[Bioc-devel] credential not recognized when git clone my packages
Hi all, I encountered the following error when trying to use git clone or git push for g...@git.bioconductor.org:packages/CRISPRseek # git clone g...@git.bioconductor.org:packages/CRISPRseek Cloning into 'CRISPRseek'... g...@git.bioconductor.org: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. Could you please let me know how to resolve this? FYI, it worked fine before the Bioc3.12 release. Thank you very much for your help! Best regards, Julie [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] activate BiocCredentials account issue
It works! Thank you! On Sat, Jan 9, 2021 at 7:21 PM Nitesh Turaga wrote: > Hi, > > This is because your account shows it is not activated. Please try to > activate your account > https://git.bioconductor.org/BiocCredentials/account_activation before > trying to log in. > > Best, > > Nitesh > > On 1/9/21, 5:58 AM, "Bioc-devel on behalf of Yuzhou Chang" < > bioc-devel-boun...@r-project.org on behalf of cyz931...@gmail.com> wrote: > > Thank you for the response! I tried to use upper case, but I still > failed > to activate the account. my package name is "IRISFGM" and the Github > link > is https://github.com/BMEngineeR/IRISFGM > > Bests, > Yuzhou > > On Fri, Jan 8, 2021 at 10:05 PM Martin Morgan > > wrote: > > > I am not sure but I think the app is case sensitive, and you have > entered > > Yuzhou.Chang. > > > > (also, in your email you didn't include the name of your package, > which > > made it a little harder to track your problem...) > > > > Martin > > > > On 1/8/21, 4:02 PM, "Bioc-devel on behalf of Yuzhou Chang" < > > bioc-devel-boun...@r-project.org on behalf of cyz931...@gmail.com> > wrote: > > > > Hi Bioconductor team, > > > > I was trying to activate my BiocCredential account. But it > showed " > > yuzhou.ch...@osumc.edu is not associated with a maintainer of a > > Bioconductor package." I am sure that I include > yuzhou.ch...@osumc.edu > > email > > address in the package DESCRIPTION file. But It does not work. > Did I > > miss > > anything else for the registration? > > > > Best regards, > > Yuzhou > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] activate BiocCredentials account issue
Hi, This is because your account shows it is not activated. Please try to activate your account https://git.bioconductor.org/BiocCredentials/account_activation before trying to log in. Best, Nitesh On 1/9/21, 5:58 AM, "Bioc-devel on behalf of Yuzhou Chang" wrote: Thank you for the response! I tried to use upper case, but I still failed to activate the account. my package name is "IRISFGM" and the Github link is https://github.com/BMEngineeR/IRISFGM Bests, Yuzhou On Fri, Jan 8, 2021 at 10:05 PM Martin Morgan wrote: > I am not sure but I think the app is case sensitive, and you have entered > Yuzhou.Chang. > > (also, in your email you didn't include the name of your package, which > made it a little harder to track your problem...) > > Martin > > On 1/8/21, 4:02 PM, "Bioc-devel on behalf of Yuzhou Chang" < > bioc-devel-boun...@r-project.org on behalf of cyz931...@gmail.com> wrote: > > Hi Bioconductor team, > > I was trying to activate my BiocCredential account. But it showed " > yuzhou.ch...@osumc.edu is not associated with a maintainer of a > Bioconductor package." I am sure that I include yuzhou.ch...@osumc.edu > email > address in the package DESCRIPTION file. But It does not work. Did I > miss > anything else for the registration? > > Best regards, > Yuzhou > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [R-pkg-devel] CRAN check texi2dvi failure
On Sat, 09 Jan 2021, Paul Gilbert writes: > I am trying to debug a problem that is appearing in the > linux and Solaris checks, but not Windows or Mac > checks, of my package tsfa as reported at > https://cran.r-project.org/web/checks/check_results_tsfa.html > > The problem is with re-building the vignette > ... > this is package 'tsfa' version '2014.10-1' > ... > checking re-building of vignette outputs ... [6s/9s] WARNING > Error(s) in re-building vignettes: > ... > Running 'texi2dvi' on 'Guide.tex' failed. > LaTeX errors: > ! LaTeX Error: \verb ended by end of line. > ... > > In responding to the threat of removal I have also > fixes some long standing warnings about adding imports > to the NAMESPACE. The new version builds with --as-cran > giving no errors or warnings with both R-devel on > win-builder (2021-01-07 r79806) and on my linux machine > (R 2021-01-08 r79812 on Linux Mint 19.3 Tricia). When I > submit it to CRAN the Windows build is OK but the same > error happens at the 'texi2dvi' step in the debian > vignette re-build. > > This seems to happens after an example that correctly > has a warning message (about Heywood cases). In my > linux build the the warning happens but the message > does not appear in the pdf output, so one possibility > is that the handling of the warning on the CRAN Unix > check machines fails to produce clean tex or suppress > output. Another possibility is that my build using > --as-cran is different from the actual CRAN build > options. For example, my 00check.log shows > ... > * checking package vignettes in ‘inst/doc’ ... OK > * checking re-building of vignette outputs ... OK > * checking PDF version of manual ... OK > * checking for non-standard things in the check directory ... OK > ... > > so I am not sure if it uses texi2dvi. (I haven't used > dvi myself for a long time.) > > I'm not sure how to debug this when I can't reproduce > the error. Suggestions would be appreciated. > > Paul Gilbert > When I run R CMD check on my Linux machine [*], I also do not get an error. But here is a guess: The error mentions \verb, and the LaTeX manual says that \verb should be followed by nonspace character. But in the vignette it is followed by a space. Maybe using \url in the vignette could fix the error? kind regards Enrico [*] R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.10 -- Enrico Schumann Lucerne, Switzerland http://enricoschumann.net __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Rd] URL checks
