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add missing pkg-config build dependency in recent R-bundle-Bioconductor easyconfigs#11104

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smoors merged 1 commit intoeasybuilders:developfrom
boegel:20200812181850_new_pr_R-bundle-Bioconductor310
Aug 13, 2020
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add missing pkg-config build dependency in recent R-bundle-Bioconductor easyconfigs#11104
smoors merged 1 commit intoeasybuilders:developfrom
boegel:20200812181850_new_pr_R-bundle-Bioconductor310

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@boegel boegel commented Aug 12, 2020

(created using eb --new-pr)

This fixes a confusing failure when installing the lpsymphony extension:

OsiAuxInfo.cpp:10:10: fatal error: CoinPragma.hpp: No such file or directory
10 | #include "CoinPragma.hpp"
  |          ^~~~~~~~~~~~~~~~
compilation terminated.

The problem was that paths passed to -I has /tmp/Rtmp0boicg/Rbuild8d44a5f2a1f/lpsymphony/src/SYMPHONY/include/coin rather than the expected <builddir>/lpsymphony/lpsymphony/src/SYMPHONY/CoinUtils/src.

This turned out to be because of a prefix=/tmp/Rtmp0boicg/Rbuild8d44a5f2a1f entry in *.pc files included in the lpsymphony sources. Not having pkg-config probably results in blindly using that path, rather than using the correct one...

@boegel boegel added the bug fix label Aug 12, 2020
@boegel boegel added this to the next release (4.2.3?) milestone Aug 12, 2020
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boegel commented Aug 13, 2020

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
node2401.golett.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz (haswell), Python 2.7.5
See https://gist.github.com/01a51248a78f250466409f108ff1a68c for a full test report.

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boegel commented Aug 13, 2020

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in this PR)
generoso-x-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/c07ea00a747eb68050e6500ba5049c23 for a full test report.

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lgtm

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smoors commented Aug 13, 2020

Going in, thanks @boegel!

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