static builder failed

[Chenhao Li]

Hi,

I was trying to build this repo (https://bitbucket.org/andreas-wilm/decontanimate/src/master/) with the 'hts_nim_static_builder' software. However, the final product was not statically linked.

Could there something wrong with the nimble file?

Here are the commands and outputs:

ubuntu@ip-10-0-3-37:~/hts-nim$ ./hts_nim_static_builder -s ../decontanimate/src/decontanimate.nim -n ../decontanimate/decontanimate.nimble
{"--debug": false, "--nim-src-file": ../decontanimate/src/decontanimate.nim, "<nim_compiler_args>": [], "--": false, "--nimble-file": ../decontanimate/decontanimate.nimble, "--tag": latest, "--deps": []}
docker run -v /home/ubuntu/decontanimate:/home/ubuntu/decontanimate -v /home/ubuntu/hts-nim:/load/ brentp/musl-hts-nim:latest /usr/local/bin/nsb -n /home/ubuntu/decontanimate/decontanimate.nimble -s /home/ubuntu/decontanimate/src/decontanimate.nim --  -d:danger -d:release
Unable to find image 'brentp/musl-hts-nim:latest' locally
latest: Pulling from brentp/musl-hts-nim
050382585609: Pull complete
abfd771006f0: Pull complete
8e509104d7b9: Pull complete
f0da7d0f3c7b: Pull complete
70d99ed0e009: Pull complete
8cb505a3e512: Pull complete
Digest: sha256:c9c9456eff1b935e32fd94c7d68d07b46d3c73bd009f77f8a348178c85704e0c
Status: Downloaded newer image for brentp/musl-hts-nim:latest
@["-n", "/home/ubuntu/decontanimate/decontanimate.nimble", "-s", "/home/ubuntu/decontanimate/src/decontanimate.nim", "--", "-d:danger", "-d:release"]
{"<nim_compiler_args>": ["-d:danger", "-d:release"], "--nim-src-file": /home/ubuntu/decontanimate/src/decontanimate.nim, "--nimble-file": /home/ubuntu/decontanimate/decontanimate.nimble, "--": true, "--deps": []}
  Verifying dependencies for decontanimate@0.0.1
 Installing cligen@>= 0.9.11
Downloading https://github.com/c-blake/cligen.git using git
  Verifying dependencies for cligen@0.9.38
 Installing cligen@0.9.38
   Success: cligen installed successfully.
      Info: Dependency on hts@>= 0.2.4 already satisfied
  Verifying dependencies for hts@0.2.18
 Installing zip@>= 0.2.1
Downloading https://github.com/nim-lang/zip using git
  Verifying dependencies for zip@0.2.1
 Installing zip@0.2.1
   Success: zip installed successfully.
Hint: used config file '/nim/config/nim.cfg' [Conf]
Hint: used config file '/nim/config/config.nims' [Conf]
Hint: system [Processing]
Hint: widestrs [Processing]
Hint: io [Processing]
Hint: decontanimate [Processing]
Hint: osproc [Processing]
Hint: strutils [Processing]
Hint: parseutils [Processing]
Hint: math [Processing]
Hint: bitops [Processing]
Hint: macros [Processing]
Hint: algorithm [Processing]
Hint: unicode [Processing]
Hint: os [Processing]
Hint: pathnorm [Processing]
Hint: osseps [Processing]
Hint: posix [Processing]
Hint: times [Processing]
Hint: options [Processing]
Hint: typetraits [Processing]
Hint: strtabs [Processing]
Hint: hashes [Processing]
Hint: streams [Processing]
Hint: cpuinfo [Processing]
Hint: linux [Processing]
Hint: bam [Processing]
Hint: hts_concat [Processing]
Hint: strformat [Processing]
Hint: simpleoption [Processing]
Hint: tables [Processing]
Hint: gzipfiles [Processing]
Hint: zlib [Processing]
Hint: logging [Processing]
/home/ubuntu/decontanimate/src/decontanimate.nim(190, 23) Warning: ref_coverage is deprecated [Deprecated]
Hint: cligen [Processing]
Hint: parseopt3 [Processing]
Hint: critbits [Processing]
Hint: argcvt [Processing]
Hint: sets [Processing]
Hint: textUt [Processing]
Hint: terminal [Processing]
Hint: colors [Processing]
Hint: termios [Processing]
Hint: wordwrap [Processing]
Hint: sysUt [Processing]
Hint: macUt [Processing]
CC: stdlib_assertions.nim
CC: stdlib_dollars.nim
CC: stdlib_io.nim
CC: stdlib_system.nim
CC: stdlib_parseutils.nim
CC: stdlib_math.nim
CC: stdlib_unicode.nim
CC: stdlib_strutils.nim
CC: stdlib_pathnorm.nim
CC: stdlib_posix.nim
CC: stdlib_times.nim
CC: stdlib_os.nim
CC: stdlib_hashes.nim
CC: stdlib_strtabs.nim
CC: stdlib_streams.nim
CC: stdlib_osproc.nim
CC: ../../../../root/.nimble/pkgs/hts-0.2.18/hts/private/hts_concat.nim
CC: ../../../../root/.nimble/pkgs/hts-0.2.18/hts/bam.nim
CC: stdlib_tables.nim
CC: ../../../../root/.nimble/pkgs/zip-0.2.1/zip/zlib.nim
CC: ../../../../root/.nimble/pkgs/zip-0.2.1/zip/gzipfiles.nim
CC: stdlib_logging.nim
CC: stdlib_critbits.nim
CC: ../../../../root/.nimble/pkgs/cligen-0.9.38/cligen/parseopt3.nim
CC: stdlib_terminal.nim
CC: stdlib_wordwrap.nim
CC: ../../../../root/.nimble/pkgs/cligen-0.9.38/cligen/textUt.nim
CC: ../../../../root/.nimble/pkgs/cligen-0.9.38/cligen/argcvt.nim
CC: ../../../../root/.nimble/pkgs/cligen-0.9.38/cligen/sysUt.nim
CC: ../../../../root/.nimble/pkgs/cligen-0.9.38/cligen.nim
CC: decontanimate.nim
Hint:  [Link]
Hint: operation successful (74494 lines compiled; 5.011 sec total; 90.461MiB peakmem; Dangerous Release Build) [SuccessX]
wrote executable: decontanimate
ubuntu@ip-10-0-3-37:~/hts-nim$ file decontanimate
decontanimate: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, with debug_info, not stripped

