[Bioc-devel] Error in BUILD report (anamiR)

2017-04-07 Thread 王棣台
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.

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

2017-04-07 Thread Gabe Becker
On Fri, Apr 7, 2017 at 12:46 PM, wrote: > On Fri, 7 Apr 2017, Hervé Pagès wrote: > > On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: >> >>> On Fri, 7 Apr 2017, Hervé Pagès wrote: >>> >>> > On 04/06/2017 03:29 AM, Michael Lawrence wrote: >>> > > On Thu, Apr 6, 2017 at 2:59 AM, Martin Morg

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

2017-04-07 Thread luke-tierney
On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: > On 04/06/2017 03:29 AM, Michael Lawrence wrote: > > On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan > > wrote: > > > On 04/06/2017 05:33 AM, Aaron Lun wrote

[Bioc-devel] Bioconductor 3.5 release: update NEWS

2017-04-07 Thread Obenchain, Valerie
Reminder to please update your NEWS files. These files are collated and included in the release announcement so it's worth polishing them up. Thanks. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the em

[Bioc-devel] Bioconductor 3.5 release: stop commits to 3.4 release branch

2017-04-07 Thread Obenchain, Valerie
Today we'll stop commits to the 3.4 release branch at COB EST. Please commit any last changes before that time. We'll wait one more day to get a final build report and then stop the release builds all together. Thanks. Valerie This email message may contain legally privileged and/or confidenti

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

2017-04-07 Thread Hervé Pagès
On 04/07/2017 05:37 AM, luke-tier...@uiowa.edu wrote: On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefull

[Bioc-devel] package 'msa' not building on veracruz2, but on toluca2 and other Mac OS systems

2017-04-07 Thread Ulrich Bodenhofer
Hi, The devel version of our package 'msa' currently does not compile on veracruz2 (R 3.4.0 alpha under OS X 10.11.6 El Capitan), but it seems to work on toluca2 (R-devel on OS X 10.9.5 Mavericks). I also checked on my Mac at home (R 3.3.3 under macOS 10.12.3 Sierra using the very latest vers

Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

2017-04-07 Thread Martin Morgan
On 04/07/2017 03:55 AM, Ramon Diaz-Uriarte wrote: Dear Martin and Valerie, I am not sure how to proceed here since the 14th is approaching and I still see this error (in both my package and at least one other package ---arrayQualityMetrics). I could comment out the plotting code for the vign

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

2017-04-07 Thread luke-tierney
On Fri, 7 Apr 2017, Hervé Pagès wrote: On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to

Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

2017-04-07 Thread Ramon Diaz-Uriarte
Dear Hervé, Thanks for your answer. I'll ignore those segfaults then. Best, R. On Fri, 07-04-2017, at 08:36:40, Hervé Pagès wrote: > Hi Ramon, > > It doesn't seem that this segfault occurs in ADaCGH2 so you can > ignore it. I can't be 100% sure but I actually expect it to go away > when thin

Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

2017-04-07 Thread Hervé Pagès
Hi Ramon, It doesn't seem that this segfault occurs in ADaCGH2 so you can ignore it. I can't be 100% sure but I actually expect it to go away when things are sorted out with the new El Capitan binaries. Unfortunately it's not something we fully control so let's wait and see... Cheers, H. On 04

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

2017-04-07 Thread Hervé Pagès
On 04/06/2017 03:29 AM, Michael Lawrence wrote: On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I get a lot of warnings because the tool seems to consider that extracting an attribute (wi

Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

2017-04-07 Thread Ramon Diaz-Uriarte
Dear Martin and Valerie, I am not sure how to proceed here since the 14th is approaching and I still see this error (in both my package and at least one other package ---arrayQualityMetrics). I could comment out the plotting code for the vignette and examples when running on El Capitan. Is thi

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-07 Thread Rainer Johannes
Hi Herve > On 7 Apr 2017, at 07:42, Hervé Pagès wrote: > > Hi Johannes, > > Thanks for contacting the developers of the packages affected by this > change. FWIW Pbase is also affected (didn't see it in your list): > I fixed Pbase - changes have not been committed to Bioc yet (asked Laurent fo