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
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 # $tags: TCGA, RNA-seq, Expression, Count # retrieve record with 'object[[AH28855]]' and then tried to retrieve the record with either h[[AH28855]] or h[[1]] I received the following error: Error in value[[3L]](cond) : failed to create a 'AnnotationHubResource' instance for hub resource âRNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlasâ of class ExpressionSet; reason: âExpressionSetResourceâ is not a defined class Did I do something wrong? Thank you for your help, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
Hi, As I pulled down the devel_core image (running boot2docker under OS X Yosemite) docker run -ti bioconductor/release_core R and then executed library(AnnotationHub) hub - AnnotationHub() and selected the recently integrated GSE62944 TCGA dataset (announced in the latest BioC newsletter, April 2015) h - hub[hub$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
