similar to: Fwd: Fedora 31 System-Wide change proposal: Automatic R runtime dependencies

Thanks, Jos? and Elliott. I can help with reviews. I attach here a list of batches of CRAN packages to be rebuilt in order (batches separated by a blank line), and the script that generates it. Hope it helps. I?aki On Wed, 24 Jun 2020 at 11:35, Elliott Sales de Andrade <quantum.analyst at gmail.com> wrote: > > I could do so, but it wouldn't be until this weekend. > > Also,

R-BiocFileCache is now branched for f32 (finally). You should be able to build it if/when the PDC comes back up. Lotta random outages right now. Tom On Mon, Jul 6, 2020 at 10:40 AM Jos? Ab?lio Matos <jamatos at fc.up.pt> wrote: > On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote: > > Over the last several days, I've been working hard to get all of the > Fedora >

Over the last several days, I've been working hard to get all of the Fedora R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and R-rtracklayer, I believe everything is built and updated to the latest versions. And of those packages, they're all ready to go when Fedora infrastructure is working reliably

Hilko, This is an experimental patch showing how to split libguestfs into subpackages, so the main libguestfs0 doesn't depend on everything. Splitting packages only works for packages which are in the appliance (ie. in appliance/packagelist or supermin.d/packages). In this patch, only zfs-fuse [which previously caused trouble for users: https://bugs.launchpad.net/bugs/1053911] has been

Hi Jos?, On Thu, 25 Jun 2020 at 20:05, Jos? Ab?lio Matos <jamatos at fc.up.pt> wrote: > > On Friday, 26 June 2020 00.45.46 WEST Elliott Sales de Andrade wrote: > > Thanks for starting off builds. However, please be careful merging to > > master, as some packages were bumped and have incompatibilities that > > should not be put in stable releases. I will try to come

Oh, and maybe in this process we could add to all packages the requirement on R(ABI) = 4 that Tom implemented. On Wed, 24 Jun 2020 at 11:42, I?aki Ucar <iucar at fedoraproject.org> wrote: > > Thanks, Jos? and Elliott. I can help with reviews. > > I attach here a list of batches of CRAN packages to be rebuilt in > order (batches separated by a blank line), and the script that

Maybe Elliott? On Tue, 23 Jun 2020 at 15:01, Tom Callaway <spotrh at gmail.com> wrote: > > At this point, I simply don't have the time. > > Tom > > On Tue, Jun 23, 2020, 6:06 AM I?aki Ucar <iucar at fedoraproject.org> wrote: >> >> On Tue, 9 Jun 2020 at 10:21, I?aki Ucar <iucar at fedoraproject.org> wrote: >> > >> > > Given

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hi, I was installing hundreds of packages on a machine with a single call to install.packages() and after a long time the call to install.packages() finally returned with the following warnings and errors: Warning messages: 1: packages ?hgu133aprobe?, ?hgu95av2.db?, ?BSgenome.Celegans.UCSC.ce2?, ?BSgenome.Mmusculus.UCSC.mm10?, ?BSgenome.Dmelanogaster.UCSC.dm3.masked?,

On Tue, 11 Aug 2020 at 02:35, Elliott Sales de Andrade <quantum.analyst at gmail.com> wrote: > > Hi Jos?, > > On Mon, 10 Aug 2020 at 11:20, Jos? Ab?lio Matos <jamatos at fc.up.pt> wrote: > > > > I tried R2spec to create the spec files necessary to have Rcpparmadillo. > > > > I noticed that it has some issues, one example is that it placed some files

Hi there I am using libvirt+lxc on fedora I just upgraded a couple boxes from f29 to f31 i am running into rather puzzling glitches on one of the boxes, and am having a hard time trying to figure what exactly is going wrong symptom being that on the faulty box, my 3 containers startup correctly, but all of them stop after some random time shortly after (approx. in the 5-10 minutes) in some

Hi, Found in the man page for update.packages: repos: character vector, the base URL(s) of the repositories to use, i.e., the URL of the CRAN master such as ?"http://cran.r-project.org"? or its Statlib mirror, ?"http://lib.stat.cmu.edu/R/CRAN"?.Can be ?NULL? to install from local files (?.tar.gz? for source packages). - Using

Hi, R has been built against FlexiBLAS in rawhide [1, 2]. These are the R packages that need to be rebuilt: R-ape-0:5.4-2.fc33.x86_64 R-expm-0:0.999.4-7.fc33.x86_64 R-gee-0:4.13.20-4.fc33.x86_64 R-gss-0:2.2.2-3.fc33.x86_64 R-igraph-0:1.2.5-3.fc33.x86_64 R-msm-0:1.6.8-5.fc33.x86_64 R-preprocessCore-0:1.50.0-4.fc33.x86_64 R-qtl-0:1.46.2-4.fc33.x86_64 R-quadprog-0:1.5.8-5.fc33.x86_64 Could

On Thu, 25 Jun 2020 at 19:01, Jos? Ab?lio Matos <jamatos at fc.up.pt> wrote: > > On Wednesday, 24 June 2020 10.42.10 WEST I?aki Ucar wrote: > > Thanks, Jos? and Elliott. I can help with reviews. > > > > I attach here a list of batches of CRAN packages to be rebuilt in > > order (batches separated by a blank line), and the script that > > generates it. Hope

On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote: > Over the last several days, I've been working hard to get all of the Fedora > R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With > the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and > R-rtracklayer, I believe everything is built and updated to the latest > versions. And of those

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

I tried R2spec to create the spec files necessary to have Rcpparmadillo. I noticed that it has some issues, one example is that it placed some files irrespectively if they were present in the tar or not. One functionality that I think it would be nice to have would to update a given spec file with the updated dependencies. What do you think of this? Regards, -- Jos? Ab?lio [[alternative

On Tue, 21 Jul 2020 at 11:05, Jos? Ab?lio Matos <jamatos at fc.up.pt> wrote: > > On Friday, 3 July 2020 18.36.17 WEST I?aki Ucar wrote: > > Nice! What if we create a group "R" on Pagure and a repo > > "fedora-scripts" or something like that? > > I would like to improve the scripts but FWIW here it comes a rough version of > the script I used.

On Fri, 3 Jul 2020 at 19:03, Jos? Ab?lio Matos <jamatos at fc.up.pt> wrote: > > On Monday, 29 June 2020 13.46.02 WEST I?aki Ucar wrote: > > But the mass rebuild process is very different, because releng doesn't > > follow any particular order (they don't need to, because nothing > > really changed). > > > > The question is whether there is any tool