R-bundle-CRAN-2023b, Brunsli-0.1 patch, and easyconfigs.py #20756

moravveji · 2024-06-07T06:58:25Z

In this PR:

the latest version of R packages from CRAN are built with R/4.3.3-gfbf-2023b (see {lang}[GCC/13.2.0,GCCcore/13.2.0,gfbf/2023b] SOCI v4.0.3, yaml-cpp v0.8.0, RStudio-Server v2023.12.1+402 w/ Java 11 R 4.3.3 #20060)
few additional dependency packages are added to the extension list
the build succeeds on Intel Sapphire Rapids with Rocky 8.9 Linux. I will try it on Intel SkyLake, CascadeLake and IceLake soon

Remarks:

As of Brotli/1.1.0-GCCcore-13.2.0 (compared to v.1.0.9), the libbrotli*-static.a are no longer built. As a result of that, building Brunsli/0.1-GCCcore-13.2.0 fails. To fix this, a new patch is introduced (Brunsli-0.1-fix-Brotli-static-library-names.patch)
This PR introduces a new .eb for libgeotiff, Brunsli, GEOS, GDAL, and so does PR {lib}[GCCcore/13.2.0] Brunsli v0.1, GDAL v3.9.0, libgeotiff v1.7.3, ... #20675. So, some care has to be practiced here to avoid duplication

moravveji · 2024-06-12T16:52:00Z

@Micket : I have just came across your PR #20675 which contains an easyconfig for GDAL/3.9.0-foss-2023b and libgeotiff/1.7.3-GCCcore-13.2.0. I must have searched deeper before placing this PR. How shall we best avoid a possible conflict between the two when merging?

[UPDATE]: I did a diff on our easyconfigs for GDAL and they are just identical, which makes life easier. The same is true for libgeotiff and GEOS.

verdurin · 2024-06-19T10:10:02Z

Test report by @verdurin
FAILED
Build succeeded for 40 out of 43 (12 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/5e5f552ce32cc2c9aebb700c3da0c0d3 for a full test report.

verdurin · 2024-06-24T09:24:48Z

@moravveji - thanks for your contribution and welcome to EasyBuild.
Certainly a bold approach to start with this one...

Could you resolve the conflicts, please, preferably by removing them from your PR and specifying them as dependencies instead.

The build failure I saw was a checksum mismatch.

boegel · 2024-06-24T12:52:04Z

To be clear: conflicts here are caused by the merge of #20675

…cluded in pr 20675

moravveji · 2024-06-25T08:04:18Z

Thanks @verdurin and @boegel for your comments. I have few questions about some (minor?) issues with this PR:

libopus gives me this error (truncated):

