Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Gábor Csárdi
The expired cert was in my initial email. This is a CA cert. If you go to https://www.ssllabs.com/ssltest/analyze.html?d=svn.r-project.org and wait for the analysis, and then expand the certification paths, then you'll see three possible paths. (For most simulated clients.) Two are trusted, one is

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Gábor Csárdi
On Sat, May 30, 2020 at 11:02 PM Jeroen Ooms wrote: [...] > > What you need to do is replace the final certificate with this one > (just copy-paste the base64 cert): https://crt.sh/?d=1720081 .Then > restart the server. You can also export this from Keychain Access on macOS, btw. find "COMODO

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Jeroen Ooms
On Sat, May 30, 2020 at 11:40 PM Duncan Murdoch wrote: > > On 30/05/2020 5:23 p.m., Bob Rudis wrote: > > I've updated the dashboard (https://rud.is/r-project-cert-status/) > > script and my notifier script to account for the entire chain in each > > cert. > > You never posted which certificate

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Duncan Murdoch
On 30/05/2020 5:23 p.m., Bob Rudis wrote: I've updated the dashboard (https://rud.is/r-project-cert-status/) script and my notifier script to account for the entire chain in each cert. You never posted which certificate has expired. Your dashboard shows they're all valid, but the download

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Bob Rudis
The browsers still shouldn't trust it. The CA cert is expired. On Sat, May 30, 2020 at 5:23 PM Bob Rudis wrote: > > I've updated the dashboard (https://rud.is/r-project-cert-status/) > script and my notifier script to account for the entire chain in each > cert. > > On Sat, May 30, 2020 at 5:16

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Bob Rudis
I've updated the dashboard (https://rud.is/r-project-cert-status/) script and my notifier script to account for the entire chain in each cert. On Sat, May 30, 2020 at 5:16 PM Bob Rudis wrote: > > # A tibble: 13 x 1 >site > > 1 beta.r-project.org > 2 bugs.r-project.org > 3

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Bob Rudis
It's the top of chain CA cert, so browsers are being lazy and helpful to humans by (incorrectly, albeit) relying on the existing trust relationship. libcurl (et al) is not nearly as forgiving. On Sat, May 30, 2020 at 5:01 PM peter dalgaard wrote: > > Odd. Safari has no problem and says

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Bob Rudis
# A tibble: 13 x 1 site 1 beta.r-project.org 2 bugs.r-project.org 3 cran-archive.r-project.org 4 cran.r-project.org 5 developer.r-project.org 6 ess.r-project.org 7 ftp.cran.r-project.org 8 journal.r-project.org 9 r-project.org 10 svn.r-project.org 11 user2011.r-project.org 12

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Gábor Csárdi
The certificate itself is ok, but some other certificate higher up in the chain is not. It is possible to have multiple certificate chains, and only one needs to be successful for to accept the certificate. Some clients are able to use an alternate chain, so they are fine, but other clients do not

Re: [Bioc-devel] request

2020-05-30 Thread Kumar, Ashwath
Hi Martin, Thanks for the reply. Thank you so much for clearing this up. I think I got confused by the build time and the snapshot time. I believe I was in the middle of editing and changing the format in the DESCRIPTION file and I think that’s the reason I see the errors in the devel version

Re: [Bioc-devel] request

2020-05-30 Thread Martin Morgan
Please view the nightly build report http://bioconductor.org/checkResults/devel/bioc-LATEST/CSSQ/ compare the time that your package had a 'snapshot' taken for the build to start Snapshot Date: 2020-05-29 16:51:41 -0400 (Fri, 29 May 2020) and commit hash and date of the last commit included in

[Bioc-devel] Nightly update not updating my DESCRIPTION information

2020-05-30 Thread Kumar, Ashwath
Hello all, I am sorry for the duplicate email if any. I didn't realize that I had replied to another email instead of writing a new one. I am the maintainer for CSSQ (https://bioconductor.org/packages/release/bioc/html/CSSQ.html). I had made some changes (Re authorship and email addresses)

Re: [Bioc-devel] Package Submission Limbo

2020-05-30 Thread Martin Morgan
Sorry that your packages have not been reviewed more promptly. We try to have an initial review in two weeks, how long a full review takes depends on many factors, including complexity of the review process. Your own packages were I believe handled relatively efficiently initially. The release

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread peter dalgaard
Odd. Safari has no problem and says certificate expires August 16 2020, but I also see the download.file issue with 4.0.1 beta: > download.file("https://www.r-project.org;, tempfile()) trying URL 'https://www.r-project.org' Error in download.file("https://www.r-project.org;, tempfile()) :

Re: [Rd] r-project.org SSL certificate issues

2020-05-30 Thread Bob Rudis
Yep. It should switch to Let's Encrypt with the automated cert renewals ASAP. On Sat, May 30, 2020 at 4:17 PM Gábor Csárdi wrote: > > On macOS 10.15.5 and R-devel: > > > download.file("https://www.r-project.org;, tempfile()) > trying URL 'https://www.r-project.org' > Error in

[Bioc-devel] Package Submission Limbo

2020-05-30 Thread Chris Eeles
Hello Bioconductor team and community, My name is Christopher Eeles and I am a software developer in the Benjamin Haibe-Kains laboratory at Princess Margaret Cancer Research Centre in Toronto, Ontario, Canada. I am concerned due to inaction on the part of my reviewer for two of my package

[Rd] r-project.org SSL certificate issues

2020-05-30 Thread Gábor Csárdi
On macOS 10.15.5 and R-devel: > download.file("https://www.r-project.org;, tempfile()) trying URL 'https://www.r-project.org' Error in download.file("https://www.r-project.org;, tempfile()) : cannot open URL 'https://www.r-project.org' In addition: Warning message: In

Re: [Bioc-devel] request

2020-05-30 Thread Kumar, Ashwath
Hello all, I am the maintainer for CSSQ (https://bioconductor.org/packages/release/bioc/html/CSSQ.html). I had made some changes (Re authorship and email addresses) to the package last night. I made sure to push them to both the master and RELEASE_3_11 branches and confirmed the changes by

[Bioc-devel] request

2020-05-30 Thread Zhen Yang
Dear Biocondcutor admins: This is Zhen Yang from Fudan University, as the maintainer of the Bioconductor package of "FEM" (https://bioconductor.org/packages/release/bioc/html/FEM.html), I would like to make some update to this package. However, my last email (yangz...@picb.ac.cn) has been