[Rd] R CMD build errors if files cannot be moved, even if they are in Rbuildignore

When a package is built it is first moved to a temporary directory (lines 962-980 in build.R). However, this moves *all* files to the temporary directory, even those in Rbuildignore; only later (lines 997-1024) are Rbuildignore files excluded. The problem with this approach is that some files in

Re: [R-pkg-devel] Announcing Bazel for R packages

On 22 September 2017 at 00:28, Siddhartha Bagaria wrote: | I agree the open source version has not been around for that long. | | But... It is picking up adoption within many other companies this year: | https://github.com/bazelbuild/bazel/wiki/Bazel-Users | | And some adoption in academia as

Re: [Bioc-devel] Cannot clone PhenStat

Fill out this form https://goo.gl/forms/eg36vcBkIUjfZfLe2 using the id I will forward to you separately. The form is processed daily, so there will be short delay before access is available. See http://bioconductor.org/developers/how-to/git/ for additional instructions. Martin On

Re: [R-pkg-devel] Announcing Bazel for R packages

I agree the open source version has not been around for that long. But... It is picking up adoption within many other companies this year: https://github.com/bazelbuild/bazel/wiki/Bazel-Users And some adoption in academia as well, e.g. http://drake.mit.edu/bazel.html On Thu, 21 Sep 2017 at

Re: [R-pkg-devel] Announcing Bazel for R packages

On 21 September 2017 at 22:40, Siddhartha Bagaria wrote: | We have released some Bazel rules for R packages. | https://github.com/grailbio/rules_r | | What is Bazel? | | Bazel is an industry tested build system that can be | used for continuous integration and testing in

Re: [Bioc-devel] Cannot clone PhenStat

Hi list, Can anyone provide guidance for this? My colleague and I would like to get the latest version in place before the 3.6 release. How can we get access to the repository now that the original maintainer has left? Do we need to contact someone else? thanks, Jeremy On 19/09/2017

Re: [R-pkg-devel] loadMethod() not available with Rscript

On 20 September 2017 at 16:44, Martyn Plummer wrote: | On Wed, 2017-09-20 at 09:45 -0500, Dirk Eddelbuettel wrote: | > Thierry, | > | > This has always been a considerable puzzle, and the source of some amusement, | > to me. It is a clear design bug in Rscript because _code that would | >

[R-pkg-devel] Announcing Bazel for R packages

Hello, We have released some Bazel rules for R packages. https://github.com/grailbio/rules_r What is Bazel? Bazel is an industry tested build system that can be used for continuous integration and testing in large monorepos (multiple software libraries as part of one

[Bioc-devel] Announcing Bazel for R packages

[x-post from r-package-devel] Hello, We have released some Bazel rules for R packages. https://github.com/grailbio/rules_r What is Bazel? Bazel is an industry tested build system that can be used for continuous integration and testing in large monorepos (multiple

Re: [Bioc-devel] Unable to push to https://git.bioconductor.org/packages/GenomicTuples

Doh, I literally spotted that the second I hit send. Sorry for the noise and thanks! On Thu, 21 Sep 2017 at 13:55 Turaga, Nitesh wrote: > Hi Peter, > > If you notice, > > On Sep 21, 2017, at 1:53 PM, Peter Hickey wrote: > > Hi Nitesh, > >

Re: [Bioc-devel] Unable to push to https://git.bioconductor.org/packages/GenomicTuples

I think my outlook messed up the formatting on my previous email, apologies. The origin is supposed to be g...@git.bioconductor.org:packages/GenomicTuples. You are currently using HTTP and are not able to push as a result of that. You can change your remote, git remote set-url origin

Re: [Bioc-devel] Unable to push to https://git.bioconductor.org/packages/GenomicTuples

Hi Peter, If you notice, On Sep 21, 2017, at 1:53 PM, Peter Hickey > wrote: Hi Nitesh, I'm unable to push changes to the GenomicTuples package to the BioC git host. $ git push fatal: remote error: FATAL: W any packages/GenomicTuples

[Bioc-devel] Unable to push to https://git.bioconductor.org/packages/GenomicTuples

Hi Nitesh, I'm unable to push changes to the GenomicTuples package to the BioC git host. $ git push fatal: remote error: FATAL: W any packages/GenomicTuples nobody DENIED by fallthru (or you mis-spelled the reponame) Following the FAQ (http://bioconductor.org/developers/how-to/git/faq/) I've

Re: [Rd] calling R API functions after engine shutdown

Calling R_ReleaseObject in a C++ destructor is not reliable - it can be bypassed by a non-local return, such as an error. Generally in R one cannot use C++ destructors reliably for anything that the R runtime wouldn't do on its own in case of a non-local return. A destructor that calls just

[Rd] calling R API functions after engine shutdown

Hi! We’ve recently come across an example where a package (minqa) creates an Rcpp Function object in a static variable. This causes R_ReleaseObject to be called by the destructor at a very late point in time - as part of the system exit function: static Function cf("c"); I’m wondering if that

Re: [Bioc-devel] maintain immunoClust

Hi, We have 2 keys on file for your package immunoClust, one is an ssh-dds key and the other is an ssh-rsa key, starting with: ssh-dss B3NzaC1kc3MAAACBAONrxcV+Ri07bvwAPLpPmzi8YvTiRQlgvT8P3P/wnFMwBUP4vmA9V2FTGSnYGJEURTznBrVvPgCy6 ssh-rsa

[Bioc-devel] maintain immunoClust

Hi all, I am maintaining the immunoClust package and need to get access to it. The SSH key is send to you via the formular several days ago. But until now I get an Permission denied (public key) message when I try to clone the repository. Thank you for help, Till Till S�rensen,

[Bioc-devel] Deadline for Packages and Data Bioc3.6

Hi Bioconductor Community, The release of Bioconductor 3.6 will be Tuesday, October 31. Please see the schedule for details: http://bioconductor.org/developers/release-schedule/ Some important deadlines that are coming up: Friday October 6 is the deadline for new package submissions. Packages

Re: [Rd] unpackPkgZip: "unable to move temporary installation" due to antivirus

This windows/anti-virus problem has been worked around in R-devel 73329. Thanks to Mike for reporting this and testing the changes. Best Tomas On 09/13/2017 01:40 AM, Mike Toews wrote: Hi, Me and an office colleague on Microsoft Windows 10 PCs are having difficulty installing any package.