the refLink table ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TranscriptDb object ... Error in .Call2("svn_time", PACKAGE = "IRanges") : IRanges internal error in svn_time(): get_svn_time() failed In addition: There were 50 or more warnings (use warnings() to see the first 50) For OS X: > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin12.4.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6 Biobase_2.20.1 [4] GenomicRanges_1.12.5 IRanges_1.18.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-5 BSgenome_1.28.0 [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.12.3 RSQLite_0.11.4 [9] rtracklayer_1.20.3 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 [13] zlibbioc_1.6.0 For RHEL: > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.12.2 AnnotationDbi_1.22.5 Biobase_2.20.0 [4] GenomicRanges_1.12.4 IRanges_1.18.3 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] BSgenome_1.28.0 Biostrings_2.28.0 DBI_0.2-7 RCurl_1.95-4.1 [5] RSQLite_0.11.4 Rsamtools_1.12.3 XML_3.96-1.1 biomaRt_2.16.0 [9] bitops_1.0-5 rtracklayer_1.20.2 stats4_3.0.1 tools_3.0.1 [13] zlibbioc_1.6.0 The warnings referenced don't look related, I don't think: 43: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]], ... : UCSC data anomaly in transcript NM_010707: the cds cumulative length is not a multiple of 3 -Mike -- Michael Steeves (steeves at raingods.net)
ADD COMMENTlink modified 4.3 years ago by Dan Tenenbaum ♦♦ 8.2k • written 4.3 years ago by Michael Steeves40
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gravatar for Dan Tenenbaum
4.3 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
On Tue, Aug 27, 2013 at 3:18 PM, Michael Steeves <steeves at="" raingods.net=""> wrote: > On OS X (10.8.4) with R 3.0.1, I'm getting an error when running the > following three lines of code: > > library(GenomicRanges) > library(GenomicFeatures) > txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename = 'refGene') > > Download the refGene table ... OK > Download the refLink table ... OK > Extract the 'transcripts' data frame ... OK > Extract the 'splicings' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TranscriptDb object ... OK > Error in list(PKGTITLE = paste("Annotation package for", dbType, > "object(s)"), : > 'version' is missing This means you have to supply a 'version' argument. See ?makeTxDbPackageFromUCSC Dan > In addition: There were 50 or more warnings (use warnings() to see the first > 50) > > If I run this on RHEL5, the same code fails in the same place, though with a > slightly different error message: > >> txdb <- makeTxDbPackageFromUCSC(genome = 'mm9', tablename = 'refGene') > Download the refGene table ... OK > Download the refLink table ... OK > Extract the 'transcripts' data frame ... OK > Extract the 'splicings' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TranscriptDb object ... Error in .Call2("svn_time", PACKAGE = > "IRanges") : > IRanges internal error in svn_time(): get_svn_time() failed > In addition: There were 50 or more warnings (use warnings() to see the first > 50) > > For OS X: > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin12.4.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6 Biobase_2.20.1 > [4] GenomicRanges_1.12.5 IRanges_1.18.1 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-5 BSgenome_1.28.0 > [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.12.3 RSQLite_0.11.4 > [9] rtracklayer_1.20.3 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 > [13] zlibbioc_1.6.0 > > For RHEL: > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GenomicFeatures_1.12.2 AnnotationDbi_1.22.5 Biobase_2.20.0 > [4] GenomicRanges_1.12.4 IRanges_1.18.3 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] BSgenome_1.28.0 Biostrings_2.28.0 DBI_0.2-7 RCurl_1.95-4.1 > [5] RSQLite_0.11.4 Rsamtools_1.12.3 XML_3.96-1.1 biomaRt_2.16.0 > [9] bitops_1.0-5 rtracklayer_1.20.2 stats4_3.0.1 tools_3.0.1 > [13] zlibbioc_1.6.0 > > The warnings referenced don't look related, I don't think: > > 43: In .extractUCSCCdsStartEnd(cdsStart[i], cdsEnd[i], exon_locs$start[[i]], > ... : > UCSC data anomaly in transcript NM_010707: the cds cumulative length is > not a multiple of 3 > > > -Mike > -- > Michael Steeves (steeves at raingods.net) > > _______________________________________________ > 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
ADD COMMENTlink written 4.3 years ago by Dan Tenenbaum ♦♦ 8.2k
On 8/27/13 6:31 PM, Dan Tenenbaum wrote: > This means you have to supply a 'version' argument. See > ?makeTxDbPackageFromUCSC Dan: This does fix the issue on OS X, however I'm still getting an error running the example from the help page on RHEL: > txdb <- makeTxDbPackageFromUCSC(version="0.01", + maintainer="Some One <so@someplace.org>", + author="Some One <so@someplace.com>", + genome="sacCer2", + tablename="ensGene") Download the ensGene table ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TranscriptDb object ... Error in .Call2("svn_time", PACKAGE = "IRanges") : IRanges internal error in svn_time(): get_svn_time() failed One of my colleagues did some investigation, and it looks like in the IRanges source code (str_utils.c) is where the problem is coming from: /* * 'out_size' should be at least 45 (for year < 10000, 44 chars will be * printed to it + '\0'). */ static int get_svn_time(time_t t, char *out, size_t out_size) { #if defined(__INTEL_COMPILER) return -1; #else /* defined(__INTEL_COMPILER) */ struct tm result; int utc_offset, n; static const char *wday2str[] = {"Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"}, *mon2str[] = {"Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"}, *svn_format = "%d-%02d-%02d %02d:%02d:%02d %+03d00 (%s, %02d %s %d)"; //localtime_r() not available on Windows+MinGW //localtime_r(&t, &result); result = *localtime(&t); #if defined(__APPLE__) || defined(__FreeBSD__) //'struct tm' has no member named 'tm_gmtoff' on Windows+MinGW utc_offset = result.tm_gmtoff / 3600; #else /* defined(__APPLE__) || defined(__FreeBSD__) */ tzset(); //timezone is not portable (is a function, not a long, on OS X Tiger) utc_offset = - (timezone / 3600); if (result.tm_isdst > 0) utc_offset++; #endif /* defined(__APPLE__) || defined(__FreeBSD__) */ n = snprintf(out, out_size, svn_format, result.tm_year + 1900, result.tm_mon + 1, result.tm_mday, result.tm_hour, result.tm_min, result.tm_sec, utc_offset, wday2str[result.tm_wday], result.tm_mday, mon2str[result.tm_mon], result.tm_year + 1900); return n >= out_size ? -1 : 0; #endif /* defined(__INTEL_COMPILER) */ } We are using the Intel compilers to build on Linux -- is this a bug, or is using the Intel compilers not supported? -Mike -- Michael Steeves (steeves@raingods.net) [[alternative HTML version deleted]]
ADD REPLYlink written 4.3 years ago by Michael Steeves40
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