linking flags

Question

linking flags

kasperdanielhansen opened this issue 4 years ago · comments

Kasper Daniel Hansen commented 4 years ago

I get a

shared -o libH5Zblosc.so H5Zblosc.o \
           libblosc.a -lz
/jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0.x/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status

All of my libraries are in non-standard locations. This is 100% likely caused by not passing the R settings for LD_FLAGS to the package in makevars.in, and should be fixable by adding a line with LDFLAGS in that file, where all the other make variables are defined. Unfortunately - right now - I don't have time to make a pull request, but I can easily test a fix on my system.

Kasper Daniel Hansen · Answer 1 · Sat Jul 04 2020 00:00:16 GMT+0800 (China Standard Time)

Sorry I wrote LD_FLAGS on time where I meant LDFLAGS. The version with _ is the compiler variable and the version without _ is the R/make variable.

Mike Smith · Answer 2 · Sat Jul 04 2020 03:54:00 GMT+0800 (China Standard Time)

Thanks for the report. Does this work for you?

BiocManager::install('grimbough/rhdf5filters', ref = "ldflags")

Kasper Daniel Hansen · Answer 3 · Mon Jul 06 2020 11:44:17 GMT+0800 (China Standard Time)

Still waiting to test. I was a bit slow over the weekend, and we have just been told our cluster is shut down for cooling / power issues. So it may take a few more days.

Mike Smith · Answer 4 · Mon Jul 06 2020 14:47:51 GMT+0800 (China Standard Time)

No worries. If this doesn't work I'll try and replicate the environment in a VM and get it compiling there.

Kasper Daniel Hansen · Answer 5 · Mon Jul 06 2020 22:51:18 GMT+0800 (China Standard Time)

The cluster is hopefully up by Wednesday (my time) or Thursday. I should also have some time to play with this at that time, so I would not go to the lengths of replicating it elsewhere, unless that is easy for you.

…

On Mon, Jul 6, 2020 at 2:48 AM Mike Smith ***@***.***> wrote: No worries. If this doesn't work I'll try and replicate the environment in a VM and get it compiling there. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABF2DHZGZP2LJM7ZDN7QZLLR2FXSLANCNFSM4OP5NFWQ> .

-- Best, Kasper

Kasper Daniel Hansen · Answer 6 · Thu Jul 09 2020 01:52:42 GMT+0800 (China Standard Time)

Using my current installation of Bioc 3.12 (devel) / R-4.0.2-patched (which is a few days out of date for various packages), I get the same old error with

BiocManager::install('grimbough/rhdf5filters')

and the error is gone with

BiocManager::install('grimbough/rhdf5filters', ref = "ldflags")

and I can verify that the linking step includes the required -L flags. So it works, thanks.

Kevin Rue-Albrecht · Answer 7 · Thu Jul 09 2020 05:32:40 GMT+0800 (China Standard Time)

BiocManager::install('grimbough/rhdf5filters', ref = "ldflags")

approved here too 👍

Mike Smith · Answer 8 · Thu Jul 09 2020 06:16:07 GMT+0800 (China Standard Time)

Great, thanks for the feedback. I've push those changes to both devel and release on Bioconductor, they should propagate soon. Let me know if there's still an issue in a few days.