Bug 1341771

Summary: Missing dependencies for R-core-devel in EPEL 5 and 6
Product: [Fedora] Fedora EPEL Reporter: Mattias Ellert <mattias.ellert>
Component: RAssignee: Tom "spot" Callaway <tcallawa>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: el6CC: tcallawa
Target Milestone: ---Keywords: Reopened
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
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Fixed In Version: R-3.3.0-5.el6 R-3.3.0-10.el5 Doc Type: If docs needed, set a value
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Last Closed: 2016-07-06 04:18:09 UTC Type: Bug
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oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
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Description Flags
Improved fix none

Description Mattias Ellert 2016-06-01 18:02:18 UTC
Description of problem:

In EPEL 5 and 6 the pkg-config returns:

$ pkg-config --libs libR
-Wl,--export-dynamic -fopenmp -L/usr/lib64/R/lib -ldl -lpthread -lc -lcurl -lidn -lssh2 -lssl -lcrypto -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lldap -lz -lrt -lR

But the R-core-devel package does not depend on libcurl-devel, libssh2-devel, openldap-devel.

Building R addons fails due to the missing deps. Also, EPEL 5 and 6 uses bundled curl, so linking against the system curl doesnät seem to be a good idea.

Compare with EPEL 7 and Fedora, where the pkg-config output does not contain these:

$ pkg-config --libs libR
-L/usr/lib64/R/lib -Wl,--export-dynamic -fopenmp -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lR

Version-Release number of selected component (if applicable):
R-3.3.0-3.el5
R-3.3.0-3.el6

How reproducible:
Always

Comment 1 Tom "spot" Callaway 2016-06-01 18:14:08 UTC
Have you considered updating to EL7? :)

Seriously. The amount of hacking I had to do to get R 3.3.0 to even _build_ for EL5/6 was disgusting.

... alright. I guess I can short-circuit the libR.pc file to refer to the bundled bits.

Comment 2 Fedora Update System 2016-06-01 18:53:50 UTC
R-3.3.0-4.el5 has been submitted as an update to Fedora EPEL 5. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-6529014854

Comment 3 Fedora Update System 2016-06-01 18:53:56 UTC
R-3.3.0-4.el6 has been submitted as an update to Fedora EPEL 6. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-a7de38e355

Comment 4 Tom "spot" Callaway 2016-06-01 18:54:21 UTC
Please, please, test this update for me.

Comment 5 Mattias Ellert 2016-06-03 06:14:49 UTC
Created attachment 1164339 [details]
Improved fix

The pkg-config command cleans up its output by removing multiple spaces and removing duplicate flags, so using the output in the sed replacement argument will not match what is in the .pc file. The original string before the cleanup must be used.

In addition, the same removal must also be done in the R/etc/Makeconf file where these flags appear in the LDFLAGS variable.

The attached patch implements these changes.

Comment 6 Fedora Update System 2016-06-03 22:17:04 UTC
R-3.3.0-4.el5 has been pushed to the Fedora EPEL 5 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-6529014854

Comment 7 Fedora Update System 2016-06-03 22:17:37 UTC
R-3.3.0-4.el6 has been pushed to the Fedora EPEL 6 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-a7de38e355

Comment 8 Tom "spot" Callaway 2016-06-06 13:55:29 UTC
-5 is building now with your fix, thanks.

Comment 9 Fedora Update System 2016-06-06 14:25:06 UTC
R-3.3.0-5.el6 has been submitted as an update to Fedora EPEL 6. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-93778a4eeb

Comment 10 Fedora Update System 2016-06-06 14:25:12 UTC
R-3.3.0-5.el5 has been submitted as an update to Fedora EPEL 5. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-ea9aef57fc

Comment 11 Fedora Update System 2016-06-07 01:47:17 UTC
R-3.3.0-5.el6 has been pushed to the Fedora EPEL 6 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-93778a4eeb

Comment 12 Fedora Update System 2016-06-07 01:48:03 UTC
R-3.3.0-5.el5 has been pushed to the Fedora EPEL 5 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-ea9aef57fc

Comment 13 Fedora Update System 2016-06-07 16:14:20 UTC
R-3.3.0-6.el5 has been submitted as an update to Fedora EPEL 5. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-050c4e8af7

Comment 14 Fedora Update System 2016-06-08 05:17:50 UTC
R-3.3.0-5.el6 has been pushed to the Fedora EPEL 6 stable repository. If problems still persist, please make note of it in this bug report.

Comment 15 Fedora Update System 2016-06-08 05:46:11 UTC
R-3.3.0-6.el5 has been pushed to the Fedora EPEL 5 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-050c4e8af7

Comment 16 Fedora Update System 2016-06-09 16:00:42 UTC
R-3.3.0-8.el5 has been submitted as an update to Fedora EPEL 5. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-09c8007e64

Comment 17 Fedora Update System 2016-06-10 07:15:59 UTC
R-3.3.0-8.el5 has been pushed to the Fedora EPEL 5 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-09c8007e64

Comment 18 Fedora Update System 2016-06-11 19:59:23 UTC
R-3.3.0-10.el5 has been submitted as an update to Fedora EPEL 5. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-367d157bc6

Comment 19 Fedora Update System 2016-06-12 23:16:57 UTC
R-3.3.0-10.el5 has been pushed to the Fedora EPEL 5 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-367d157bc6

Comment 20 Fedora Update System 2016-07-06 04:17:59 UTC
R-3.3.0-10.el5 has been pushed to the Fedora EPEL 5 stable repository. If problems still persist, please make note of it in this bug report.