Re: [Bioc-devel] forceAndCall is not a SPECIAL function ERROR when using ShortRead readAligned function
Try updating to R-alpha (3.2.0) instead of R-devel (3.3.0). Dan - Original Message - From: Nicolas Delhomme nicolas.delho...@umu.se To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioC-devel bioc-de...@stat.math.ethz.ch Sent: Friday, March 27, 2015 11:12:00 AM Subject: Re: [Bioc-devel] forceAndCall is not a SPECIAL function ERROR when using ShortRead readAligned function Easy enough :-) I'm running the RnaSeqTutorial package vignette and the chunks 6, 7 and 8 fail with that forceAndCall error. My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11). Nico --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- On 27 Mar 2015, at 19:09, Dan Tenenbaum dtene...@fredhutch.org wrote: I think we'd need to see your files in order to try to reproduce this. Dan - Original Message - From: Nicolas Delhomme nicolas.delho...@umu.se To: bioC-devel bioc-de...@stat.math.ethz.ch Sent: Friday, March 27, 2015 11:04:17 AM Subject: [Bioc-devel] forceAndCall is not a SPECIAL function ERROR when using ShortRead readAligned function Hej Bioc! I've got the following error and can't really track its origin. Cheers, Nico aln2 - readAligned(getwd(),pattern=subset.bam$,type=BAM) Error: Input/Output 'readAligned' failed to parse files dirPath: '/Users/delhomme/Documents/Git/RnaSeqTutorial' pattern: 'subset.bam$' type: 'BAM' error: forceAndCall is not a SPECIAL function sessionInfo() R Under development (unstable) (2015-02-11 r67792) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) 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] stats4parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.25.9 GenomicAlignments_1.3.32 Rsamtools_1.19.49GenomicRanges_1.19.48 [5] GenomeInfoDb_1.3.16 Biostrings_2.35.12 XVector_0.7.4 IRanges_2.1.43 [9] S4Vectors_0.5.22 BiocParallel_1.1.21 BiocGenerics_0.13.10 RnaSeqTutorial_0.3.2 [13] easyRNASeq_2.3.4 locfit_1.5-9.1 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4 bitops_1.0-6 futile.options_1.0.0 tools_3.2.0 [6] zlibbioc_1.13.3biomaRt_2.23.5 annotate_1.45.4 RSQLite_1.0.0 lattice_0.20-30 [11] DBI_0.3.1 DESeq_1.19.0 genefilter_1.49.2 hwriter_1.3.2 grid_3.2.0 [16] LSD_3.0Biobase_2.27.3 AnnotationDbi_1.29.20 XML_3.98-1.1 survival_2.38-1 [21] limma_3.23.11 latticeExtra_0.6-26 geneplotter_1.45.0 lambda.r_1.1.7 edgeR_3.9.14 [26] intervals_0.15.0 genomeIntervals_1.23.2 splines_3.2.0 xtable_1.7-4 RCurl_1.95-4.5 --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] forceAndCall is not a SPECIAL function ERROR when using ShortRead readAligned function
That did it, sorry for whining too early :-\ Nico --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- On 27 Mar 2015, at 19:13, Dan Tenenbaum dtene...@fredhutch.org wrote: Try updating to R-alpha (3.2.0) instead of R-devel (3.3.0). Dan - Original Message - From: Nicolas Delhomme nicolas.delho...@umu.se To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioC-devel bioc-de...@stat.math.ethz.ch Sent: Friday, March 27, 2015 11:12:00 AM Subject: Re: [Bioc-devel] forceAndCall is not a SPECIAL function ERROR when using ShortRead readAligned function Easy enough :-) I'm running the RnaSeqTutorial package vignette and the chunks 6, 7 and 8 fail with that forceAndCall error. My R-devel is rather outdated, I'm updating it to see if that is the reason (2015-02-11). Nico --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- On 27 Mar 2015, at 19:09, Dan Tenenbaum dtene...@fredhutch.org wrote: I think we'd need to see your files in order to try to reproduce this. Dan - Original Message - From: Nicolas Delhomme nicolas.delho...@umu.se To: bioC-devel bioc-de...