[Bioc-devel] disable windows build for EiR development

Can you please disable the windows build for eiR in the development branch? Thanks. Kevin Horan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] openbabel 2.4.1

The package ChemmineOB depends on the external library OpenBabel. There is now a new version of it, version 2.4.1. Could you please install this on all three operating systems (just for devel )? You can find general OpenBabel build instructions here

Re: [Bioc-devel] git help

o bioc-devel so that it’s public and other maintainers/users know that there is an issue with your package. Best, Nitesh On Jan 3, 2018, at 2:31 PM, Kevin Horan wrote: Nitesh, I am one of the maintainers for the ChemmineR package on bioconductor. I have a bad duplicate commit problem I

Re: [Bioc-devel] git help

t, Nitesh On Jan 3, 2018, at 4:28 PM, Kevin Horan wrote: Nitesh, I tried to re-construct the repo starting from what is left in the SVN repository, but I couldn't get all the branches to come over and it just generally looks too different to easily replace the bioc repo.

Re: [Bioc-devel] git help

overlay all the commits including the new release on top of this (RELEASE_3_6). If you have any questions further on this, please ask before pushing to Bioconductor. Best, Nitesh On Jan 3, 2018, at 7:10 PM, Kevin Horan wrote: Nitesh, That sounds great, thanks. Kevin On 01/03/2018 01

Re: [Bioc-devel] git help

of RELEASE_3_6 branch commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e Author: Hervé Pagès Date: Mon Oct 30 12:39:24 2017 -0400 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch commit e3a8d2122a65305c478276e538faace277ea9ed6 Author: Kevin Horan Date: Fri Jun 30 20:12

Re: [Bioc-devel] git help

fixed. Please re-clone your repository. Best, Nitesh On Jan 8, 2018, at 8:39 PM, Kevin Horan wrote: Nitesh, Sorry, just saw your email now. You can go ahead and make those changes. Thanks for all your help. Kevin On 01/07/2018 11:22 AM, Turaga, Nitesh wrote: Hi Kevin, One last

[Bioc-devel] rsvg on mac

The ChemmineR build is failing on the mac due to a new dependency not being available, the package "rsvg". Would it be possible to install that on the mac build machine? Thanks. http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html Kevin

[Bioc-devel] release build of ChemmineR failing

The release version of ChemmineR is failing on windows. It seems to be a build script issue though, possibly something on your side. The package was building fine a few weeks ago and I have not modified it. Can you please have a look? Thanks. "C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e "libr

[Bioc-devel] release build of ChemmineR failing

The release version of ChemmineR is failing on windows. It seems to be a build script issue though, possibly something on your side. The package was building fine a few weeks ago and I have not modified it. Can you please have a look? Thanks. "C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e "libr

Re: [Bioc-devel] rsvg on mac

is on the rsvg landing page: > > https://cran.r-project.org/web/packages/rsvg/index.html > > Nothing we can do until CRAN makes them available. > > Valerie > > > On 02/07/2018 08:29 AM, Kevin Horan wrote: >> The ChemmineR build is failing on the mac due to a n

Re: [Bioc-devel] release build of ChemmineR failing

reporting the problem. It is not clear to me why do you > need a Makefile to build your vignette in first place, could you maybe > explain the motivation behind it? > > Cheers, > Andrzej > > > On Wed, Feb 7, 2018 at 5:37 PM, Kevin Horan > mailto:kho...@globalrecordings

Re: [Bioc-devel] rsvg on mac

tly > to the build system maintenance and really only serves a purpose in > this window of time where binaries are not available for devel. > > cc'ing Herve in case he has more to add. > > > Valerie > > > > > On 02/12/2018 12:25 PM, Kevin Horan wrote:

Re: [Bioc-devel] rsvg on mac

licts/instabilities when installing new components. Given that our resources are limited, it wouldn't make much sense that we do this for those CRAN packages for which the binaries are only temporarily unavailable. Cheers, H. On 02/13/2018 12:56 PM, Kevin Horan wrote: Valerie, Ok, I unde

Re: [Bioc-devel] rsvg on mac

tan in devel aren't available. You >> can see this on the rsvg landing page: >> >> https://cran.r-project.org/web/packages/rsvg/index.html >> <https://cran.r-project.org/web/packages/rsvg/index.html> >> >> Nothing we can do

Re: [Bioc-devel] rsvg on mac

ports. > I'm not sure why you are asking us (again) to install the rsvg system > dependency on the Mac builders. Did I misunderstand what you wanted? > > Valerie > > > On 05/09/2018 07:41 AM, Kevin Horan wrote: >> >> ��� Now that this past bioc release is do

[Bioc-devel] rsvg missing on merida2

My package, ChemmineR, is failing to build because of a missing package, rsvg. This package was there during the last release cycle, and is still present on the release build machines. I'm just wondering if this package is going to return or not? It's been about a week since the build broke

[Bioc-devel] current openbabel version on tokay2

te. Thanks. Kevin Horan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] ChemmineOB build failing on windows

Bioc, The build of ChemmineOB is failing on windows, which is also causing 3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to build the package on my own windows machine (Windows Server 2012 R2 Standard) without any error. I used R devel. The content of this package has not b

Re: [Bioc-devel] ChemmineOB build failing on windows

ndows. Kevin On 4/23/20 12:52 PM, Hervé Pagès wrote: On 4/23/20 12:45, Hervé Pagès wrote: On 4/23/20 10:45, Kevin Horan wrote: Bioc, The build of ChemmineOB is failing on windows, which is also causing 3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to build the package on m

[Bioc-devel] is it possible to disable i386 builds on bioconductor

    I have a package which randomly segfaults when running my unit tests only on windows i386, but never on x64, or any other OS. I can't imagine there are many out there still running i386 systems are there? Is it possible to just disable the i386 build on bioconductor so that the tests are

Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

ts, and you have a script to run the unit tests run_tests.R then something like    R -d valgrind -f run_tests.R may be productive. valgrind is slow so it pays to narrow the problem down as much as possible. Maartin On 2/8/21, 12:43 PM, "Bioc-devel on behalf of Kevin Horan" < bi

[Bioc-devel] missing packages on nebbiolo1

The packages eiR and ChemmineOB are failing to build because nebbiolo1 is missing the packages RUnit and RSQLite. Could those be installed please? Thank you. https://master.bioconductor.org/checkResults/3.17/bioc-LATEST/eiR/nebbiolo1-checksrc.html https://master.bioconductor.org/checkResult