System library issues with 3.5.1 build(s?) about r-base-feedstock

[vilhelmen]

@vilhelmen Are you trying to pin the build when running install/create? If yes, the syntax is how you referred to the specific builds above: name=version=build, e.g. compare the following:

$ conda create --dry-run -n test-r-build r-base=3.5.1=h391c2eb_5
$ conda create --dry-run -n test-r-build r-base=3.5.1=he45234b_1005

Something like that. I'm running a conda config --env --add pinned_packages r-base=3.5.1=h391c2eb_5 and crossing my fingers that R doesn't switch to he45234b_1005 when a different package is installed at a later date.

[vilhelmen]

Also, is there a way to pin a particular build? I can't find anything on it and my guesses at syntax aren't working.

[jdblischak]

Also, is there a way to pin a particular build? I can't find anything on it and my guesses at syntax aren't working.

@vilhelmen Are you trying to pin the build when running install/create? If yes, the syntax is how you referred to the specific builds above: name=version=build, e.g. compare the following:

$ conda create --dry-run -n test-r-build r-base=3.5.1=h391c2eb_5
$ conda create --dry-run -n test-r-build r-base=3.5.1=he45234b_1005

[mingwandroid]

Our compilers don't look for system libraries (there is a way of linking to CentOS6 libs but it requires manually installing CDT packages).

conda-forge has its own GDAL package that you should use when build r-rgdal.

(r-rgdal is broken in main right now, don't get me started)

Please get started with a bug report.

[vilhelmen]

Please get started with a bug report.

No worries, they are aware. My understanding of the situation is that they're undergoing package rebuilds which is incomplete but the new packages have made it to main so nothing works right yet. Or something like that.

There are other R packages that are not provided by conda and have to be installed through R that have library dependencies seemingly not available in the main conda channels directly (V8, for example).

Is he45234b_1005's behavior (not being able to compile/build/link/etc with system libraries) intentional and h391c2eb_5 (working with system libraries) a fluke, or is it the opposite? Is there some sort of tag on the package I'm not seeing?

[mingwandroid]

In general our compilers are moving towards increased isolation from system libraries (you can add them manually with -I/usr/include and -L/usr/lib, depending on the build system).

I appreciate that sometimes the end user has little option but to mix in some system libraries so it's not ideal. If our compilers were to be made capable of looking in system folders, should it do that before the sysroot or after it? I think this needs an env. variable adding but I don't think we'll get round to this any time soon.

[vilhelmen]

That's fair, I understand the complexities involved and how much of a pain it can be. Is it possible to add the -I and -L flags into the Makeconfs file? I'm not really an R person and my attempts to brute force it were unsuccessful.

I'll bring it up with some downstream users and see what they know.

[isuruf]

Going to close this as 3.5.1 is old. Please open a new issue if the problem is in newer versions.