R 3.5.0 for iomkl 2018a #6466

edmondac · 2018-06-16T09:50:39Z

Here's our R 3.5.0 using iomkl 2018a. I don't know if you'd rather this came with 2018.02...?

It's still building here to test, but I wanted to ask that question sooner rather than later!

This PR is a prerequisite for Bioconductor 3.7, which has at least one library that requires R 3.5.0.

boegel · 2018-06-19T08:09:52Z

@edmondac R 3.5.0 is our target for foss/2018b and intel/2018b (cfr. #6424 & #6409 resp.), but we should also update the (dependency and) extension versions when doing that...

edmondac · 2018-06-19T15:36:50Z

Hi @boegel - so what would you like me to do with this PR?

boegel · 2018-06-19T17:31:07Z

@edmondac I think we should either update the extensions as well, or abandon this...

boegel

@edmondac Thanks a lot for looking into updating the extension versions... How did you go about this, did you go through them manually, or using some script?

boegel · 2018-06-20T12:25:17Z

easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-iomkl-2018a-Mesa-17.3.6.eb

+
+name = 'libGLU'
+version = '9.0.0'
+versionsuffix = '-Mesa-17.3.6'


@edmondac This is basically the same as the existing libGLU-9.0.0-iomkl-2018a.eb, so I don't see the point?

Just use ('libGLU', '9.0.0') in the R easyconfig instead?

Sorry - missed that one. I'd changed the dep but not removed the file.

boegel · 2018-06-20T12:25:33Z

easybuild/easyconfigs/g/GEOS/GEOS-3.6.2-iomkl-2018a.eb

+homepage = 'http://trac.osgeo.org/geos'
+description = """GEOS (Geometry Engine - Open Source) is a C++ port of the  Java Topology Suite (JTS)"""
+
+toolchain = {'name': 'iomkl', 'version': '2018a'}


This easyconfig isn't actually required to resolve a dependency?

Good point - removed.

I updated using easy_update, then a little tinkering.

It's still building here with the updated apps, it's about half way through them...

boegel · 2018-06-21T06:43:14Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+        'checksums': ['49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372'],
+    }),
+    ('clValid', '0.6-6', {
+        'checksums': ['bcf781238a2a831a7ec8909d27251731e3115a0541a9ea9795e5ec4d903938d1'],


@edmondac I'm getting a different checksum here: c13ef1b6258e34ba53615b78f39dbe4d8ba47b976b3c24a3eedaecf5ffba19ed (fresh download)...

edmondac · 2018-06-21T08:23:56Z

I've fixed the checksum - they must have changed the tgz.

I reverted RSQLite to 2.0 because I didn't feel like I had time to make a new patch - since RSQLite-2.0-icc.patch doesn't apply any more.

I've just reverted randomForestSRC too as the new one segfaults (like randomForest) with iomkl 2018a

Building again here... I'll let you know when it completes...

… patch for matrixStats, fix checksum for penalized, update patch for imager, add gee extension

boegel

@edmondac all suggestions are tackled in bear-rsg#1, if you merge that PR this one will be updated accordingly, and then it should be good to go

boegel · 2018-06-21T06:44:44Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+}
+
+# !! order of packages is important !!
+# packages updated on Mar 15 2018


@edmondac Please fix this date

boegel · 2018-06-21T06:47:48Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+    ('GMP', '6.1.2'),  # for igraph
+    ('NLopt', '2.4.2'),  # for nloptr
+    ('FFTW', '3.3.7'),  # for fftw
+    ('libsndfile', '1.0.28'),  # for seewave


missing ICU dependency, see #6371

boegel · 2018-06-21T06:48:24Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+    ('formatR', '1.5', {
+        'checksums': ['874c197ae3720ec11b44984a055655b99a698e1912104eb9034c11fdf6104da7'],
+    }),
+    ('gtools', version, {


@edmondac this should say '3.5.0', not version (probably a side effect of using easy_update?)

boegel · 2018-06-21T06:53:26Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+        'checksums': ['bcf781238a2a831a7ec8909d27251731e3115a0541a9ea9795e5ec4d903938d1'],
+    }),
+    ('matrixStats', '0.53.1', {
+        'checksums': ['df70bc9fb64716a7a633b5d0c2a2422b2c8d93ac5e64574528a325505df9712e'],


patch is missing here, see #6278

boegel · 2018-06-21T06:56:35Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+        'checksums': ['c007d6eaf6335a15c1912b0804276ff39abce27b7a61539a91b8fda653629252'],
+    }),
+    ('penalized', '0.9-50', {
+        'checksums': ['66ed84b967f70fd49702318e43e129c2ff60bb0631b81fe2617671d1ebbbc060'],