[Brent Pedersen]

hmm, that is odd. I see:

(base) brentp@lorax:~/src/decontanimate$ file ./decontanimate
./decontanimate: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, with debug_info, not stripped
(base) brentp@lorax:~/src/decontanimate$ ldd ./decontanimate
	statically linked

[Chenhao Li]

Thanks for the quick response!

Were you able to run the binary without libhts.so? It still complains about missing library on my machine.

[Brent Pedersen]

i'll look into this today. thanks for letting me know.

[Brent Pedersen]

I think this is fixed. It now says:

$ file ./decontanimate
./decontanimate: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), statically linked, with debug_info, not stripped

just requires getting the latest docker container from brentp:musl-hts-nim.

[Chenhao Li]

Thanks! I am getting an error when running it though:

ubuntu@ip-10-0-3-37:~/hts-nim$ file decontanimate
decontanimate: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), statically linked, with debug_info, not stripped
ubuntu@ip-10-0-3-37:~/hts-nim$ ./decontanimate
could not load: libz.so.1
compile with -d:nimDebugDlOpen for more information
ubuntu@ip-10-0-3-37:~/hts-nim$

I guess it is probably a problem with the decontanimate then...

[Brent Pedersen]

you're right. I was able to get it to work with:

../hts-nim/hts_nim_static_builder -s src/decontanimate.nim -n decontanimate.nimble -- --dynlibOverride:"z"

[Chenhao Li]

Thank you very much! This worked like a charm.

[Brent Pedersen]

great! thanks for pointing this out.