Re: [Bioc-devel] BiocCredentials email issue

2020-03-29 Thread Turaga, Nitesh
Hi, I've reset your email to mdwilker...@outlook.com Please activate your BiocCredentials account to gain access to your account. https://git.bioconductor.org/BiocCredentials/account_activation/ Best. Nitesh On 3/28/20, 11:52 AM, "Bioc-devel on behalf of Matt Wilkerson" wrote: Hello

Re: [Bioc-devel] Re phospphonormalizer package

2020-03-29 Thread Turaga, Nitesh
I changed your email address, please try again now with sohrab.sar...@blueprintgenetics.com. On 3/28/20, 12:02 PM, "Bioc-devel on behalf of Sohrab Saraei" wrote: I have been trying to log in to my bioconductor account for sometime now, but unfortunately no luck. I trie to reset my

Re: [Rd] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

2020-03-29 Thread Paul Murrell
Hi I have created an R branch that contains a potential fix ... https://svn.r-project.org/R/branches/R-symfam/ This allows, for example, ... cairo_pdf(symbolfamily="OpenSymbol") ... to specify that the OpenSymbol family should be used as the "symbol" font (e.g., for "plotmath") in R. This

Re: [Rd] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

2020-03-29 Thread Iñaki Ucar
Thanks, Paul. I've created a bug report to keep track of this (https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17748), and taken the liberty of adding you to CC. We'll need to cherry-pick the fix for R 3.6.3 in Fedora 31. Iñaki On Sun, 29 Mar 2020 at 21:15, Paul Murrell wrote: > > Hi > >

Re: [Rd] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

2020-03-29 Thread Paul Murrell
Hi Thanks for your input on this Iñaki and Nicolas. I am starting testing an R fix for this problem today. As suggested, the plan is to allow the R user to specify a font family other than "symbol" for plotmath output (or, more generally, in R parlance, for 'font=5' or 'fontface=5') on a

Re: [Rd] is.vector could handle AsIs class better

2020-03-29 Thread Gabriel Becker
Jan, I believe it's because it has "a non-NULL attribute other than names" as per the documentation. In this case its class of "AsIs". Best, ~G On Sun, Mar 29, 2020 at 6:29 AM Jan Gorecki wrote: > Dear R-devel, > > AsIs class seems to be well handled by `typeof` and `mode` function. > Those

[Bioc-devel] Docker image submission

2020-03-29 Thread Carlos Biagi Jr
Dear all, I tried to submit a docker image right now but I received an error message saying that the repository does not have a DESCRIPTION file. I followed all the steps in https://github.com/Bioconductor/bioconductor_docker/blob/master/best_practices.md link. How should I proceed? Because in

[Rd] is.vector could handle AsIs class better

2020-03-29 Thread Jan Gorecki
Dear R-devel, AsIs class seems to be well handled by `typeof` and `mode` function. Those two functions are being referred when explaining `is.vector` behaviour in manual. Yet `is.vector` does not seem to be handling AsIs class the same way. is.vector(1L) #[1] TRUE is.vector(I(1L)) #[1] FALSE Is

Re: [Rd] status of Java & rJava?

2020-03-29 Thread Spencer Graves
  I spoke too soon in saying that everything worked with OpenJDK:  "R CMD check Ecfun_0.2-4.tar.gz" using "https://github.com/sbgraves237/Ecfun; worked fine on my Mac but failed with "error: DLL 'rJava' not found: maybe not installed for this architecture?" under Windows 10. 

Re: [Rd] status of Java & rJava?

2020-03-29 Thread Adrian Trapletti
Simon, Java is still one of the most popular languages out there, in particular in large organizations. See e.g. https://www.tiobe.com/tiobe-index/ . However, there has been a lot of confusion because of Oracle's licencing change in 2019. But the good news is, there are more alternatives than

Re: [Rd] status of Java & rJava?

2020-03-29 Thread Spencer Graves
On 2020-03-28 23:07, Prof Brian Ripley wrote: On 29/03/2020 04:07, Simon Urbanek wrote: Spencer, you could argue that Java is dead since Oracle effectively killed it by removing all public downloads, but if you manage to get hold of a Java installation then it works just fine with R. To