R-hub/community

AlanInglis

@AlanInglis

Hey all. I'm new to this and Im confused as to how to interpret the error results from my tests. It appears that the errors are outside of my control!?
https://builder.r-hub.io/status/vivid_0.1.0.tar.gz-cf5dc8a8606447ea9e62a83aa8ae436f

CLR

@clozanoruiz

@AlanInglis not vompletely sure, but seems that at least one of the sysreqs (udunits) can't be installed? Perhaps because it needs to be something like udunits-dev in sysreqdb? @gaborcsardi ?

Gábor Csárdi

@gaborcsardi

The proj4 dependency failed to install:

4924#> configure: error: libproj and/or proj.h/proj_api.h not found in standard search locations.
4925#> *** Install PROJ library and if necessary set PKG_CPPFLAGS/PKG_LIBS accordingly.
4926#> ERROR: configuration failed for package ‘proj4’
4927#> * removing ‘/home/docker/R/proj4’

Even though libproj-dev is installed. You can try to install proj4 in the rhub/ubuntu-gcc-release container, to see why this fails.

Gábor Csárdi

@gaborcsardi

Oh, @clozanoruiz is actually right, it is a sysreqs error for udunits.

Should be fixed with r-hub/sysreqsdb@88a1bc2

AlanInglis

@AlanInglis

thanks for all your help

Dr. CB

@cbdsabc_twitter

Is there a place to see if updates were made to the subsystems - it seems as if the xml2 system library went missing sometime today - all my builds are failing for various reasons related to xml2 - for instance httr and biomaRt can't install without it.

Gábor Csárdi

@gaborcsardi

System libraries like libxml2 should be installed as needed. If they are not, please open an issue. I don't think httr needs libxml2, but biomaRt might.

Lluís

@llrs

Hi! Many thanks for this great service! It has helped me in several submissions to CRAN.

Is there some way to know which environmental variables accepted by R does R-hub use?

Gábor Csárdi

@gaborcsardi

It uses all of them that you pass in env_vars.

Lluís

@llrs

Oh, thanks! Now I see I had a PR modifying env_vars, so I knew that in the past

Tim Keitt

@thk686

After a bit of a hiatus, I am resubmitting a package, so my knowledge is a bit out of date. I used the rhub package as recommended and get this output:

E checking whether package 'kdtools' can be installed (1m 56.1s)
Installation failed.
See 'C:/Users/USERJagAGNdIct/kdtools.Rcheck/00install.out' for details.

Is there a way to find the contents of the file 00install.out?

Tim Keitt

@thk686

I assume it lives on the windows build machine but is there a way to access it from rhub?

Gábor Csárdi

@gaborcsardi

R-hub sends an email, which has a link to "artifacts". The artifacts have the 00install.out file.

Tim Keitt

@thk686

Ah, perfect. Thanks. I did not get the file for some reason -- sometimes our mail system blocks things even before reaching spam. I did get one from the win-builder site however.

Gábor Csárdi

@gaborcsardi

If you didn't get an email from R-hub, but you know the id of the check (you can list your last checks with rhub::list_my_checks()), then you can go to https://artifacts.r-hub.io/<id> to see the artifacts. E.g. https://artifacts.r-hub.io/pak_0.1.2.9001.tar.gz-d05e09824dc940119ecef9704ed82810 (this is not an actual id, but they have this form).

You can also use the ids in the output of list_my_checks() to get the artifacts URL. E.g.:

❯ chk <- rhub::get_check("badcafe")
❯ chk$urls()$artifacts
[1] "https://artifacts.r-hub.io/pkgdepends_0.1.1.9000.tar.gz-badcafe........"

Tim Keitt

@thk686

Nice

Vittorio Orlandi

@vittorioorlandi

Hi, I'm running check_for_cran on a package of mine and on Fedora Linux distributions (one of which is a default platform for check_for_cran) I'm getting: configure: error: GNU MP not found, or not 4.1.4 or up, see http://gmplib.org when trying to install gmp, a dependency. I had this dependency in a previous version of the package, which I believe I also checked using check_for_cran (or something similar within rhub) without issue.

I’m not exactly sure what to do here, as the fix would be on the Linux environment side it seems. I imagine I could find some Linux distribution on which this passes, but that seems unsatisfying and CRAN will still probably pick up on it when I submit. I’d greatly appreciate any recommendations.
Thank you,
Vittorio

Gábor Csárdi

@gaborcsardi

I am afraid you'd need to show an example that fails. Thanks!

Vittorio Orlandi

@vittorioorlandi

Sorry about that. I've created a toy package to illustrate that does practically nothing but import gmp. When I run rhub::check_for_cran() within the package, I get a PREPERROR from the test on the fedora-clang-devel platform. The check log and full description of the error can be found at: https://builder.r-hub.io/status/testProj_0.0.0.9000.tar.gz-5cc68ccedb7e4268ac4803a596edff93 under the Installing Package Dependencies heading. Apologies if that's not what you were looking for.

Gábor Csárdi

@gaborcsardi

Thanks, should be fixed here: r-hub/sysreqsdb@a32cb32
A minimal package is a great reproducible example, thanks! For these kind of failures, it is enough if you point us to the log of the failing build.

Vittorio Orlandi

@vittorioorlandi

Great, thanks very much!

Naeem Khoshnevis

@Naeemkh

Thanks for developing and maintaining such an amazing tool. I get PREPERROR on Ubuntu Linux 20.04.1 LTS, R-devel, GCC (ubuntu-gcc-devel),
Error : Bioconductor does not yet build and check packages for R version 4.2; see https://bioconductor.org/install.
Is it expected? Should I submit an issue?

Gábor Csárdi

@gaborcsardi

That error message is printed but it should be ignored. The real error is probably elsewhere. Can you point me to the log?

Naeem Khoshnevis

@Naeemkh

Thanks. Here is the log: https://builder.r-hub.io/status/original/CausalGPS_0.2.6.tar.gz-90c802066279458794d3b0c1aecfa798

Naeem Khoshnevis

@Naeemkh

Hi @gaborcsardi, I was wondering if you have any updates on the PREPERROR issue. Thanks.

Naeem Khoshnevis

@Naeemkh

I am trying to submit a package to CRAN. It passes all system's tests/checks (as far as I tested), for example,

Debian Linux, R-devel, clang, ISO-8859-15 locale (debian-clang-devel)
Fedora Linux, R-devel, clang, gfortran (fedora-clang-devel)
macOS 10.13.6 High Sierra, R-release, brew (macos-highsierra-release)
Windows Server 2008 R2 SP1, R-devel, 32/64 bit (windows-x86_64-devel).

However, it returns PREPERROR on Ubuntu Linux 20.04.1 LTS, R-devel, GCC (ubuntu-gcc-devel). The error message is:
Error: No such container: CausalGPS_0.2.5.9000.tar.gz-cc24a1be31644c2a888e959ece4d3211-1.
Does anyone have any thoughts about this? And Based on your experience, is it safe to submit it to CRAN?

John H Maindonald

@jhmaindonald

I am getting the error:

I am getting the error.

validate_email('john@statsresearch.co.nz')
Error in curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired
Odd thing is, I did have this working whenI submitted a package to r-hub a few days ago.
john@statsresearch, which I used for the package, is now a validated email address on
github, it was not at the time.

John H Maindonald

@jhmaindonald

Near the end of the file
https://builder.r-hub.io/status/original/qra_0.2.5.tar.gz-26a96b02650e9573feb530cd5f109fe5
is the message
See
‘/export/home/XBeQbXx/qra.Rcheck/00check.log’
for details.
How do I get to see that file?
I have been quite unable to do anything with rhub from the command line. Any help in dealing with the SSL certificate issue noted in my previous message would be very welcome.

Gábor Csárdi

@gaborcsardi

The SSL certificate problem is because of an old openssl or libressl library bug. Is this Linux or macOS? Which version of macOS?

John H Maindonald

@jhmaindonald

Thanks. macOS Mojave 10.14.6

Gábor Csárdi

@gaborcsardi

Yeah, so this is a bug in the libressl that comes with mojave and apple did not fix it. You can fix it manually. You need to edit /etc/ssl/cert.pem (make a backup copy first), and remove the cert that expired on Sep 30 14:01:15 2021 GMT. Its entry starts with ## Digital Signature Trust Co., until the end of the cert, the first -----END CERTIFICATE----- line.

you can test it with something like

curl -v https://builder.r-hub.io >/dev/null

from a shell. This should fail before, and not fail after your edit.

Depending on which browser you use, you might need to update that as well, at least I had to update chrome.

Gábor Csárdi

@gaborcsardi

^ this is the system curl at /usr/bin/curl, if you use curl from brew or another source, that probably does not need this fix. But R does need it, nevertheless.

John H Maindonald

@jhmaindonald

Thanks a lot. That worked. In emacs I had to do C-x C-f /sudo::/etc/ssl/cert.pem

Ramanth Addala

@Ramanth

Hi Everyone,
Im trying to publish a package to CRAN and it failed with Error that the installation of package is not successful on Solaris OS.
I tried R-Hub later to test and i got the run result after 12Hrs, and the installation has no issues.

Is there a difference on the Solaris Installation wrt CRAN and R-Hub?

Gábor Csárdi

@gaborcsardi

Yes, probably several differences. How does your package fail, and how did you try R-hub?

Ramanth Addala

@Ramanth

in the CRAN website , it shows it failed installation as above

and i uploaded the package to the rhub builder website and i chose the solaris option

Gábor Csárdi

@gaborcsardi

If you click on ERROR it will show you why it failed to install.

Which Solaris option? There are two.

Which package is this?

Ramanth Addala

@Ramanth

oh ya, on clicking the ERROR i navigated to a page, but that doesnt have any info its broken, it gave me a 404 page
i dropped a mail to cran system admin, yet to get a reply from them

And on the R-Hub its the second option
Oracle Solaris 10, x86, 32 bit, R release, Oracle Developer Studio 12.6

Ramanth Addala

@Ramanth

Which package is this?
factset.protobuf.stach.v2

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