Re: [Bioc-devel] BiocManager not installing latest release version of DepecheR

2019-11-14 Thread Aaron Lun
I would assume that "BiocManager::install()" won't update an existing set of BioC packages unless explicitly prompted. If that's the case, shouldn't the instructions at http://bioconductor.org/install/ specify "BiocManager::install(version='3.10')"? On Wed, Nov 13, 2019 at 1:04 PM Shepherd, Lori

[Bioc-devel] R CMD build error for new package.

2019-11-14 Thread Kumar, Ashwath
Hello, I am trying to submit a new package to Bioconductor and received the automated R CMD check report and it seems to have failed. For reference the R CMD build error is from the creating vignette step. Quitting from lines 56-61 (CSSQ.Rmd) Error: processing vignette 'CSSQ.Rmd' failed with

Re: [Rd] class() |--> c("matrix", "arrary") [was "head.matrix ..."]

2019-11-14 Thread Pages, Herve
On 11/14/19 05:47, Hadley Wickham wrote: > On Sun, Nov 10, 2019 at 2:37 AM Martin Maechler > wrote: >> >>> Gabriel Becker >>> on Sat, 2 Nov 2019 12:37:08 -0700 writes: >> >> > I agree that we can be careful and narrow and still see a >> > nice improvement in behavior.

Re: [R-pkg-devel] Using FORTRAN libraries and compiler options

2019-11-14 Thread Dirk Eddelbuettel
On 14 November 2019 at 16:42, Rampal S. Etienne wrote: | I couldn't find a call to dgemm in the mvtnorm package. Do you have | other suggestions for packages that may be calling this? The mirror of CRAN at GitHub allows convenient search. Looking for 'user:cran dgemm' give 620+ code hits; the

Re: [Rd] class() |--> c("matrix", "arrary") [was "head.matrix ..."]

2019-11-14 Thread Hadley Wickham
On Sun, Nov 10, 2019 at 2:37 AM Martin Maechler wrote: > > > Gabriel Becker > > on Sat, 2 Nov 2019 12:37:08 -0700 writes: > > > I agree that we can be careful and narrow and still see a > > nice improvement in behavior. While Herve's point is valid > > and I understand his

Re: [Bioc-devel] Python Z trees to hclust

2019-11-14 Thread Bernat Gel Moreno
Hi Peter, Thanks for the advice and pointers to the relevant files. After reading the Fortran code and thinking about it I ended up coding from scratch my own pure R function to set the plotting order of an hclust object. It might not be as fast as the Fortran implementation, but it works