Re: [Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error
Hi Raymond, This should be fixed now in GenomeInfoDb 1.10.3 (release) and 1.11.8 (devel). Both packages should become available via biocLite() in the next 24 hours or so. Thanks again for reporting the issue and for your patience. Cheers, H. On 02/01/2017 12:32 PM, Hervé Pagès wrote: Hi Raymond, On 02/01/2017 04:39 AM, Raymond Cavalcante wrote: Hello, I was wondering if any progress has been made on fixing this? I looked through recent commits for GenomeInfoDb, but there didn't seem to be anything related to this problem. Not yet. Please expect a couple more days before this is resolved. Thanks for your patience, H. Thanks, Raymond On Jan 25, 2017, at 23:01, Obenchain, Valerie wrote: Thanks for the report. It looks like the directory structure has changed. I'll work on this tomorrow and will post back when it's fixed. Valerie On 01/25/2017 06:29 PM, Raymond Cavalcante wrote: Hello, I'm suddenly encountering errors with GenomeInfoDb::Seqinfo(): GenomeInfoDb::Seqinfo(genome='hg19') Error in file(file, "rt") : cannot open connection In addition: Warning message: In file(file, "rt") : URL 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt': status was '404 Not Found' I'm not sure how to fix this issue, as it seems to be more of an NCBI problem. Any help would be greatly appreciated. Thanks, Raymond Cavalcante ___ 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. ___ 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
Re: [Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error
Hi Raymond, On 02/01/2017 04:39 AM, Raymond Cavalcante wrote: Hello, I was wondering if any progress has been made on fixing this? I looked through recent commits for GenomeInfoDb, but there didn't seem to be anything related to this problem. Not yet. Please expect a couple more days before this is resolved. Thanks for your patience, H. Thanks, Raymond On Jan 25, 2017, at 23:01, Obenchain, Valerie wrote: Thanks for the report. It looks like the directory structure has changed. I'll work on this tomorrow and will post back when it's fixed. Valerie On 01/25/2017 06:29 PM, Raymond Cavalcante wrote: Hello, I'm suddenly encountering errors with GenomeInfoDb::Seqinfo(): GenomeInfoDb::Seqinfo(genome='hg19') Error in file(file, "rt") : cannot open connection In addition: Warning message: In file(file, "rt") : URL 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt': status was '404 Not Found' I'm not sure how to fix this issue, as it seems to be more of an NCBI problem. Any help would be greatly appreciated. Thanks, Raymond Cavalcante ___ 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. ___ 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
Re: [Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error
Hello, I was wondering if any progress has been made on fixing this? I looked through recent commits for GenomeInfoDb, but there didn't seem to be anything related to this problem. Thanks, Raymond > On Jan 25, 2017, at 23:01, Obenchain, Valerie > wrote: > > Thanks for the report. It looks like the directory structure has > changed. I'll work on this tomorrow and will post back when it's fixed. > > Valerie > > >> On 01/25/2017 06:29 PM, Raymond Cavalcante wrote: >> Hello, >> >> I'm suddenly encountering errors with GenomeInfoDb::Seqinfo(): >> GenomeInfoDb::Seqinfo(genome='hg19') >>> Error in file(file, "rt") : cannot open connection >>> In addition: Warning message: >>> In file(file, "rt") : >>> URL >>> 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt': >>> status was '404 Not Found' >> I'm not sure how to fix this issue, as it seems to be more of an NCBI >> problem. Any help would be greatly appreciated. >> >> Thanks, >> Raymond Cavalcante >> ___ >> 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error
Thanks for the report. It looks like the directory structure has changed. I'll work on this tomorrow and will post back when it's fixed. Valerie On 01/25/2017 06:29 PM, Raymond Cavalcante wrote: > Hello, > > I'm suddenly encountering errors with GenomeInfoDb::Seqinfo(): > >>> GenomeInfoDb::Seqinfo(genome='hg19') >> Error in file(file, "rt") : cannot open connection >> In addition: Warning message: >> In file(file, "rt") : >> URL >> 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt': >> status was '404 Not Found' > I'm not sure how to fix this issue, as it seems to be more of an NCBI > problem. Any help would be greatly appreciated. > > Thanks, > Raymond Cavalcante > ___ > 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error
Hello, I'm suddenly encountering errors with GenomeInfoDb::Seqinfo(): > > GenomeInfoDb::Seqinfo(genome='hg19') > Error in file(file, "rt") : cannot open connection > In addition: Warning message: > In file(file, "rt") : > URL > 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt': > status was '404 Not Found' I'm not sure how to fix this issue, as it seems to be more of an NCBI problem. Any help would be greatly appreciated. Thanks, Raymond Cavalcante ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