== 2024-06-19 09:07:10,961 filetools.py:837 WARNING IOError occurred while trying to download https://downloads.xiph.org/releases/opus/opus-1.5.2.tar.gz to /eb/maint/sources/l/libopus/opus-1.5.2.tar.gz: <urlopen error [SSL: TLSV1_ALERT_PROTOCOL_VERSION] tlsv1 alert protocol version (_ssl.c:877)>
== 2024-06-19 09:07:11,430 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): Couldn't find file opus-1.5.2.tar.gz anywhere, and downloading it didn't work either... Paths attempted (in order): /tmp/eb-oc9o47pd/files_pr20756/l/libopus/l/libopus/opus-1.5.2.tar.gz, /tmp/eb-oc9o47pd/files_pr20756/l/libopus/libopus/opus-1.5.2.tar.gz, /tmp/eb-oc9o47pd/files_pr20756/l/libopus/opus-1.5.2.tar.gz, /home/software/src/easybuild/local/l/libopus/opus-1.5.2.tar.gz, /home/software/src/easybuild/local/libopus/opus-1.5.2.tar.gz, /home/software/src/easybuild/local/opus-1.5.2.tar.gz, /eb/maint/local/l/libopus/opus-1.5.2.tar.gz, /eb/maint/local/libopus/opus-1.5.2.tar.gz, /eb/maint/local/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/l/libopus/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/libopus/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/opus-1.5.2.tar.gz, /eb/maint/software/EasyBuild/4.9.2/easybuild/easyconfigs/l/libopus/opus-1.5.2.tar.gz, /eb/maint/software/EasyBuild/4.9.2/easybuild/easyconfigs/libopus/opus-1.5.2.tar.gz, /eb/maint/software/EasyBuild/4.9.2/easybuild/easyconfigs/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/l/libopus/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/libopus/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/opus-1.5.2.tar.gz, /tmp/eb-oc9o47pd/files_pr20756/l/libopus/opus-1.5.2.tar.gz, /tmp/eb-oc9o47pd/files_pr20756/libopus/opus-1.5.2.tar.gz, /tmp/eb-oc9o47pd/files_pr20756/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/l/libopus/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/libopus/opus-1.5.2.tar.gz, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/opus-1.5.2.tar.gz, /eb/maint/software/EasyBuild/4.9.2/easybuild/easyconfigs/l/libopus/opus-1.5.2.tar.gz, /eb/maint/software/EasyBuild/4.9.2/easybuild/easyconfigs/libopus/opus-1.5.2.tar.gz, /eb/maint/software/EasyBuild/4.9.2/easybuild/easyconfigs/opus-1.5.2.tar.gz, /eb/maint/sources/l/libopus/opus-1.5.2.tar.gz, /eb/maint/sources/libopus/opus-1.5.2.tar.gz, /eb/maint/sources/opus-1.5.2.tar.gz, https://downloads.xiph.org/releases/opus/opus-1.5.2.tar.gz, https://sources.easybuild.io/l/libopus/opus-1.5.2.tar.gz  (at easybuild/framework/easyblock.py:975 in obtain_file)

However, the very correct download URL is in the list: https://downloads.xiph.org/releases/opus/opus-1.5.2.tar.gz. So, I am not sure how to fix this

The PR {lib}[GCCcore/13.2.0] Brunsli v0.1, GDAL v3.9.0, libgeotiff v1.7.3, ... #20675 was put in before this PR, and it contained GEOS, libgeotiff and GDAL which I have removed from the current PR (commit 9059f2a). However, to build Brunsli against Brotli, a patch is needed, which is included in the current PR, and is missing from the other one. That is why I have not removed Brunsli from here.
How do you propose to proceed here?
For the R-bundle-CRAN itself, I get the following error:
```
== 2024-06-19 10:09:58,752 easyblock.py:4285 WARNING build failed (first 300 chars): Checksum verification for extension source signal_1.8-0.tar.gz failed
```
I know as a fact that the developers/maintainers of the R package signal have changed the source while keeping the version number. As a result, the fingerprint has changed under the hood. Because the same package is used in older versions of R-bundle-CRAN module, on most systems, the older signal-1.8-0.tar.gz source file is found from the cached source paths with the outdated fingerprint. Therefore, the checksum fails here. The easy solution I found was to remove the source .tar.gz file and use eb --force --inject-checksums=sha256 ... to get an updated fingerprint. So, unless the source is manually removed from all test systems, this step is always gonna fail

Thanks in advance

Flamefire · 2024-06-25T11:24:25Z

  == 2024-06-19 09:07:10,961 filetools.py:837 WARNING IOError occurred while trying to download https://downloads.xiph.org/releases/opus/opus-1.5.2.tar.gz to /eb/maint/sources/l/libopus/opus-1.5.2.tar.gz: <urlopen error [SSL: TLSV1_ALERT_PROTOCOL_VERSION] tlsv1 alert protocol version (_ssl.c:877)>
  However, the very correct download URL is in the list: `https://downloads.xiph.org/releases/opus/opus-1.5.2.tar.gz`. So, I am not sure how to fix this

Looks like an SSL issue. Might be intermediate.

