Hello Bioconductor team, We are the creator and maintainers of the CINdex Bioconductor package. Last few days, we are seeing build errors in our package (See below). The package builds fine in Mac OS, but is giving the following error on Ubuntu OS. http://bioconductor.org/checkResults/release/bioc-LATEST/CINdex/malbec1-buildsrc.html We have not made any changes to our package, and did not have any errors previously. Is there some action we need to take on our part ? Please advise. Thanks, Krithika Attaching package: 'Biobase' The following object is masked from 'package:AnnotationHub': cache =========================================================================== Welcome to oligo version 1.42.0 =========================================================================== Loading required package: DBI Warning: closing unused connection 5 (hg19ToHg18.over.chain) Loading ideogram... Quitting from lines 230-240 (PrepareInputData.Rmd) Error: processing vignette 'PrepareInputData.Rmd' failed with diagnostics: Bad Request Execution halted
[Bioc-devel] CINdex package build error in Linux
3 messages · Krithika Bhuvaneshwar, Obenchain, Valerie, Yuriy Gusev
1 day later
Hi Krithika, I believe this was related to a problem with getTable() in rtracklayer: https://github.com/lawremi/rtracklayer/issues/5 rtracklayer 1.39.5 built successfully today and the error in CINdex has cleared up: https://bioconductor.org/packages/3.7/bioc/html/CINdex.html Valerie
On 01/18/2018 08:19 AM, Krithika Bhuvaneshwar wrote:
Hello Bioconductor team, We are the creator and maintainers of the CINdex Bioconductor package. Last few days, we are seeing build errors in our package (See below). The package builds fine in Mac OS, but is giving the following error on Ubuntu OS. http://bioconductor.org/checkResults/release/bioc-LATEST/CINdex/malbec1-buildsrc.html We have not made any changes to our package, and did not have any errors previously. Is there some action we need to take on our part ? Please advise. Thanks, Krithika Attaching package: 'Biobase' The following object is masked from 'package:AnnotationHub': cache =========================================================================== Welcome to oligo version 1.42.0 =========================================================================== Loading required package: DBI Warning: closing unused connection 5 (hg19ToHg18.over.chain) Loading ideogram... Quitting from lines 230-240 (PrepareInputData.Rmd) Error: processing vignette 'PrepareInputData.Rmd' failed with diagnostics: Bad Request Execution halted _______________________________________________ Bioc-devel at r-project.org<mailto:Bioc-devel at 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.
Great news! Thanks Valerie Best Regards Yuriy On Fri, Jan 19, 2018 at 11:40 AM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:
Hi Krithika, I believe this was related to a problem with getTable() in rtracklayer: https://github.com/lawremi/rtracklayer/issues/5 rtracklayer 1.39.5 built successfully today and the error in CINdex has cleared up: https://bioconductor.org/packages/3.7/bioc/html/CINdex.html Valerie On 01/18/2018 08:19 AM, Krithika Bhuvaneshwar wrote: Hello Bioconductor team, We are the creator and maintainers of the CINdex Bioconductor package. Last few days, we are seeing build errors in our package (See below). The package builds fine in Mac OS, but is giving the following error on Ubuntu OS.http://bioconductor.org/checkResults/release/bioc-LATEST/CINdex/malbec1-buildsrc.html We have not made any changes to our package, and did not have any errors previously. Is there some action we need to take on our part ? Please advise. Thanks, Krithika Attaching package: 'Biobase' The following object is masked from 'package:AnnotationHub': cache =========================================================================== Welcome to oligo version 1.42.0 =========================================================================== Loading required package: DBI Warning: closing unused connection 5 (hg19ToHg18.over.chain) Loading ideogram... Quitting from lines 230-240 (PrepareInputData.Rmd) Error: processing vignette 'PrepareInputData.Rmd' failed with diagnostics: Bad Request Execution halted [[alternative HTML version deleted]]
_______________________________________________Bioc-devel at r-project.org mailing listhttps://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.
Yuriy Gusev, Ph.D., Associate Professor Innovation Center for Biomedical Informatics (ICBI) Georgetown University Medical Center 2115 Wisconsin Ave NW, Suite 110 Washington DC 20007 Tel. (202) 687-5094; Fax (202) 687-5011 Email: yg63 at georgetown.edu ORCID ID: orcid.org/0000-0001-7371-4715 Website:icbi.georgetown.edu/ edX MOOC: https://www.edx.org/course/demystifying-biomedical-big-data-users-georgetownx-biox-201-01x [[alternative HTML version deleted]]