Re: [Bioc-devel] ExperimentHub broken in bioc-devel?
It should be up in bioc-devel soon. It failed to build last night do to other package dependencies failing. All should be remedied by tomorrows build. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Levi Waldron <lwaldron.resea...@gmail.com> Sent: Saturday, June 3, 2017 2:34:15 PM To: Obenchain, Valerie Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] ExperimentHub broken in bioc-devel? Thanks Val! 2.9.4 isn't in bioc-devel yet, but I got it through Subversion and am up and running again. On Sat, Jun 3, 2017 at 11:26 AM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Levi, > > Lori fixed this bug last week. You'll need AnnotationHub >= 2.9.4. > > Val > > > On 06/03/2017 05:55 AM, Levi Waldron wrote: > > It works for me when I have an existing cache, but not after removing the > > cache: > > > >> unlink("~/.ExperimentHub", recursive=TRUE) > >> suppressPackageStartupMessages(library(curatedMetagenomicData)) > >> ExperimentHub() > > updating metadata: retrieving 1 resource > > > > |=== > ==| > > 100% > > snapshotDate(): 2016-12-12 > > *Error in gzfile(file, "rb") : cannot open the connection* > > In addition: Warning message: > > In gzfile(file, "rb") : > > cannot open compressed file '/Users/lwaldron//. > ExperimentHub/index.rds', > > probable reason 'No such file or directory' > >> sessionInfo() > > R version 3.4.0 Patched (2017-06-02 r72758) > > Platform: x86_64-apple-darwin15.6.0 (64-bit) > > Running under: macOS Sierra 10.12.4 > > > > Matrix products: default > > BLAS: > > /System/Library/Frameworks/Accelerate.framework/Versions/ > A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib > > LAPACK: > > /Library/Frameworks/R.framework/Versions/3.4/ > Resources/lib/libRlapack.dylib > > > > 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 > > base > > > > other attached packages: > > [1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0 > > > > loaded via a namespace (and not attached): > > [1] Rcpp_0.12.11 IRanges_2.11.3 > > [3] digest_0.6.12 mime_0.5 > > [5] R6_2.2.1 xtable_1.8-2 > > [7] DBI_0.6-1 stats4_3.4.0 > > [9] RSQLite_1.1-2 BiocInstaller_1.27.2 > > [11] httr_1.2.1curl_2.6 > > [13] S4Vectors_0.15.2 tools_3.4.0 > > [15] Biobase_2.37.2shiny_1.0.3 > > [17] httpuv_1.3.3 yaml_2.1.14 > > [19] compiler_3.4.0AnnotationDbi_1.39.1 > > [21] memoise_1.1.0 htmltools_0.3.6 > > [23] interactiveDisplayBase_1.15.0 > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > -- Levi Waldron http://www.waldronlab.org Assistant Professor of Biostatistics CUNY School of Public Health US: +1 646-364-9616 Skype: levi.waldron [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ExperimentHub broken in bioc-devel?
Thanks Val! 2.9.4 isn't in bioc-devel yet, but I got it through Subversion and am up and running again. On Sat, Jun 3, 2017 at 11:26 AM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Levi, > > Lori fixed this bug last week. You'll need AnnotationHub >= 2.9.4. > > Val > > > On 06/03/2017 05:55 AM, Levi Waldron wrote: > > It works for me when I have an existing cache, but not after removing the > > cache: > > > >> unlink("~/.ExperimentHub", recursive=TRUE) > >> suppressPackageStartupMessages(library(curatedMetagenomicData)) > >> ExperimentHub() > > updating metadata: retrieving 1 resource > > > > |=== > ==| > > 100% > > snapshotDate(): 2016-12-12 > > *Error in gzfile(file, "rb") : cannot open the connection* > > In addition: Warning message: > > In gzfile(file, "rb") : > > cannot open compressed file '/Users/lwaldron//. > ExperimentHub/index.rds', > > probable reason 'No such file or directory' > >> sessionInfo() > > R version 3.4.0 Patched (2017-06-02 r72758) > > Platform: x86_64-apple-darwin15.6.0 (64-bit) > > Running under: macOS Sierra 10.12.4 > > > > Matrix products: default > > BLAS: > > /System/Library/Frameworks/Accelerate.framework/Versions/ > A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib > > LAPACK: > > /Library/Frameworks/R.framework/Versions/3.4/ > Resources/lib/libRlapack.dylib > > > > 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 > > base > > > > other attached packages: > > [1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0 > > > > loaded via a namespace (and not attached): > > [1] Rcpp_0.12.11 IRanges_2.11.3 > > [3] digest_0.6.12 mime_0.5 > > [5] R6_2.2.1 xtable_1.8-2 > > [7] DBI_0.6-1 stats4_3.4.0 > > [9] RSQLite_1.1-2 BiocInstaller_1.27.2 > > [11] httr_1.2.1curl_2.6 > > [13] S4Vectors_0.15.2 tools_3.4.0 > > [15] Biobase_2.37.2shiny_1.0.3 > > [17] httpuv_1.3.3 yaml_2.1.14 > > [19] compiler_3.4.0AnnotationDbi_1.39.1 > > [21] memoise_1.1.0 htmltools_0.3.6 > > [23] interactiveDisplayBase_1.15.0 > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > -- Levi Waldron http://www.waldronlab.org Assistant Professor of Biostatistics CUNY School of Public Health US: +1 646-364-9616 Skype: levi.waldron [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] ExperimentHub broken in bioc-devel?
It works for me when I have an existing cache, but not after removing the cache: > unlink("~/.ExperimentHub", recursive=TRUE) > suppressPackageStartupMessages(library(curatedMetagenomicData)) > ExperimentHub() updating metadata: retrieving 1 resource |=| 100% snapshotDate(): 2016-12-12 *Error in gzfile(file, "rb") : cannot open the connection* In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/Users/lwaldron//.ExperimentHub/index.rds', probable reason 'No such file or directory' > sessionInfo() R version 3.4.0 Patched (2017-06-02 r72758) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib 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 base other attached packages: [1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.11 IRanges_2.11.3 [3] digest_0.6.12 mime_0.5 [5] R6_2.2.1 xtable_1.8-2 [7] DBI_0.6-1 stats4_3.4.0 [9] RSQLite_1.1-2 BiocInstaller_1.27.2 [11] httr_1.2.1curl_2.6 [13] S4Vectors_0.15.2 tools_3.4.0 [15] Biobase_2.37.2shiny_1.0.3 [17] httpuv_1.3.3 yaml_2.1.14 [19] compiler_3.4.0AnnotationDbi_1.39.1 [21] memoise_1.1.0 htmltools_0.3.6 [23] interactiveDisplayBase_1.15.0 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel