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fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON #15051

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boegel
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@boegel boegel commented Feb 25, 2022

(created using eb --new-pr)

fix for:

CMake Error at Code/cmake/Modules/RDKitUtils.cmake:49 (add_library):
  Target "RDInchiLib" links to target "Boost::system" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  External/INCHI-API/CMakeLists.txt:76 (rdkit_library)

probably started failing after CMakeMake was enhanced in easybuilders/easybuild-easyblocks#2461

@boegel boegel added the bug fix label Feb 25, 2022
@boegel boegel added this to the next release (4.5.4?) milestone Feb 25, 2022
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boegel commented Feb 25, 2022

@boegelbot please test @ generoso

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@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=15051 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15051 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8186

Test results coming soon (I hope)...

- notification for comment with ID 1050957912 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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My guess is that the correct fix is to remove the

configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib "

line(s)

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boegel commented Feb 25, 2022

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (3 easyconfigs in total)
node3103.skitty.os - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/e87a9bc3102c8d741ff2a1b1e7f72a8f for a full test report.

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Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (3 easyconfigs in total)
cns3 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/b3e4757a16c5a958881f8526cba1d5d8 for a full test report.

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boegel commented Feb 25, 2022

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3524.doduo.os - Linux RHEL 8.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/628db2801c4df7d9dfec5d268c70745b for a full test report.

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boegel commented Mar 28, 2022

My guess is that the correct fix is to remove the

configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib "

line(s)

Why would those be wrong?
Also, doesn't that leave the door open to accidentally picking up Boost from the OS?

edit: tried this suggestion, doesn't help, but adding -DBoost_NO_BOOST_CMAKE=ON does work.
The -DBoost_INCLUDE_DIR and -DBoost_LIBRARY_DIR_RELEASE must stay though, only using -DBoost_NO_BOOST_CMAKE results in:

-- Could NOT find Boost (missing: serialization) (found suitable version "1.71.0", minimum required is "1.58.0")
== Using strict rotor definition
CMake Error at /software/CMake/3.15.3-GCCcore-8.3.0/share/cmake-3.15/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find Boost (missing: system iostreams) (found suitable version
  "1.71.0", minimum required is "1.58.0")

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lgtm

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Going in, thanks @boegel!

@SebastianAchilles SebastianAchilles merged commit 06faa04 into easybuilders:develop Mar 28, 2022
@boegel boegel deleted the 20220225163240_new_pr_RDKit2020033 branch March 28, 2022 13:09
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4 participants