[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

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

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,

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

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

[Bioc-devel] Bioconductor 3.5 release: update NEWS

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

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

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

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

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

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

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

Re: [Rd] [bug] in cut.POSIXt(..., breaks = )

This is a simple fix. I just extract the part of cut.R that calculated breaks by a number, then convert the breaks format, provide the breaks manually to cut again. I used lubridate as_datetime because it's simpler. Of course it can be replaced with as.POSIXct. The breaks are always formatted in

Re: [R-pkg-devel] Help with Windows build failure

So actually 'Biarch: false’ didn’t help at all, same problem: https://win-builder.r-project.org/KhXyGby5Yhjm/ Does anyone know if the win builder machines have both 32-bit and 64-bit Python installed and in the PATH? -- Alexandre Sieira CISA, CISSP, ISO 27001 Lead Auditor "The truth is rarely

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

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

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

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

Re: [R-pkg-devel] Help with Windows build failure

Hi, Dirk. Thank you for responding. I do sympathize with your frustrations, due to the exact complexity you are mentioning and also my ignorance on how R packages compile on Windows, I had SnakeCharmR signal ‘OS_type: Unix’ for the longest time. The thing is that AFAIK this works on Windows

Re: [Rd] failure of make check-all

The warning that dummy_ii returns address of local variable is benign, this function is intended to do so. I've silenced it in R-devel. Tomas On 04/06/2017 03:51 PM, Therneau, Terry M., Ph.D. wrote: Peter, Retry how much of it? That is, where does it go in the sequence from svn up to

Re: [R-pkg-devel] R CMD check not finding my vignettes

Can you send the tarball please, I can take a look, Uwe On 07.04.2017 12:09, David Hugh-Jones wrote: Hi Uwe, Indeed yes, but my built tarball has got the files in inst/doc as shown. If I then run 'R CMD check' on that tarball, I get the error quoted. Is there something happening that I don't

Re: [R-pkg-devel] R CMD check not finding my vignettes

Hi Uwe, Indeed yes, but my built tarball has got the files in inst/doc as shown. If I then run 'R CMD check' on that tarball, I get the error quoted. Is there something happening that I don't understand? Incidentally, the tarball also has files in the vignettes directory: (a) the original .Rmd

Re: [Rd] Hyperbolic tangent different results on Windows and Mac

On Mon, Mar 27, 2017 at 12:33 PM, Jeroen Ooms wrote: > For future reference: > https://sourceforge.net/p/mingw-w64/mailman/message/35747206/ > > On Wed, Mar 22, 2017 at 2:12 PM, Jeroen Ooms wrote: > > This looks like a bug in mingw-w64 CRT. The

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

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

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

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

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

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

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

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

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

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

Re: [R-pkg-devel] maintainer built vignette

Please note that packages with a FOSS licences cannot have BuildVignettes: no Such FOSS Packages with a vignette (typically as pdf) need the sources that produced the vignette. Hence, if you really want to ship a vignette including code that is hardly executable on CRAN systems, reply to the

Re: [R-pkg-devel] R CMD check not finding my vignettes

I do not know devtools, but the vignette sources should be placed in ./vignettes and then R CMD build will put the files into the relevant places automatically. Best, Uwe Ligges On 07.04.2017 07:55, David Hugh-Jones wrote: Okay, so this got tumbleweeded... so should I file a bug? D On