Static build with libRmath-nim library causing undefined reference

[ruqianl]

Hi @brentp ,

I have been trying to build static binaries of my CLT [sscocaller] (https://gitlab.svi.edu.au/biocellgen-public/sscocaller.git) some of the instructions from your hts_nim_static_builder. On top of hts-nim, sscocaller also depends on the libRmath-nim library and I have been getting the undefined reference error.

I have used the docker image:

docker run -it -v $PWD:/mnt/mcfiles/ brentp/musl-hts-nim /bin/bash
and then nsb

/usr/local/bin/nsb -s src/sscocaller.nim -n sscocaller.nimble -- --d:release --threads:on

@m..@s..@s..@[e-mail]@spkgs@sdistributions-0.1.0@[e-mail].c:(.text+0x15): undefined reference to `dbinom'

/usr/lib/gcc/x86_64-alpine-linux-musl/9.3.0/../../../../x86_64-alpine-linux-musl/bin/ld: /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sdistributions-0.1.0@[e-mail].c.o: in function dbinom__UYyjXXE0GgmIfuGpc2rPqA': @m..@s..@s..@[e-mail]@spkgs@sdistributions-0.1.0@[e-mail].c:(.text+0x15): undefined reference to dbinom'
collect2: error: ld returned 1 exit status
Error: execution of an external program failed: 'gcc -o /mnt/mcfiles/src/xx_exe_out /root/.cache/nim/sscocaller_r/stdlib_assertions.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_dollars.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_locks.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_sharedlist.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_formatfloat.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_io.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_system.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_parseutils.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_math.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_algorithm.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_unicode.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_strutils.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_times.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_os.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_hashes.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_tables.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_sequtils.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_sets.nim.c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sunicodedb-0.9.0@sunicodedb@sproperties_data.nim.c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sunicodedb-0.9.0@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sunicodedb-0.9.0@sunicodedb@stypes_data.nim.c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sunicodedb-0.9.0@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sregex-0.16.2@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sdocopt-0.6.8@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@shts-0.3.12@shts@sprivate@shts_concat.nim.c.o /root/.cache/nim/sscocaller_r/stdlib_strformat.nim.c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@shts-0.3.12@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@shts-0.3.12@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@[e-mail].c.o /root/.cache/nim/sscocaller_r/@m..@s..@s..@[e-mail]@spkgs@sdistributions-0.1.0@[e-mail].c.o /root/.cache/nim/sscocaller_r/stdlib_streams.nim.c.o /root/.cache/nim/sscocaller_r/@msscocaller.nim.c.o -pthread -lm -lrt -static -no-pie -fno-pie /usr/lib/libm.a /usr/local/lib/libhts.a /usr/local/lib/libdeflate.a /usr/local/lib/libz.a /usr/local/lib64/libzip.a /usr/lib/libbz2.a /usr/lib/liblzma.a /usr/lib/libpthread.a /usr/lib/libopenblas.a /usr/lib/libgfortran.a /usr/lib/libquadmath.a /usr/lib/libssl.a /usr/lib/libcrypto.a /usr/lib/libdl.a /usr/lib/libc.a /usr/lib/librt.a /usr/lib/libpcre.a /usr/lib/libd4binding.a -ldl'
error compiling code

I was wondering if you any idea/suggestion/direction of where to look at to fix this.

Thank you very much.
Ruqian

[Brent Pedersen]

Hi,
sorry for delay. I would take the docker file and the directory and add R (and libRmath libraries if they aren't installed by default) to the docker file and add path to libRmath.a (If that's what it's called.) to docker/docker.nim.cfg.

Let me know if any questions.
-Brent

[ruqianl]

Hi Brent,

Thanks a lot! That worked!

https://gitlab.svi.edu.au/biocellgen-public/sscocaller

Best,
Ruqian

[Brent Pedersen]

great! I added your project here: https://github.com/brentp/hts-nim/wiki/Example-uses-of-hts-nim