Re: [Bioc-devel] Error in BUILD report (anamiR)
Thank you for your efforts. Since the windows ERROR is out of your control we will undeprecate your package. 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 Herv�� Pag��s <hpa...@fredhutch.org> Sent: Thursday, May 4, 2017 1:24:49 PM To: ̨; Obenchain, Valerie; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Error in BUILD report (anamiR) Hi Ti-Tai, Not much you or we can do about this. Hopefully the RMySQL Windows binary (currently 0.10.11) will soon be fixed on CRAN. Thanks for keeping an eye on the build results for anamiR. Best, H. On 05/04/2017 08:28 AM, ̨ wrote: > Hi all, > > It turns out that this error is related to the RMySQL package(CRAN), > and only happened in windows operating system. > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rstats-2Ddb_RMySQL_issues_190=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=EttA79WmCSlSiTmcSwggrVyANbs5AysI8hyEOfn4MeI= > > It looks like it can be solved only if we downgraded the RMySQL version now. > Can I choose not to import the newest RMySQL version while being tested in > the BUILDREPORT? > > > Ti-Tai > > > ��: Obenchain, Valerie [valerie.obench...@roswellpark.org] > �ļ�: 2017��4��16�� ���� 10:58 > ��: ̨; bioc-devel@r-project.org > ��ּ: Re: [Bioc-devel] Error in BUILD report (anamiR) > > It looks like this has been resolved on today's report: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=YqN2fHnUtseqzRMY6V06EubUXBY_m568PYWkUh0Zhb8= > > Valerie > > > On 04/07/2017 02:21 PM, ̨ wrote: >> Hi all, >> >> I got en error when it tries to create vignette in BUILD: >> tokay2 Windows Server 2012 R2 Standard / x64 >> >> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with >> diagnostics: >> could not run statement: Lost connection to MySQL server during query >> >> But for Linux or Mac, it all works. >> I have no idea how to solve this problem. >> >> Many thanks, >> Ti-Tai >> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=qn1gkdYoqG_1sfJjLb27oOtHp3x8K4Brjgt_SaWXkIE= >> > > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=qn1gkdYoqG_1sfJjLb27oOtHp3x8K4Brjgt_SaWXkIE= > -- Herv�� Pag��s 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 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] Error in BUILD report (anamiR)
Hi Ti-Tai, Not much you or we can do about this. Hopefully the RMySQL Windows binary (currently 0.10.11) will soon be fixed on CRAN. Thanks for keeping an eye on the build results for anamiR. Best, H. On 05/04/2017 08:28 AM, 王棣台 wrote: Hi all, It turns out that this error is related to the RMySQL package(CRAN), and only happened in windows operating system. https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rstats-2Ddb_RMySQL_issues_190=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=EttA79WmCSlSiTmcSwggrVyANbs5AysI8hyEOfn4MeI= It looks like it can be solved only if we downgraded the RMySQL version now. Can I choose not to import the newest RMySQL version while being tested in the BUILDREPORT? Ti-Tai 從: Obenchain, Valerie [valerie.obench...@roswellpark.org] 寄件日期: 2017年4月16日 上午 10:58 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Error in BUILD report (anamiR) It looks like this has been resolved on today's report: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=YqN2fHnUtseqzRMY6V06EubUXBY_m568PYWkUh0Zhb8= Valerie On 04/07/2017 02:21 PM, 王棣台 wrote: Hi all, I got en error when it tries to create vignette in BUILD: tokay2 Windows Server 2012 R2 Standard / x64 Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: could not run statement: Lost connection to MySQL server during query But for Linux or Mac, it all works. I have no idea how to solve this problem. Many thanks, Ti-Tai [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=qn1gkdYoqG_1sfJjLb27oOtHp3x8K4Brjgt_SaWXkIE= 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGog=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VSEps9beT-guh1-ZsGnrNtM76EXvC0sLDGAvbHiyf7o=qn1gkdYoqG_1sfJjLb27oOtHp3x8K4Brjgt_SaWXkIE= -- 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] Error in BUILD report (anamiR)
Hi all, It turns out that this error is related to the RMySQL package(CRAN), and only happened in windows operating system. https://github.com/rstats-db/RMySQL/issues/190 It looks like it can be solved only if we downgraded the RMySQL version now. Can I choose not to import the newest RMySQL version while being tested in the BUILDREPORT? Ti-Tai 從: Obenchain, Valerie [valerie.obench...@roswellpark.org] 寄件日期: 2017年4月16日 上午 10:58 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Error in BUILD report (anamiR) It looks like this has been resolved on today's report: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/07/2017 02:21 PM, 王棣台 wrote: > Hi all, > > I got en error when it tries to create vignette in BUILD: > tokay2 Windows Server 2012 R2 Standard / x64 > > Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: > could not run statement: Lost connection to MySQL server during query > > But for Linux or Mac, it all works. > I have no idea how to solve this problem. > > Many thanks, > Ti-Tai > > [[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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in BUILD report (anamiR)
It looks like this has been resolved on today's report: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/07/2017 02:21 PM, 王棣台 wrote: > Hi all, > > I got en error when it tries to create vignette in BUILD: > tokay2 Windows Server 2012 R2 Standard / x64 > > Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: > could not run statement: Lost connection to MySQL server during query > > But for Linux or Mac, it all works. > I have no idea how to solve this problem. > > Many thanks, > Ti-Tai > > [[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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Error in BUILD report (anamiR)
Hi all, I got en error when it tries to create vignette in BUILD: tokay2 Windows Server 2012 R2 Standard / x64 Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: could not run statement: Lost connection to MySQL server during query But for Linux or Mac, it all works. I have no idea how to solve this problem. Many thanks, Ti-Tai [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
