Fix compilation error by removing 'shallow' for Nim 2.0 compatibility #236

kojix2 · 2024-07-12T11:50:05Z

This is a follow-up to PR #235.

When attempting to compile mosdepth, I encountered an error related to shallow.

mosdepth on docopt is 📦 v0.3.8 via 👑 v2.0.8 
❯ nimble build -Y mosdepth.nimble
  Verifying dependencies for [email protected]
     Info:  Dependency on hts@>= 0.3.22 already satisfied
  Verifying dependencies for [email protected]
     Info:  Dependency on [email protected] already satisfied
  Verifying dependencies for [email protected]
     Info:  Dependency on regex@>= 0.11.1 already satisfied
  Verifying dependencies for [email protected]
     Info:  Dependency on unicodedb@>= 0.7.2 already satisfied
  Verifying dependencies for [email protected]
     Info:  Dependency on https://github.com/brentp/d4-nim@>= 0.0.3 already satisfied
  Verifying dependencies for [email protected]
   Building mosdepth/mosdepth using c backend
/Users/kojix2/Nim/mosdepth/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/kojix2/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bam/auxtags.nim(63, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/kojix2/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bam/auxtags.nim(66, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/kojix2/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(507, 3) Error: undeclared identifier: 'shallow'
candidates (edit distance, scope distance); see '--spellSuggest': 
 (3, 4): 'alloc'
 (3, 4): 'dealloc'
 (3, 4): 'realloc'
       Tip: 12 messages have been suppressed, use --verbose to show them.
nimble.nim(304)          buildFromDir

    Error:  Build failed for the package: mosdepth

It appears to be the same issue as reported in #209.

Removing shallow resolved the compilation issue, and the tests passed successfully.

mosdepth on  docopt [!?] is 📦 v0.3.8 via 👑 v2.0.8 
❯ nim c -r tests/all.nim 
Hint: used config file '/opt/homebrew/Cellar/nim/2.0.8/nim/config/nim.cfg' [Conf]
Hint: used config file '/opt/homebrew/Cellar/nim/2.0.8/nim/config/config.nims' [Conf]
Hint: used config file '/Users/kojix2/Nim/mosdepth/nim.cfg' [Conf]
Hint: used config file '/Users/kojix2/Nim/mosdepth/tests/nim.cfg' [Conf]
...............................................................................................................................................................................
/Users/kojix2/Nim/mosdepth/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/kojix2/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bam/auxtags.nim(63, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/kojix2/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bam/auxtags.nim(66, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/kojix2/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(608, 15) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(611, 17) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(614, 19) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(627, 15) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(544, 6) Hint: 'to_tuples' is declared but not used [XDeclaredButNotUsed]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(549, 6) Hint: 'main' is declared but not used [XDeclaredButNotUsed]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(767, 6) Hint: 'check_chrom' is declared but not used [XDeclaredButNotUsed]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(782, 6) Hint: 'check_cram_has_ref' is declared but not used [XDeclaredButNotUsed]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(9, 8) Warning: imported and not used: 'strformat' [UnusedImport]
/Users/kojix2/Nim/mosdepth/mosdepth.nim(11, 8) Warning: imported and not used: 'times' [UnusedImport]
/Users/kojix2/Nim/mosdepth/tests/funcs.nim(4, 8) Warning: imported and not used: 'os' [UnusedImport]
/Users/kojix2/Nim/mosdepth/tests/all.nim(1, 8) Warning: imported and not used: 'funcs' [UnusedImport]
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/exceptions.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/since.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/ctypes.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/sysatomics.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/ansi_c.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/memory.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/syslocks.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/threadtypes.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/digitsutils.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/miscdollars.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/assertions.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/iterators.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/coro_detection.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/dragonbox.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/schubfach.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/formatfloat.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/objectdollar.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/dollars.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/typedthreads.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/stacktraces.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/bitops_utils.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/countbits_impl.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system/repr_v2.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/widestrs.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/syncio.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/system.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/core/locks.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/exitprocs.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/core/macros.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/parseutils.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/bitops.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/fenv.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/math.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/algorithm.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/typetraits.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/enumutils.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/strbasics.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/unicode.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/jsutils.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/strimpl.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/strutils.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/streams.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/options.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/posix/posix.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/times.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/hashes.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/outparams.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/collections/sets.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/collections/sequtils.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/osseps.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/pathnorm.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/oserrors.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/oscommon.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/ospaths2.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/ossymlinks.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/osfiles.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/osdirs.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/envvars.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/private/osappdirs.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/std/cmdline.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/os.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/strformat.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/colors.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/posix/termios.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/terminal.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/unittest.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/private/hts_concat.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/utils.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/simpleoption.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bam.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/vcf.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/fai.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bgzf.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/csi.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bgzf/bgzi.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/stats.nim
CC: ../../../.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/collections/tables.nim
CC: ../int2str.nim
CC: ../../../.nimble/pkgs2/unicodedb-0.12.0-4452416471e2fe8726eb6070ed6ea7368171cc09/unicodedb/properties_data.nim
CC: ../../../.nimble/pkgs2/unicodedb-0.12.0-4452416471e2fe8726eb6070ed6ea7368171cc09/unicodedb/properties.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/common.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/types.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/exptype.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/scanner.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/parser.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/exptransformation.nim
CC: ../../../.nimble/pkgs2/unicodedb-0.12.0-4452416471e2fe8726eb6070ed6ea7368171cc09/unicodedb/types_data.nim
CC: ../../../.nimble/pkgs2/unicodedb-0.12.0-4452416471e2fe8726eb6070ed6ea7368171cc09/unicodedb/types.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nodematch.nim
CC: ../../../../../opt/homebrew/Cellar/nim/2.0.8/nim/lib/pure/collections/deques.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nfa.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/litopt.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nfatype.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/compiler.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nfamatch.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nfafindall.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nfamatch2.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nfafindall2.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex/nfamacro.nim
CC: ../../../.nimble/pkgs2/regex-0.21.0-3e6b482026bcd9113b0e05026d641248e6c51709/regex.nim
CC: ../../../.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/util.nim
CC: ../../../.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt.nim
CC: ../depthstat.nim
CC: ../mosdepth.nim
CC: funcs.nim
CC: all.nim
Hint:  [Link]
ld: warning: ignoring duplicate libraries: '-lm'
Hint: mm: orc; threads: on; opt: none (DEBUG BUILD, `-d:release` generates faster code)
81827 lines; 1.253s; 167.652MiB peakmem; proj: /Users/kojix2/Nim/mosdepth/tests/all.nim; out: /Users/kojix2/Nim/mosdepth/tests/all [SuccessX]
Hint: /Users/kojix2/Nim/mosdepth/tests/all [Exec]

