Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
On 04/09/2015 05:57 AM, Ludwig Geistlinger wrote: Here you go ... sessionInfo() R Under development (unstable) (2015-03-09 r67969) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationHub_1.99.72 BiocInstaller_1.17.5 Yes, this should be AnnotationHub 1.99.81. Should be installed with BiocInstaller::biocLite(AnnotationHub) You can check that status of your Bioconductor installation with BiocInstaller::biocValid() loaded via a namespace (and not attached): [1] Rcpp_0.11.5 IRanges_2.1.43 [3] digest_0.6.8 bitops_1.0-6 [5] mime_0.2 GenomeInfoDb_1.3.13 [7] R6_2.0.1 xtable_1.7-4 [9] DBI_0.3.1stats4_3.2.0 [11] RSQLite_1.0.0httr_0.6.1 [13] S4Vectors_0.5.22 RJSONIO_1.3-0 [15] stringr_0.6.2Biobase_2.27.2 [17] RCurl_1.95-4.5 shiny_0.11.1 [19] httpuv_1.3.2 parallel_3.2.0 [21] BiocGenerics_0.13.6 AnnotationDbi_1.29.17 [23] htmltools_0.2.6 interactiveDisplayBase_1.5.1 Please provide sessionInfo() The class is defined in AnnotationHub in devel. Perhaps it is not suitably exported. On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed library(AnnotationHub) hub - AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter, April 2015) h - hub[hub$rdataclass == ExpressionSet] h AnnotationHub with 1 record # snapshotDate(): 2015-03-26 # names(): AH28855 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: ExpressionSet # $title: RNA-Sequencing and clinical data for 7706 tumor samples from The C... # $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706 tum... # $taxonomyid: 9606 # $genome: hg19 # $sourcetype: tar.gz # $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 # $sourcelastmodifieddate: NA # $sourcesize: NA # $tags: TCGA, RNA-seq, Expression, Count # retrieve record with 'object[[AH28855]]' and then tried to retrieve the record with either h[[AH28855]] or h[[1]] I received the following error: Error in value[[3L]](cond) : failed to create a 'AnnotationHubResource' instance for hub resource ‘RNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlas’ of class ExpressionSet; reason: “ExpressionSetResource� is not a defined class Did I do something wrong? Thank you for your help, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ 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 -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] New package for copy number detection from targeted sequencing using off-target reads
I am happy to announce that our CopywriteR tool is now available on the development branch of Bioconductor. CopywriteR extracts copy number information from targeted sequencing using off-target reads (for more information, see Kuilman et al, Genome Biology 16:49, 2015). This new method allows copy number detection in the absence of a reference, and circumvents some of the problems experienced when performing copy number analysis using on-target reads. CopywriteR can be applied to sequencing data from target enrichment on small gene panels, and to data obtained from various other techniques including chromatin immunoprecipitation. We believe that CopywriteR constitutes a widely applicable alternative to available tools. We are looking forward to further improve the tool and would be happy to receive any feedback. Best regards, Thomas -- Thomas Kuilman, PhD Department of Molecular Oncology Netherlands Cancer Institute 1066 CX Amsterdam The Netherlands Phone: +31-20-5121841 On 9 Apr 2015, at 21:05, bioc-devel-requ...@r-project.orgmailto:bioc-devel-requ...@r-project.org bioc-devel-requ...@r-project.orgmailto:bioc-devel-requ...@r-project.org wrote: Send Bioc-devel mailing list submissions to bioc-devel@r-project.orgmailto:bioc-devel@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioc-devel or, via email, send a message with subject or body 'help' to bioc-devel-requ...@r-project.orgmailto:bioc-devel-requ...@r-project.org You can reach the person managing the list at bioc-devel-ow...@r-project.orgmailto:bioc-devel-ow...@r-project.org When replying, please edit your Subject line so it is more specific than Re: Contents of Bioc-devel digest... Today's Topics: 1. Announcing a new package: FlowRepositoryR (Josef Spidlen) 2. Re: AnnotationHub: ExpressionSetResource Error in Docker devel_core (Vincent Carey) 3. Re: AnnotationHub: ExpressionSetResource Error in Docker devel_core (Ludwig Geistlinger) 4. Re: AnnotationHub: ExpressionSetResource Error in Docker devel_core (Martin Morgan) 5. Fwd: Proposed biocViews for Hi-C assay (Nathaniel Hayden) 6. Disabling commits to release today; Update NEWS files, biocViews (Dan Tenenbaum) -- Message: 1 Date: Thu, 9 Apr 2015 05:19:00 -0700 From: Josef Spidlen jspid...@bccrc.camailto:jspid...@bccrc.ca To: bioc-devel@r-project.orgmailto:bioc-devel@r-project.org Subject: [Bioc-devel] Announcing a new package: FlowRepositoryR Message-ID: camew6ujmas4texaourttmhnut977octwq+kgnzxlauktdtp...@mail.gmail.commailto:camew6ujmas4texaourttmhnut977octwq+kgnzxlauktdtp...