R-hub/community

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

Ramanth Addala

@Ramanth

Hi @gaborcsardi any idea on this issue?

Gábor Csárdi

@gaborcsardi

I was hoping that you could get any information on why/how if failed on CRAN?

Alexander Murph

@sirmurphalot

I pushed an update to an R package that I wrote to CRAN. How long until this update shows up on GitHub's CRAN mirror? (the update hit cran 12/13)

Gábor Csárdi

@gaborcsardi

It will show up when I fix the failing update script: https://github.com/r-hub/cranatgh/actions

Gevengene

@Gevengene

Hi guyz, I am having some issues in using Gitter in Rstudio. can some one guide me? i.e.Error in .getColonyPeaks2(sum.y, n = nrow, plot) : Not enough peaks found.

Does anyone know how to solve this?

Ramanth Addala

@Ramanth

This is related to my earlier issue that the package failing on solaris os
We tried checking it again and this time we got failure on rhub with above error

and the same package works fine in other os/platforms , we are assuming that this is because of unavailbility of a depdency RProtobuf for solaris platform

is our assumption correct?
How should we upload to cran in such cases? any guidance would be helpful

Gábor Csárdi

@gaborcsardi

CRAN does not check packages on Solaris any more.

Ramanth Addala

@Ramanth

Thats news!! and is this in effect and any annoucement for this

Matt Jones

@mbjones

Hey folks, I am having a trouble with build failures due to remote dependencies that should be working fine. In particular, when I try to build on linux platforms, such as debian, the build fails because it can't build package dependencies that seem to have C-library requirements from other packages. Here's the error I see:

```ERROR: dependencies ‘redland’, ‘XML’ are not available for package ‘datapack’

removing ‘/home/docker/R/datapack’
Warning messages:
1: In i.p(...) : installation of package ‘xml2’ had non-zero exit status
2: In i.p(...) : installation of package ‘XML’ had non-zero exit status
3: In i.p(...) :
installation of package ‘openssl’ had non-zero exit status
4: In i.p(...) :
installation of package ‘roxygen2’ had non-zero exit status
5: In i.p(...) : installation of package ‘httr’ had non-zero exit status
6: In i.p(...) :
installation of package ‘redland’ had non-zero exit status
7: In i.p(...) :>

```

datapack depends on redland, which builds and tests fine -- but for some reason the recursive dependencies on xml2, openssl, etc. seem to be failing. Any thoughts on why I might be seeing this?

Gábor Csárdi

@gaborcsardi

Can you point us to a full log?

Matt Jones

@mbjones

https://builder.r-hub.io/status/datapack_1.4.1.tar.gz-620e711860ed4979962663e3f7da4c18

Matt Jones

@mbjones

What confuses me is that it seems to install libxml2-dev on line 51, but then I see this later in the log:

 985#> Package libxml-2.0 was not found in the pkg-config search path.

 986#> Perhaps you should add the directory containing `libxml-2.0.pc'

 987#> to the PKG_CONFIG_PATH environment variable

Gábor Csárdi

@gaborcsardi

Yes, it is because of this:

  68#> Some packages could not be installed. This may mean that you have
  69#> requested an impossible situation or if you are using the unstable
  70#> distribution that some required packages have not yet been created
  71#> or been moved out of Incoming.
  72#> The following information may help to resolve the situation:
  73#> The following packages have unmet dependencies:
  74#> libcurl4-gnutls-dev : Conflicts: libcurl4-openssl-dev but 7.81.0-1 is to be installed
  75#> libcurl4-openssl-dev : Conflicts: libcurl4-gnutls-dev but 7.81.0-1 is to be installed
  76#> E: Unable to correct problems, you have held broken packages.

Unfortunately your package depends on Redland, which brings in libcurl4-gnutls-dev and we need libcurl4-openssl-dev for curl, and it is not possible to install both at the same time. There is no fix for this I am afraid.

You could manually solve it by installing one Debian package first, and then the R package depending on it, then removing that Debian package, installing the other one, and the R package that depends on it. But on R-hub you cannot do that, we assume that all (build-time) system dependencies can be installed at the same time.

Matt Jones

@mbjones

thanks Gabor. So, when you say "we need libcurl4-openssl-dev", which package is the "we"? We build and tested redland itself on rhub last week when we released a new version, and didn't hit this issue there. So why does it get triggered for a package that just depends on the redland R package? Is there something we could change in our dependencies to avoid the need for libcurl4-openssl-dev?

Gábor Csárdi

@gaborcsardi

curl needs libcurl4-openssl-dev

Matt Jones

@mbjones

ok. thanks. I will look into whether we can switch the redland curl dependency -- librdf is C code that we don't maintain, but maybe it will be just as happy with the openssl-based curl libs.

Paulo Felipe

@paulofelipe

Hello everyone,

I'm having problems with checking the package I'm developing only when I use the "linux-x86_64-rocker-gcc-san" platform. For some reason, Rcpp installation is failing. I investigated but could not find the cause. If anyone can help me, I'd appreciate it. I'm sorry if this is a basic question, but this is the first package I'm trying to publish on CRAN.

The error:

2323#> attributes.cpp:404:20: error: ‘std::string’ {aka ‘class std::cxx11::basic_string’} has no member named ‘back’
2324#> 404 | if(sig.back() == '}')
2325#> | ^~~~
2326#> attributes.cpp:408:20: error: ‘std::string’ {aka ‘class std::cxx11::basic_string’} has no member named ‘front’
2327#> 408 | if(sig.front() == '{')
2328#> | ^~~~~
2329#> attributes.cpp: In function ‘bool Rcpp::attributes::checkRSignature(const Rcpp::attributes::Function&, std::string)’:
2330#> attributes.cpp:2813:45: error: ‘>>’ should be ‘> >’ within a nested template argument list
2331#> 2813 | Rcpp::as>(pargs_cv);
2332#> | ^~
2333#> | > >
2334#> make: ** [/usr/local/lib/R/etc/Makeconf:177: attributes.o] Error 1
2335#> ERROR: compilation failed for package ‘Rcpp’
2336#> removing ‘/home/docker/R/Rcpp’

Thanks in advance!

henry senyondo

@henrykironde

Has CRAN improved the way packages are submitted? Could packages be submitted through a POST request, or do we still have to do it through the submission form? Or do we have any GitHub actions that can do this?

Gábor Csárdi

@gaborcsardi

devtools::submit_cran() can submit semi-automatically, it will ask some interactive questions and then sends a POST. You still need to OK the confirmation email. Look at the devtools code if you want to do this from the CI.

1 reply

Houtao Deng

@softwaredeng

hey, the intrees package was archived on 2022-02-03 because the RRF package it depends on had an issue and was archived. RRF has been live on CRAN 2022-02-24, but intrees is still unavailable. Any thoughts?

intrees link: https://cran.r-project.org/web/packages/inTrees/index.html

Gábor Csárdi

@gaborcsardi

Hi, what is your question?

Houtao Deng

@softwaredeng

sorry - the question is how can I make inTrees back to CRAN?

6 replies

Naeem Khoshnevis

@Naeemkh

Does anyone know why I get this warning on Rhub: Requires (indirectly) orphaned package: ‘gtools’. As far as I can check, the gtools package has not been orphaned.

Gábor Csárdi

@gaborcsardi

Seems orphaned to me: https://cran.r-project.org/web/packages/gtools/

Naeem Khoshnevis

@Naeemkh

Thanks, @gaborcsardi . I was confused with the archived package. My mistake. Do I have an option to handle this situation? My package is indirectly dependent on gtools. Thanks.

Gábor Csárdi

@gaborcsardi

Unfortunately the repository policy says:

Orphaned CRAN packages should not be strict requirements (in the ‘Depends’, ‘Imports’ or ‘LinkingTo’ fields, including indirectly). They are allowed in ‘Suggests’ if used conditionally, although this is discouraged.

https://cran.r-project.org/web/packages/policies.html

You can also take over as the maintainer of the gtools package and then it won't be orphaned. Not a great solution, but sometimes it is still better than removing the functionality that depends on it.

Naeem Khoshnevis

@Naeemkh

Thanks, @gaborcsardi!

kgoldfeld

@kgoldfeld

I am getting some interesting messages when trying to run some checks, and wondering if it is me, or something bigger than me. For example when I try rhub::check_for_cran() I get this:

Error in match_platform(platforms): Unknown R-hub platform, see rhub::platforms() for a list.

1 reply

Gábor Csárdi

@gaborcsardi

Yeah, if anyone here hasn't seen it yet: https://twitter.com/rhub_/status/1542039387369885698

Hi all, unfortunately we temporarily need to stop our Windows and Linux builders, to sort out some billing issues. Hopefully we'll be able to turn them back on soon. We'll tweet here once we have more information.

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