* The PR [{lib}[GCCcore/13.2.0] Brunsli v0.1, GDAL v3.9.0, libgeotiff v1.7.3, ... #20675](https://github.com/easybuilders/easybuild-easyconfigs/pull/20675) was put in before this PR, and it contained GEOS, libgeotiff and GDAL which I have removed from the current PR (commit [9059f2a](https://github.com/easybuilders/easybuild-easyconfigs/commit/9059f2a554da79bd24ec9e84cf3fe829197e68df)). However, to build `Brunsli` against `Brotli`, a patch is needed, which is included in the current PR, and is missing from the other one. That is why I have not removed Brunsli from here.
  How do you propose to proceed here?

The patch is not required as it is handled in the EC you mentioned: https://github.com/easybuilders/easybuild-easyconfigs/pull/20675/files#diff-0ea948e4665fcb18be3b5d531fc2c022b3124c586df87e5cb05eea1c7f69b268R30

However I think the patch is clearer than the sed used there. I suggest to merge current develop into your branch, remove the sed line and instead add your patch (needs to be done during resolving the merge conflict)
This should result in a small change only to that EC.

  ```
  == 2024-06-19 10:09:58,752 easyblock.py:4285 WARNING build failed (first 300 chars): Checksum verification for extension source signal_1.8-0.tar.gz failed
  ```
  I know as a fact that the developers/maintainers of the R package `signal` have changed the source while keeping the version number. As a result, the fingerprint has changed under the hood. Because the same package is used in older versions of `R-bundle-CRAN` module, on most systems, the older `signal-1.8-0.tar.gz` source file is found from the cached source paths with the outdated fingerprint. Therefore, the checksum fails here. The easy solution I found was to remove the source .tar.gz file and use `eb --force --inject-checksums=sha256 ...` to get an updated fingerprint. So, unless the source is manually removed from all test systems, this step is always gonna fail

3 steps:

Open an issue with the maintainers of that package telling them not to do that (again)
Compare the new and old version of the archive contents
If they are the same just add an alternate checksum : 'source': ('checksum1', 'checksum2'),

Flamefire · 2024-06-26T07:06:12Z

@moravveji I created a PR to resolve the conflicts stopping this from being merged: moravveji#1

Feel free to handle it yourself, just wanted to offer it to get this merged as we like to use it at our site too. So thanks for the effort of updating this monstrous EC

moravveji · 2024-06-26T07:36:27Z

@moravveji I created a PR to resolve the conflicts stopping this from being merged: moravveji#1

Feel free to handle it yourself, just wanted to offer it to get this merged as we like to use it at our site too. So thanks for the effort of updating this monstrous EC

Thanks @Flamefire for your new branch. I think I already handled the conflicts in my current branch, by updating the develop branch in my own fork. Yet, I have to remove more EC from this PR with another commit, which I will do once the first round of checks are completed.

For signal-1.8-0.tar.gz I compared (diff) the extracted old and new sources, and the difference between the two is only in the sources/DESCRIPTION file. So, it is pretty safe to have two checksums for a single source filename. If I understood your comment correctly, then the accepted syntax for two checksums (or even more) per one extension source can look like the following, right?

    ('signal', '1.8-0', {
        'checksums': ['0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7', # old source file
                      '23ff303856ff09734e8ef280cec94556a15cdc702727ae5d02f8cfa4d8f473b7'], # new source file
    }),

easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-33-GCCcore-13.2.0.eb

Flamefire · 2024-06-26T09:27:24Z

For signal-1.8-0.tar.gz I compared (diff) the extracted old and new sources, and the difference between the two is only in the sources/DESCRIPTION file. So, it is pretty safe to have two checksums for a single source filename. If I understood your comment correctly, then the accepted syntax for two checksums (or even more) per one extension source can look like the following, right?
    ('signal', '1.8-0', {
        'checksums': ['0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7', # old source file
                      '23ff303856ff09734e8ef280cec94556a15cdc702727ae5d02f8cfa4d8f473b7'], # new source file
    }),

Almost: it must be a tuple, not a list, i.e. "()" instead of "[]"

moravveji · 2024-06-26T10:26:58Z

This should be easy ;-)
In the EC for Brunsli, I have a long line for the checksum, which leads to the following error:

/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb:20:10: E127 continuation line over-indented for visual indent

I have tried different ways to get around this (such as using \ for line continuation, or using newline and simply splitting the line into two), but so far, no success. The line looks like this:

checksums = [
    {'v0.1.tar.gz': '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'},
    {'Brunsli-0.1-fix-Brotli-static-library-names.patch': \
         '0b921fb4839f0b0223c1bf08499e84afd5d428f448664fd1337173f45a815704'},
]

Can someone plz give an advice?

easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb

Co-authored-by: Alexander Grund <[email protected]>

moravveji · 2024-06-26T17:39:41Z

    ('signal', '1.8-0', {
        'checksums': ['0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7', # old source file
                      '23ff303856ff09734e8ef280cec94556a15cdc702727ae5d02f8cfa4d8f473b7'], # new source file
    }),

Almost: it must be a tuple, not a list, i.e. "()" instead of "[]"

Well, seems like EB is clever enough to spot the trick, and refuse to accept it. I get this error now:

AssertionError: False is not true : No checksum issues:
Checksums missing for one or more sources/patches of extension signal in R-bundle-CRAN-2024.06-foss-2023b.eb: found 1 sources + 0 patches vs 2 checksums

Makes me think if it is legitimate to make an exception here, and remove the checksums only for this specific extension (signal), given that the checksums are strongly recommended, but not enforced.

Flamefire · 2024-06-27T07:57:42Z

Makes me think if it is legitimate to make an exception here, and remove the checksums only for this specific extension (signal), given that the checksums are strongly recommended, but not enforced.

The syntax was wrong, my mistake, sorry: moravveji#2

branfosj · 2024-06-27T08:10:09Z

easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2024.06-foss-2023b.eb

+        'checksums': ('0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7',   # older source
+                      '23ff303856ff09734e8ef280cec94556a15cdc702727ae5d02f8cfa4d8f473b7'),  # newer source


Suggested change

'checksums': ('0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7', # older source

'23ff303856ff09734e8ef280cec94556a15cdc702727ae5d02f8cfa4d8f473b7'), # newer source

'checksums': [

('89cba854167a2b051a58cf3b73ccbf74eeb47c890ac39720611cd41f86b94684',

'0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7'),

],

Or this, yes. To me it looks better on 2 lines for the single list element though. I also took the liberty to improve the error message seen here: moravveji#2

I see the many green lights again. So, thanks @Flamefire for the nice fix.
All the necessary adjustments after the recent merges are included here.
So, it this PR ready for testing?

Test report coming up. I don't expect any issues. Just takes a while to install 1115 extensions ;-)

I have seen surprises at test step ... so, I stay tuned. On our machines it took roughly 6 hours to build (including dependencies).

Fix checksum

Flamefire · 2024-06-28T15:41:57Z

Test report by @Flamefire
SUCCESS
Build succeeded for 25 out of 25 (2 easyconfigs in total)
n1336 - Linux RHEL 8.7 (Ootpa), x86_64, Intel(R) Xeon(R) Platinum 8470 (icelake), Python 3.8.13
See https://gist.github.com/Flamefire/bed936187da64cede291f782af3e27ee for a full test report.

Flamefire · 2024-08-13T12:50:06Z

After #20898 was merged this only partially applies now.

R-bundle is likely the same as the merged one, but might be wort to compare
Brunsli is still using the sed approach instead of the patch
The minor fix to the EC tests

Not sure if it is worth following up on this although I would. Will be a very small PR I guess.

moravveji · 2024-08-13T16:49:45Z

after the other PR was merged, I got disappointed, and lost interest in this one. So, please feel free to either follow it up or close it. Thanks in advance.