Is this a topic for Google Summer of Code? See https://github.com/rstats-gsoc/gsoc2021/wiki On 2021-01-09 12:34 p.m., Dirk Eddelbuettel wrote: > > The idea of 'white lists' to prevent known (and 'tolerated') issues, note, > warnings, ... from needlessly reappearing is very powerful and general, and > can go much further than just URL checks. > > I suggested several times in the past that we can look at the format Debian > uses in its 'lintian' package checker and its override files -- which are > used across thousands of packages there. But that went nowhere so I stopped. > > This issue needs a champion or two to implement a prototype as well as a > potential R Core / CRAN sponsor to adopt it. But in all those years no smoke > has come out of any chimneys so ... ¯\_(ツ)_/¯ is all we get. > > Dirk > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] URL checks
The idea of 'white lists' to prevent known (and 'tolerated') issues, note, warnings, ... from needlessly reappearing is very powerful and general, and can go much further than just URL checks. I suggested several times in the past that we can look at the format Debian uses in its 'lintian' package checker and its override files -- which are used across thousands of packages there. But that went nowhere so I stopped. This issue needs a champion or two to implement a prototype as well as a potential R Core / CRAN sponsor to adopt it. But in all those years no smoke has come out of any chimneys so ... ¯\_(ツ)_/¯ is all we get. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Demo for linking native routines between R packages
On Sat, Jan 9, 2021 at 4:45 PM Joshua Ulrich wrote: [...] > > That said, WRE does list two packages that register native routines > from other packages: > > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Linking-to-native-routines-in-other-packages > > There are a bunch more, see here: https://github.com/search?q=org%3Acran+R_RegisterCCallable=code Here is another very minimal example: https://github.com/DavisVaughan/cexport#cexport Gabor [...] [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Demo for linking native routines between R packages
Hi David, On Wed, Jan 6, 2021 at 4:00 AM Jitao David Zhang wrote: > > Dear Davis, Dirk, Jan, and r-devel subscribers, > > I hope you have had a good start in the new year. > > For your information: I have updated the GitHub repository to demonstrate > linking native routines between R packages ( > https://github.com/Accio/demo-linking-native), especially by listing the > prior art and the project by Davis to give the readers more background and > history of the topic. And I took the liberty to acknowledge your > contribution, criticism and help to improve this baby project. > > In any case, I wish there is a link from WRE to a small demo (not > necessarily mine!) where linking native routine is implemented in a > minimalistic example for teaching and demonstration purposes. That will > help people a lot in my opinion. > R-core will probably be reluctant to link to an external example they have very little control over. For example, what if the process changes and the external source doesn't get updated? That said, WRE does list two packages that register native routines from other packages: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Linking-to-native-routines-in-other-packages I'd be open to including a vignette in xts that discusses the process of linking to zoo. That would have the benefit of needing to be updated if the process changes. We can discuss off-list if you're interested in collaborating on it. > Best regards, > David > > -- > Jitao David Zhang > > http://jdzhang.me/ > m...@jdzhang.me > > Schützengasse 20 > 4125 Riehen, Switzerland > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] activate BiocCredentials account issue
Thank you for the response! I tried to use upper case, but I still failed to activate the account. my package name is "IRISFGM" and the Github link is https://github.com/BMEngineeR/IRISFGM Bests, Yuzhou On Fri, Jan 8, 2021 at 10:05 PM Martin Morgan wrote: > I am not sure but I think the app is case sensitive, and you have entered > Yuzhou.Chang. > > (also, in your email you didn't include the name of your package, which > made it a little harder to track your problem...) > > Martin > > On 1/8/21, 4:02 PM, "Bioc-devel on behalf of Yuzhou Chang" < > bioc-devel-boun...@r-project.org on behalf of cyz931...@gmail.com> wrote: > > Hi Bioconductor team, > > I was trying to activate my BiocCredential account. But it showed " > yuzhou.ch...@osumc.edu is not associated with a maintainer of a > Bioconductor package." I am sure that I include yuzhou.ch...@osumc.edu > email > address in the package DESCRIPTION file. But It does not work. Did I > miss > anything else for the registration? > > Best regards, > Yuzhou > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