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hello to those working with flow cytometry data, we are excited to announce that our package, FlowRepositoryR, is now available in BioConductor (devel). This package provides a light interface to access FlowRepository (https://flowrepository.org/) data from within R. FlowRepository is a public repository currently containing 456 flow cytometry experiments (datasets). 218 of those are public at this point and the numbers are growing as researchers keep submitting data as part of their publications. FlowRepositoryR provides an easy access requiring very little R experience. Basic operations, such as locating a dataset, reviewing metadata and downloading files can be done in one or two lines of code. I would argue that this can actually be easier, faster and more reliable than having to open your web browser and start clicking around. Access to both, public and private experiments is supported. All access is read-only at this point, but we will look into adding write functionality after the current BioConductor release. Please let me know if you have any feedback, suggestions or feature requests. Cheers, Josef -- Josef Spidlen, Ph.D. Staff Scientist, Terry Fox Laboratory, BC Cancer Agency 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada Tel. +1 604-675-8000, ex. 7755 [[alternative HTML version deleted]] -- Message: 2 Date: Thu, 9 Apr 2015 08:47:38 -0400 From: Vincent Carey st...@channing.harvard.edumailto:st...@channing.harvard.edu To: Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.demailto:ludwig.geistlin...@bio.ifi.lmu.de Cc: bioc-devel@r-project.orgmailto:bioc-devel@r-project.org bioc-devel@r-project.orgmailto:bioc-devel@r-project.org Subject: Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core Message-ID: caant7+xslifcnc_igq5yeeanz7awurtkctpeqb-r+2n4+xr...@mail.gmail.commailto:caant7+xslifcnc_igq5yeeanz7awurtkctpeqb-r+2n4+xr...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Please provide sessionInfo() The class is defined in AnnotationHub in devel. Perhaps it is not suitably exported.
Re: [Bioc-devel] AnnotationHub: Error in Docker release_core
Hi, On Thu, Apr 9, 2015 at 10:27 AM, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Error in file(con, r) : cannot open the connection In addition: Warning message: In file(con, r) : unable to resolve 'annotationhub.bioconductor.org' That's strange, on linux it's working. Seems related to network unavailability inside Docker with Mac OS X (I know, not a very insightful suggestion...). BTW: are the docker scripts that were used to create the bioc dockers under http://www.bioconductor.org/help/docker/ somewhere available? https://github.com/Bioconductor/bioc_docker E. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Fwd: Proposed biocViews for Hi-C assay
From Aaron Lun. On a related note, there's now a number of packages involved in analyzing Hi-C data, e.g., GoTHiC, HiTC, GenomicInteractions and diffHic. Would it be worth adding a BiocViews term for the Hi-C assay (maybe under Technology - Sequencing)? Cheers, Aaron -- Aaron Lun PhD student Bioinformatics Division - Smyth Lab Walter and Eliza Hall Institute of Medical Research ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] AnnotationHub: Error in Docker release_core
Dear Elena, thank you for your quick response. Seems as I have make this up to early - it works now for me as well, must have been a pure connection issue. Thx for pointing me to the docker scripts (I must have overread it, is ac tually also stated under http://bioconductor.org/help/docker/). Sorry for the inconvenience!! Best, Ludiwg Hi, On Thu, Apr 9, 2015 at 10:27 AM, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Error in file(con, r) : cannot open the connection In addition: Warning message: In file(con, r) : unable to resolve 'annotationhub.bioconductor.org' That's strange, on linux it's working. Seems related to network unavailability inside Docker with Mac OS X (I know, not a very insightful suggestion...). BTW: are the docker scripts that were used to create the bioc dockers under http://www.bioconductor.org/help/docker/ somewhere available? https://github.com/Bioconductor/bioc_docker E. -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
Here you go ... sessionInfo() R Under development (unstable) (2015-03-09 r67969) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationHub_1.99.72 BiocInstaller_1.17.5 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 IRanges_2.1.43 [3] digest_0.6.8 bitops_1.0-6 [5] mime_0.2 GenomeInfoDb_1.3.13 [7] R6_2.0.1 xtable_1.7-4 [9] DBI_0.3.1stats4_3.2.0 [11] RSQLite_1.0.0httr_0.6.1 [13] S4Vectors_0.5.22 RJSONIO_1.3-0 [15] stringr_0.6.2Biobase_2.27.2 [17] RCurl_1.95-4.5 shiny_0.11.1 [19] httpuv_1.3.2 parallel_3.2.0 [21] BiocGenerics_0.13.6 AnnotationDbi_1.29.17 [23] htmltools_0.2.6 interactiveDisplayBase_1.5.1 Please provide sessionInfo() The class is defined in AnnotationHub in devel. Perhaps it is not suitably exported. On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed library(AnnotationHub) hub - AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter, April 2015) h - hub[hub$rdataclass == ExpressionSet] h AnnotationHub with 1 record # snapshotDate(): 2015-03-26 # names(): AH28855 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: ExpressionSet # $title: RNA-Sequencing and clinical data for 7706 tumor samples from The C... # $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706 tum... # $taxonomyid: 9606 # $genome: hg19 # $sourcetype: tar.gz # $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 # $sourcelastmodifieddate: NA # $sourcesize: NA # $tags: TCGA, RNA-seq, Expression, Count # retrieve record with 'object[[AH28855]]' and then tried to retrieve the record with either h[[AH28855]] or h[[1]] I received the following error: Error in value[[3L]](cond) : failed to create a 'AnnotationHubResource' instance for hub resource âRNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlasâ of class ExpressionSet; reason: âExpressionSetResourceâ is not a defined class Did I do something wrong? Thank you for your help, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ 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
[Bioc-devel] Announcing a new package: FlowRepositoryR
Hello to those working with flow cytometry data, we are excited to announce that our package, FlowRepositoryR, is now available in BioConductor (devel). This package provides a light interface to access FlowRepository (https://flowrepository.org/) data from within R. FlowRepository is a public repository currently containing 456 flow cytometry experiments (datasets). 218 of those are public at this point and the numbers are growing as researchers keep submitting data as part of their publications. FlowRepositoryR provides an easy access requiring very little R experience. Basic operations, such as locating a dataset, reviewing metadata and downloading files can be done in one or two lines of code. I would argue that this can actually be easier, faster and more reliable than having to open your web browser and start clicking around. Access to both, public and private experiments is supported. All access is read-only at this point, but we will look into adding write functionality after the current BioConductor release. Please let me know if you have any feedback, suggestions or feature requests. Cheers, Josef -- Josef Spidlen, Ph.D. Staff Scientist, Terry Fox Laboratory, BC Cancer Agency 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada Tel. +1 604-675-8000, ex. 7755 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed library(AnnotationHub) hub - AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter, April 2015) h - hub[hub$rdataclass == ExpressionSet] h AnnotationHub with 1 record # snapshotDate(): 2015-03-26 # names(): AH28855 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: ExpressionSet # $title: RNA-Sequencing and clinical data for 7706 tumor samples from The C... # $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706 tum... # $taxonomyid: 9606 # $genome: hg19 # $sourcetype: tar.gz # $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 # $sourcelastmodifieddate: NA # $sourcesize: NA # $tags: TCGA, RNA-seq, Expression, Count # retrieve record with 'object[[AH28855]]' and then tried to retrieve the record with either h[[AH28855]] or h[[1]] I received the following error: Error in value[[3L]](cond) : failed to create a 'AnnotationHubResource' instance for hub resource RNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlas of class ExpressionSet; reason: ExpressionSetResource is not a defined class Did I do something wrong? Thank you for your help, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
Please provide sessionInfo() The class is defined in AnnotationHub in devel. Perhaps it is not suitably exported. On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de wrote: Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed library(AnnotationHub) hub - AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter, April 2015) h - hub[hub$rdataclass == ExpressionSet] h AnnotationHub with 1 record # snapshotDate(): 2015-03-26 # names(): AH28855 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: ExpressionSet # $title: RNA-Sequencing and clinical data for 7706 tumor samples from The C... # $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706 tum... # $taxonomyid: 9606 # $genome: hg19 # $sourcetype: tar.gz # $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 # $sourcelastmodifieddate: NA # $sourcesize: NA # $tags: TCGA, RNA-seq, Expression, Count # retrieve record with 'object[[AH28855]]' and then tried to retrieve the record with either h[[AH28855]] or h[[1]] I received the following error: Error in value[[3L]](cond) : failed to create a 'AnnotationHubResource' instance for hub resource ‘RNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlas’ of class ExpressionSet; reason: “ExpressionSetResource” is not a defined class Did I do something wrong? Thank you for your help, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
