[Bioc-devel] XML package on tokay2

Some Bioconductor packages depend on CRAN XML package. For example http://bioconductor.org/checkResults/devel/bioc-LATEST/mzID/tokay2-install.html This dependency is not available on tokay2 machine. I also noticed this XML package is orphaned on CRAN. What are the plans regarding this core

[Bioc-devel] whitespace or or end of line format conflict in git merge

While resolving conflicts according to this protocol https://master.bioconductor.org/developers/how-to/git/resolve-conflicts/ I ran into a quite a number of seeming duplications of the file content between HEAD and upstream/master. It looks like either some sort of whitespace or end of line

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Yes! Now it works. Thank you! On Tue, Oct 10, 2017 at 2:01 PM Vladislav Petyuk <pet...@gmail.com> wrote: > Done. Do you see it? > > On Tue, Oct 10, 2017 at 1:37 PM Turaga, Nitesh < > nitesh.tur...@roswellpark.org> wrote: > >> I believe you have the wrong form. &

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

ster.bioconductor.org/developers/how-to/git/faq/ (point #3) > > > Best, > > Nitesh > > > > > On Oct 10, 2017, at 4:30 PM, Vladislav Petyuk <pet...@gmail.com> wrote: > > > > Here is the link I was using. > > > https://docs.google.com/forms/d/e/1FAIpQL

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Here is the link I was using. https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform On Tue, Oct 10, 2017 at 1:28 PM Vladislav Petyuk <pet...@gmail.com> wrote: > done > > On Tue, Oct 10, 2017 at 1:24 PM Turaga, Nitesh < > nitesh.t

Re: [Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

l. > > > > Nitesh > > > >> On Oct 10, 2017, at 4:10 PM, Vladislav Petyuk <pet...@gmail.com> wrote: > >> > >> pet...@gmail.com > >> > >> On Tue, Oct 10, 2017 at 1:08 PM Turaga, Nitesh < > nitesh.tur...@roswellpark.org>

Re: [Bioc-devel] mzR: pwiz is now the default backend

Are there going to be any noticeable changes for the package users? Does it break compatibility? Do I need to install something extra (like ProteoWizard)? On Tue, May 23, 2017 at 9:10 AM Laurent Gatto wrote: > > Dear developer, > > For those who use mzR to access raw mass

[Bioc-devel] error related to kmp_runtime.cpp(6480)

My package passes all the builds except OS X. http://www.bioconductor.org/checkResults/devel/bioc-LATEST/MSnID/veracruz2-buildsrc.html Interestingly, the build goes just fine (with the same arguments) on my laptop, which is OS X 10.12.3. Given that kmp_runtime.cpp is from OpenMP and chunk 25 in

Re: [Bioc-devel] Challenges with package installation on fresh R

Dan, Herve, thanks for taking a look. This gives some leads. On Thu, Jun 25, 2015 at 7:26 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Hervé Pagès hpa...@fredhutch.org To: Vladislav Petyuk pet...@gmail.com, Dan Tenenbaum dtene...@fredhutch.org Cc

Re: [Bioc-devel] Challenges with package installation on fresh R

, Vladislav Petyuk pet...@gmail.com wrote: Dan, Herve, thanks for taking a look. This gives some leads. On Thu, Jun 25, 2015 at 7:26 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Hervé Pagès hpa...@fredhutch.org To: Vladislav Petyuk pet...@gmail.com

Re: [Bioc-devel] Challenges with package installation on fresh R

the issue posted https://github.com/hadley/devtools/issues/864 On Fri, Jun 26, 2015 at 2:36 PM, Vladislav Petyuk pet...@gmail.com wrote: It looks like devtools::package_deps is forcing type to be binary. if (identical(type, both)) { type - binary } devtools::package_deps

Re: [Bioc-devel] Challenges with package installation on fresh R

Just added the full output to the README.md file https://github.com/vladpetyuk/toypack/blob/master/README.md On Thu, Jun 25, 2015 at 12:28 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Vladislav Petyuk pet...@gmail.com To: Bioc-devel@r-project.org

Re: [Bioc-devel] Challenges with package installation on fresh R

). On Thu, Jun 25, 2015 at 1:08 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Vladislav Petyuk pet...@gmail.com To: Dan Tenenbaum dtene...@fredhutch.org Cc: Bioc-devel@r-project.org Sent: Thursday, June 25, 2015 12:55:56 PM Subject: Re: [Bioc-devel

[Bioc-devel] Challenges with package installation on fresh R

Hi all, I ran into a problem with dependencies during package installation. Here is an example that intends to reproduce the problem https://github.com/vladpetyuk/toypack Majority of the packages (in Imports/Depends/Suggests and their Imports/Depends/Suggests) install just fine. However there is

Re: [Bioc-devel] reproducible with mclapply?

:25 PM, Vladislav Petyuk pet...@gmail.com wrote: There are different ways set.seed can be used. The way it is suggested on the aforementioned stackoverflow post is basically a two stage process. First seed is provided by a user (set.seed(1)). That is user can change the outcome from run

Re: [Bioc-devel] reproducible with mclapply?

There are different ways set.seed can be used. The way it is suggested on the aforementioned stackoverflow post is basically a two stage process. First seed is provided by a user (set.seed(1)). That is user can change the outcome from run to run. Based on that seed, a vector of randomized seeds

[Bioc-devel] Mavericks Not Supported message

Hi, Could someone tell me about the possible causes of ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... message for OS X Mavericks? http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Mavericks is the OS I developed my package on. Thank you, Vlad [[alternative HTML version