this checksum is also wrong, should be c12b3259e019f91c7bd02827ea3a27f842d9c15950fa6cc114dff23c89c297d1, see also #6083 (comment)

boegel · 2018-06-21T07:04:07Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+        'checksums': [
+            'fc9ba74519388c194e14bae39d41f3fec8c2aade0177df364f61753f0fbf8a3d',  # glasso_1.8.tar.gz
+            '87e966b6651c2d9ccd8a2c2ba842eef8dcbeaa3fdd25085bb1d5aff6e79f409c',  # glasso-1.8-ifort-no-fixed.patch
+


missing extension: gee (cfr. #6376)

boegel · 2018-06-21T10:58:55Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+        'checksums': [
+            'fc9ba74519388c194e14bae39d41f3fec8c2aade0177df364f61753f0fbf8a3d',  # glasso_1.8.tar.gz
+            '87e966b6651c2d9ccd8a2c2ba842eef8dcbeaa3fdd25085bb1d5aff6e79f409c',  # glasso-1.8-ifort-no-fixed.patch
+


this patch no longer applies...

boegel · 2018-06-21T10:59:56Z

easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb

+        'checksums': [
+            'fc9ba74519388c194e14bae39d41f3fec8c2aade0177df364f61753f0fbf8a3d',  # glasso_1.8.tar.gz
+            '87e966b6651c2d9ccd8a2c2ba842eef8dcbeaa3fdd25085bb1d5aff6e79f409c',  # glasso-1.8-ifort-no-fixed.patch
+


gee extension is missing (cfr. #6376)

fixes for R-3.5.0-iomkl-2018a-X11-20180131.eb

boegel · 2018-06-21T19:35:43Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2476.golett.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/cf4e1e755bbe9071f72a1cc4aa30f51a for a full test report.

boegel · 2018-06-21T23:18:20Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2012.delcatty.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/3c1159f2af875928c4b81f7959d4e3b1 for a full test report.

boegel · 2018-06-23T10:42:46Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node3236.victini.os - Linux centos linux 7.5.1804, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 2.7.5
See https://gist.github.com/7ac0721c01771859ee401d50cd50fc12 for a full test report.

boegel · 2018-06-23T14:58:45Z

Going in, thanks @edmondac!

edmondac added 5 commits June 16, 2018 10:48

R 3.5.0 for iomkl 2018a

26a62dc

Removing unnecessary headers

0e0631d

Fixing dep conflict

3d104c8

Fixing multi-variant deps

67380a5

Don't need that easyconfig

a09a3bc

easybuilders deleted a comment from boegelbot Jun 19, 2018

boegel added the update label Jun 19, 2018

Updated extensions

e0609f7

boegel requested changes Jun 20, 2018

View reviewed changes

edmondac added 3 commits June 20, 2018 13:26

Deps and fixes

ea68d4e

Removing unnecessary files

0c26d46

Reverting randomForest to 4.6-12 as 4.6-14 segfaults...

53d62b1

easybuilders deleted a comment from boegelbot Jun 21, 2018

boegel requested changes Jun 21, 2018

View reviewed changes

Reverting randomForestSRC as 2.6.1 is segfaulting

55e1a94

add missing ICU dep, bump RSQLite to 2.1.1 & drop unneeded patch, add…

d2d4bb1

… patch for matrixStats, fix checksum for penalized, update patch for imager, add gee extension

boegel mentioned this pull request Jun 21, 2018

fixes for R-3.5.0-iomkl-2018a-X11-20180131.eb bear-rsg/easybuild-easyconfigs#1

Merged

boegel requested changes Jun 21, 2018

View reviewed changes

edmondac and others added 3 commits June 21, 2018 16:47

Reverting imager to 0.40.2 as the patch doesn't apply to 0.41.1

cf240bf

Merge branch 'r-3.5.0-iomkl' into r-3.5.0-iomkl

fee91bd

Merge pull request #1 from boegel/r-3.5.0-iomkl

0bb50c8

fixes for R-3.5.0-iomkl-2018a-X11-20180131.eb

boegel approved these changes Jun 21, 2018

View reviewed changes

boegel added this to the 3.6.2 milestone Jun 21, 2018

edmondac mentioned this pull request Jun 23, 2018

Bioconductor 3.7 iomkl 2018a R 3.5.0 #6497

Merged

boegel merged commit 7ad68e0 into easybuilders:develop Jun 23, 2018

edmondac deleted the r-3.5.0-iomkl branch December 16, 2019 09:04

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R 3.5.0 for iomkl 2018a #6466

R 3.5.0 for iomkl 2018a #6466

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R 3.5.0 for iomkl 2018a #6466

R 3.5.0 for iomkl 2018a #6466

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