NCBI C++ Toolkit v27.0.0

[gouriano]

ncbi-cxx-toolkit-public/27.0.0

The Toolkit is a public-domain collection of portable libraries, consisting of a cross-platform application framework and a set of utilities and supporting classes to work with biological data. It serves as a foundation of multiple projects at NCBI.
Please add recently released v27.0.0

Sources:
https://github.com/ncbi/ncbi-cxx-toolkit-public
Documentation:
https://ncbi.github.io/cxx-toolkit
Conan recipe
https://conan.io/center/ncbi-cxx-toolkit-public

---

• I've read the contributing guidelines.
• I've used a recent Conan client version close to the currently deployed.
• I've tried at least one configuration locally with the conan-center hook activated.

[gouriano]

It seems I am truly lost.
The build log says

/home/conan/w/prod/BuildSingleReference/.conan/data/ncbi-cxx-toolkit-public/27.0.0///build/014b985dcbed46bcb70edaa7e50b6036af9430f4/src/src/objtools/pubseq_gateway/protobuf/psg_protobuf.pb.cc:2411: undefined reference to `google::protobuf::RepeatedPtrFieldstd::string::Clear()'

but, psg_protobuf.pb.cc is file generated by protoc code generator.
Why it does not find something which is supposed to be in protobuf libraries?
Everything builds fine on my local computer.
The only difference is that Conan center uses GCC v7.2, while I use GCC v7.3
Could it be because if this? I very much doubt.
I do not know, this is even not our code that fails.

[gouriano]

"This commit is being built" -- What is going on? It cannot take this long.

[gouriano]

"This commit cannot be built " - why? I did not receive any email notifications and when I click "details", I see "forbidden".

[SSE4]

@prince-chrismc can you help to get valid logs here?

[jcar87]

Hi @gouriano - thanks for reaching out.
The build for the last commit on this PR failed due to a transient issue with our CI system - unfortunately once it reaches that stage, it is unable to update the status or post a comment, regardless of where it failed (or if it failed at all). Please bear in mind that the checks that we publish on the bottom are informative and not necessarily indicative of whether the PR can be merged or not. The public information is the summary posted as a comment on the PR itself.

I have triggered a manual build of this pull request - thanks for bringing this to our attention and apologies it failed the first time and the information was not very clear.

[gouriano]

Thank you very much!

[gouriano]

grpc/1.50.1:8bbc1d1764ae82b18112552fd99ce3f38de9e8c5 - Missing
ERROR: Missing binary: grpc/1.50.1:8bbc1d1764ae82b18112552fd99ce3f38de9e8c5
ERROR: Missing prebuilt package for 'grpc/1.50.1'

This does not look like our fault

[jcar87]

grpc/1.50.1

Indeed - this happened because it was using cached artifacts from an earlier run before changes to grpc were merged - I'll ensure this PR runs taking that into account.

[gouriano]

Again, missing GRPC
I believe this is a probelm on Conan center's side

ERROR: Missing binary: grpc/1.50.1:8bbc1d1764ae82b18112552fd99ce3f38de9e8c5
grpc/1.50.1: WARN: Can't find a 'grpc/1.50.1' package for the specified settings, options and dependencies:
ERROR: Missing prebuilt package for 'grpc/1.50.1'

[github-actions]

Hooks produced the following warnings for commit 57f713b

ncbi-cxx-toolkit-public/27.0.0@#eaff0510f5387781fee2f26fbea8b30a

post_package_info(): WARN: [CMAKE FILE NOT IN BUILD FOLDERS (KB-H019)] cpp_info.components["core"].build_modules is not a dictionary
post_package_info(): WARN: [CMAKE FILE NOT IN BUILD FOLDERS (KB-H019)] cpp_info.components["core"].build_modules is not a dictionary

[uilianries]

Suggested change

print("Package requires ", pkg)

Please, do not use print(), prefer self.output.info(). Requirements you can avoid, because is already listed by conan when solving the graph.

[github-actions]

Hooks produced the following warnings for commit ccb7ba0

ncbi-cxx-toolkit-public/27.0.0@#00482585ed2552642bcc211014875195

post_package_info(): WARN: [CMAKE FILE NOT IN BUILD FOLDERS (KB-H019)] cpp_info.components["core"].build_modules is not a dictionary
post_package_info(): WARN: [CMAKE FILE NOT IN BUILD FOLDERS (KB-H019)] cpp_info.components["core"].build_modules is not a dictionary

[gouriano]

I would greatly appreciate the explanation of
c3i/conan-v2/pr-merge — This commit cannot be built
thanks

[github-actions]

Hooks produced the following warnings for commit 4237d6e

ncbi-cxx-toolkit-public/27.0.0@#8be8ebec5ca22704236f0d0f2d6a1361

post_package_info(): WARN: [CMAKE FILE NOT IN BUILD FOLDERS (KB-H019)] cpp_info.components["core"].build_modules is not a dictionary
post_package_info(): WARN: [CMAKE FILE NOT IN BUILD FOLDERS (KB-H019)] cpp_info.components["core"].build_modules is not a dictionary

[gouriano]

Missing binaries is not our fault. If you do not want to "build missing", then provide prebuilt binaries.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[vakatov]

@gouriano - can '--build=missing' be used?