@stat.math.ethz.ch Sent: Friday, March 27, 2015 11:04:17 AM Subject: [Bioc-devel] forceAndCall is not a SPECIAL function ERROR when using ShortRead readAligned function Hej Bioc! I've got the following error and can't really track its origin. Cheers, Nico aln2 - readAligned(getwd(),pattern=subset.bam$,type=BAM) Error: Input/Output 'readAligned' failed to parse files dirPath: '/Users/delhomme/Documents/Git/RnaSeqTutorial' pattern: 'subset.bam$' type: 'BAM' error: forceAndCall is not a SPECIAL function sessionInfo() R Under development (unstable) (2015-02-11 r67792) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) 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] stats4parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.25.9 GenomicAlignments_1.3.32 Rsamtools_1.19.49GenomicRanges_1.19.48 [5] GenomeInfoDb_1.3.16 Biostrings_2.35.12 XVector_0.7.4 IRanges_2.1.43 [9] S4Vectors_0.5.22 BiocParallel_1.1.21 BiocGenerics_0.13.10 RnaSeqTutorial_0.3.2 [13] easyRNASeq_2.3.4 locfit_1.5-9.1 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4 bitops_1.0-6 futile.options_1.0.0 tools_3.2.0 [6] zlibbioc_1.13.3biomaRt_2.23.5 annotate_1.45.4 RSQLite_1.0.0 lattice_0.20-30 [11] DBI_0.3.1 DESeq_1.19.0 genefilter_1.49.2 hwriter_1.3.2 grid_3.2.0 [16] LSD_3.0Biobase_2.27.3 AnnotationDbi_1.29.20 XML_3.98-1.1 survival_2.38-1 [21] limma_3.23.11 latticeExtra_0.6-26 geneplotter_1.45.0 lambda.r_1.1.7 edgeR_3.9.14 [26] intervals_0.15.0 genomeIntervals_1.23.2 splines_3.2.0 xtable_1.7-4 RCurl_1.95-4.5 --- Nicolas Delhomme The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --- ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] request to create BSgenome Bos_taurus_UMD3.1.1
So I went ahead and did BSgenome.Btaurus.UCSC.bosTau8. It should become available via biocLite() in the next couple of hours (in BioC devel only). H. On 03/26/2015 12:54 AM, Hervé Pagès wrote: Hi Byungkuk, On 03/25/2015 10:17 PM, Byungkuk Min wrote: Dear Dr.Pages, I've been trying to build a BSgenome for Bos_taurus_UMD3.1.1 from NCBI http://www.ncbi.nlm.nih.gov/assembly/GCF_03055.6/. But I'm getting the same error message... library(BSgenome) forgeBSgenomeDataPkg(/PATH/TO/genome.fa) Error: Line starting '1 ...' is malformed! I don't have much knowledge of R, so creating a custom BSgenome seems out of my league. I would like to kindly request the bovine BSgenome package. Do you really need *that* particular assembly (GCF_03055.6). Otherwise, there are already some bovine BSgenome packages available: library(BSgenome) grep(Btaurus, available.genomes(), value=TRUE) [1] BSgenome.Btaurus.UCSC.bosTau3 [2] BSgenome.Btaurus.UCSC.bosTau3.masked [3] BSgenome.Btaurus.UCSC.bosTau4 [4] BSgenome.Btaurus.UCSC.bosTau4.masked [5] BSgenome.Btaurus.UCSC.bosTau6 [6] BSgenome.Btaurus.UCSC.bosTau6.masked We don't have bosTau8 yet, which is the latest bovine assembly available at UCSC (they added it in June 2014) but I could add it. Note that despite its name (also Bos_taurus_UMD_3.1.1), bosTau8 is not the same assembly as the one you picked up on NCBI. Yours is: http://www.ncbi.nlm.nih.gov/assembly/GCF_03055.6 (the latest, from 2014/11/25), but bosTau8 is: http://www.ncbi.nlm.nih.gov/assembly/GCF_03055.5 (much older, from 2009/12/01) Anyway, if we ignore chrM and the thousands of scaffolds that are included in these assemblies, the sequences of the main chromosomes (i.e. chr1 to chr29 + chrX) are exactly the same in the 2 assemblies. So maybe the BSgenome package for bosTau8 will do? Note that the main advantage of making a BSgenome package for a UCSC assembly (instead of using an NCBI assembly) is that the BSgenome object then interoperates nicely with the TxDb object that one can easily make from one of the UCSC tracks available for that assembly (using the makeTxDbFromUCSC() function from the GenomicFeatures package). H. Thank you! *Byungkuk Min* Ph.D Candidate University of Science Technology, http://ust.ac.kr Korea Research Institute of Bioscience and Biotechnology http://www.kribb.re.kr 125 Gwahangno, Yuseong-Gu, Daejeon, Korea (305-806) Laboratory : 042-860-4423 FAX : 042-860-4608 Cell phone : 010-5209-7377 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