[Suite] mosdepth-suite
  [OK] depthstat min
  [OK] test-quantize-args
  [OK] linear-search
  [OK] lookup
  [OK] threshold-args
  [OK] name splitting

mosdepth is a project that focuses on speed, so I understand if you don't want to remove optimization code. Please note that this is just a suggestion from someone not very familiar with Nim.
Thank you for your great project and hard work.

Related to brentp#209

brentp · 2024-08-27T19:24:28Z

hi @kojix2 , I apologize for ignoring this. I just went and did the same thing today. It would have saved me some time if I'd used your PR instead 🤦 .

kojix2 · 2024-08-28T02:02:30Z

No problem! I'm glad you found the same solution. Maybe I can help again next time.

It might be helpful to add the build instructions to the README.
I'm sure some people would like to compile mosdepth themselves (although you can quickly figure it out by looking at the CI workflow).

brentp · 2024-08-28T15:16:58Z

if you make a PR for build docs in readme, I'll accept this time! :)

kojix2 added 2 commits July 12, 2024 19:14

Update docopt version to 0.7.1

3e1e460

Remove shallow, deprecated in Nim 2.0

1615027

Related to brentp#209

kojix2 changed the title ~~Shallow~~ Fix compilation error by removing 'shallow' for Nim 2.0 compatibility Jul 12, 2024

brentp force-pushed the master branch from edab58f to 3ca1038 Compare August 27, 2024 18:42

brentp closed this Aug 27, 2024

kojix2 deleted the shallow branch August 28, 2024 02:02

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Fix compilation error by removing 'shallow' for Nim 2.0 compatibility #236

Fix compilation error by removing 'shallow' for Nim 2.0 compatibility #236

kojix2 commented Jul 12, 2024

brentp commented Aug 27, 2024

kojix2 commented Aug 28, 2024

brentp commented Aug 28, 2024

Fix compilation error by removing 'shallow' for Nim 2.0 compatibility #236

Fix compilation error by removing 'shallow' for Nim 2.0 compatibility #236

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kojix2 commented Jul 12, 2024

brentp commented Aug 27, 2024

kojix2 commented Aug 28, 2024

brentp commented Aug 28, 2024