[gouriano]

Conan center builds the package the way they like it, not the way I do. That is the whole point of testing, I believe.

[conan-center-bot]

Conan v1 pipeline ✔️

All green in build 2 (7c14c2f56192e526a2cb255ecf07fbac5a7c9fd6):

• ncbi-cxx-toolkit-public/27.0.0:
  All packages built successfully! (All logs)

---

Conan v2 pipeline ❌

Note: Conan v2 builds are now mandatory. Please read our discussion about it.

The v2 pipeline failed. Please, review the errors and note this is required for pull requests to be merged. In case this recipe is still not ported to Conan 2.x, please, ping @conan-io/barbarians on the PR and we will help you.

See details:

Failure in build 2 (7c14c2f56192e526a2cb255ecf07fbac5a7c9fd6):

• ncbi-cxx-toolkit-public/27.0.0:
  CI failed to create some packages (All logs)

  Logs for packageID 818aca088dd2f881a39eef796fdb4678f2a673c1:

  [settings]
  arch=x86_64
  build_type=Release
  compiler=gcc
  compiler.cppstd=17
  compiler.libcxx=libstdc++11
  compiler.version=11
  os=Linux
  [options]
  */*:shared=False
  

  [...]
  ERROR: Missing binary: libpng/1.6.39:52e28526917bc008177a3c5cf92ea21144c3ecd5
  ERROR: Missing binary: libtiff/4.4.0:8c80bceaef92005659f72b3c891e2eb977a4e133
  ERROR: Missing binary: libunwind/1.6.2:46f376d86f56bc7c9d777b2b4895e141b61a9588
  ERROR: Missing binary: libxml2/2.11.6:227df3a5a5dd47e7e96b967bdb50f722321f9790
  ERROR: Missing binary: libxslt/1.1.34:10df644640dc33c3059ae4561609d321211221b8
  ERROR: Missing binary: openssl/3.2.1:710bb705c1bca5f69a9b481f9d1f13873004145b
  ERROR: Missing binary: pcre/8.45:22df55d12fd0a729491762b4508bc4ddf8b50a38
  ERROR: Missing binary: protobuf/3.21.12:0a68446b9947784d37544a468d7db3ff36a7d85d
  ERROR: Missing binary: sqlite3/3.41.1:46fbaf6d13261d8e27269f7addcf948d9d8e7b59
  
  sqlite3/3.41.1: WARN: Can't find a 'sqlite3/3.41.1' package binary '46fbaf6d13261d8e27269f7addcf948d9d8e7b59' for the configuration:
  [settings]
  arch=x86_64
  build_type=Release
  compiler=gcc
  compiler.version=11
  os=Linux
  [options]
  build_executable=True
  disable_gethostuuid=False
  enable_column_metadata=True
  enable_dbpage_vtab=False
  enable_dbstat_vtab=False
  enable_default_secure_delete=False
  enable_default_vfs=True
  enable_explain_comments=False
  enable_fts3=False
  enable_fts3_parenthesis=False
  enable_fts4=False
  enable_fts5=False
  enable_json1=False
  enable_math_functions=True
  enable_preupdate_hook=False
  enable_rtree=True
  enable_soundex=False
  enable_unlock_notify=True
  fPIC=True
  omit_deprecated=False
  omit_load_extension=False
  shared=False
  threadsafe=1
  use_alloca=False
  use_uri=False
  
  ERROR: Missing prebuilt package for 'backward-cpp/1.6', 'grpc/1.50.1', 'libdwarf/20191104', 'libpng/1.6.39', 'libtiff/4.4.0', 'libunwind/1.6.2', 'libxml2/2.11.6', 'libxslt/1.1.34', 'openssl/3.2.1', 'pcre/8.45', 'protobuf/3.21.12', 'sqlite3/3.41.1'. You can try:
      - List all available packages using 'conan list sqlite3/3.41.1:* -r=remote'
      - Explain missing binaries: replace 'conan install ...' with 'conan graph explain ...'
      - Try to build locally from sources using the '--build=missing' argument
  
  More Info at 'https://docs.conan.io/2/knowledge/faq.html#error-missing-prebuilt-package'
  

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