Flamefire · 2024-08-29T10:39:50Z

I added the remaining changes of yours to #21180 and #21181, so you can close this PR

moravveji · 2024-08-29T10:50:21Z

@Flamefire : Thanks for that.

moravveji added 3 commits June 7, 2024 07:26

easyconfig for R/4.4.0-gfbf-2023a

b453b7c

R-bundle-CRAN/2024.06-foss-2023b and its dependencies

fdd3802

removing duplicate extensions

8c18bfa

moravveji mentioned this pull request Jun 7, 2024

Missing libbrotlidec-static.a in version 1.1.0 google/brotli#1174

Open

bedroge mentioned this pull request Jun 7, 2024

{lib}[GCCcore/13.2.0] Brunsli v0.1, GDAL v3.9.0, libgeotiff v1.7.3, ... #20675

Merged

Ehsan Moravveji and others added 2 commits June 12, 2024 17:12

fixing Brunsli dependency on Brotli

ed0a71a

explaining Brunsli patch

2b14b1a

moravveji added 3 commits June 13, 2024 08:02

removing inconsistent .eb for R and CRAN bundle from the index only

52e6c3f

add R-bundle-CRAN easyconfig again

e6da9b3

updating patch checksum

f95706c

moravveji changed the title ~~WIP: R-bundle-CRAN-2023b and 12 updated dependencies~~ R-bundle-CRAN-2023b and 12 updated dependencies Jun 14, 2024

boegel added the update label Jun 19, 2024

boegel added this to the 4.x milestone Jun 19, 2024

removing duplicate eb files for gdal, goes and ligeotiff; they are in…

9059f2a

…cluded in pr 20675

Flamefire mentioned this pull request Jun 26, 2024

Merge develop to R-cran moravveji/easybuild-easyconfigs#1

Open

Merge branch 'develop' into R-cran-2023b

78bb775

moravveji added 4 commits June 26, 2024 10:01

fix checksum continuation

26e5531

easyconfig for R/4.4.0-gfbf-2023a

a05bd60

Merge branch 'develop' into R-cran-2023b

0a8f28f

wrong R sneaked into this PR

b39bd1b

bedroge reviewed Jun 26, 2024

View reviewed changes

easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-33-GCCcore-13.2.0.eb Outdated Show resolved Hide resolved

removing ImageMagick to adapt to PR#20892

7f49486

moravveji added 4 commits June 26, 2024 11:29

missing end bracket

56de33e

adding alternative checksum for signal, in case older source is recycled

8064c66

trying explicit continuation line

11f02ad

one bloody space

9dc3483

Flamefire reviewed Jun 26, 2024

View reviewed changes

easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb Outdated Show resolved Hide resolved

removing hidden spaces

f488ffd

Co-authored-by: Alexander Grund <[email protected]>

Flamefire added 2 commits June 27, 2024 10:08

Test: Improve checksum error message

12e57e3

Fix checksum of signal extension

0aa6231

branfosj reviewed Jun 27, 2024

View reviewed changes

Merge pull request #2 from Flamefire/fix-cs

0e54869

Fix checksum

moravveji changed the title ~~R-bundle-CRAN-2023b and 12 updated dependencies~~ R-bundle-CRAN-2023b, Brunsli-0.1 patch, and easyconfigs.py Jun 28, 2024

moravveji requested review from bedroge, Flamefire and branfosj June 28, 2024 08:38

Flamefire approved these changes Jun 28, 2024

View reviewed changes

moravveji mentioned this pull request Jul 1, 2024

Choice of R version for the 2023b toolchain #20947

Closed

This was referenced Aug 14, 2024

Replace sed in Brunsli by proper patch #21180

Open

Add some more packages to R-bundle-CRAN-2024.06-foss-2023b #21181

Open

moravveji closed this Aug 29, 2024

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R-bundle-CRAN-2023b, Brunsli-0.1 patch, and easyconfigs.py #20756

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		'checksums': ('0a604949bae91410a150a22cfa02d954f5b83166cc7a73e5409554d00e0417a7', # older source
		'23ff303856ff09734e8ef280cec94556a15cdc702727ae5d02f8cfa4d8f473b7'), # newer source

R-bundle-CRAN-2023b, Brunsli-0.1 patch, and easyconfigs.py #20756

R-bundle-CRAN-2023b, Brunsli-0.1 patch, and easyconfigs.py #20756

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