When there are patches involved and you're going to a newer version of the source, you have to check if the patches still apply and if they are still needed.
If they still seem to be needed, but don't apply any longer, you have to create a new patch for the new version. And as can be seen in your output below, the patches fails to apply. We're also working to fix the current 3.3.2 version of AUGUSTUS in EasyBuild. There are a couple of small changes to the easyconfig to make the resulting installation work better. You are also doing a couple of mistakes below. You should normally not set optarch, unless you're building for a different architecture then the one you're building on. And when using a intel based easyconfig you should use intel compatible options, -march=xxxx is in principle only for GCC. On 12/4/19 12:25 PM, [email protected] wrote: > hi all [absolute beginner to eb] > > struggling a bit trying to build AUGUSTUS 3.3.3 (source code changes: > https://fossies.org/diffs/augustus/3.3.2_vs_3.3.3/) > > I have used the previous version 3.3.2 and then > $ eb AUGUSTUS-3.3.3-intel-2019a.eb --inject-checksums --force > > reviewed, replaced (3.2 to 3.3 >>> %s/3.2/3.3/g) and renamed the files: > AUGUSTUS-3.3.2_fix-hardcoding.patch >>> AUGUSTUS-3.3.3_fix-hardcoding.patch > AUGUSTUS-3.3.2_additional_fix_hardcoding.patch >>> > AUGUSTUS-3.3.3_additional_fix_hardcoding.patch > > confirmed files sha256sum and replaced them on file AUGUSTUS-3.3.3- > intel-2019a.eb > > $ eb --buildpath=/tmp --job-cores=32 --optarch=march=skylake-avx512 --dry-run > AUGUSTUS-3.3.3-intel-2019a.eb -r > $ eb --buildpath=/tmp --job-cores=32 --optarch=march=skylake-avx512 > AUGUSTUS-3.3.3-intel-2019a.eb -r > > Log throws this errors: > # '-fgnu89-inline' is required to avoid linking errors with older glibc's, > == 2019-12-04 10:33:19,174 run.py:587 INFO parse_log_for_error msg: Command > used: patch -b -p1 -i /home/apps/eb/software/EasyBuild/4.0.1/easybuild/ > easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch > == 2019-12-04 10:33:19,175 run.py:589 INFO parse_log_for_error (some may be > harmless) regExp (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.? > \w) found: > == 2019-12-04 10:33:19,175 run.py:546 WARNING Found 2 errors in command output > (output: Hunk #1 FAILED at 15., 1 out of 1 hunk FAILED -- saving rejects to > file auxprogs/bam2wig/Makefile.rej) > == 2019-12-04 10:33:19,225 build_log.py:164 ERROR EasyBuild crashed with an > error (at easybuild/base/exceptions.py:124 in __init__): Couldn't apply patch > file /home/apps/eb/software/EasyBuild/4.0.1/easybuild/easyconfigs/a/AUGUSTUS/ > AUGUSTUS-3.3.3_fix-hardcoding.patch. Process exited with code 1: patching file > auxprogs/bam2wig/Makefile > == 2019-12-04 10:33:19,227 build_log.py:164 ERROR EasyBuild crashed with an > error (at easybuild/base/exceptions.py:124 in __init__): build failed (first > 300 chars): Couldn't apply patch file /home/apps/eb/software/EasyBuild/4.0.1/ > easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch. Process > exited with code 1: patching file auxprogs/bam2wig/Makefile > == 2019-12-04 10:33:19,227 build_log.py:164 ERROR EasyBuild crashed with an > error (at easybuild/base/exceptions.py:124 in __init__): Build of /home/apps/ > eb/software/EasyBuild/4.0.1/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3- > intel-2019a.eb failed (err: "build failed (first 300 chars): Couldn't apply > patch file /home/apps/eb/software/EasyBuild/4.0.1/easybuild/easyconfigs/a/ > AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch. Process exited with code 1: > patching file auxprogs/bam2wig/Makefile\nHunk #1 FAILED at 15.\n1 out of 1 > hunk FAILED -- saving rejects to file auxprogs/bam2wig/Makefile.") (at > easybuild/main.py:147 in build_and_install_software) > > The only diffs I can see from the new 3.3.3 auxprogs/bam2wig/Makefile are > (https://fossies.org/diffs/augustus/3.3.2_vs_3.3.3/auxprogs/bam2wig/Makefile-diff.html) > - removes TABIX (which the patch files hashes out anyway) --- > https://github.com/easybuilders/easybuild-easyconfigs/blob/4.0.x/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch > - mkdir -p ../../bin > > Would you guys be able to point me in the direction to debugging this further? > > Apologies if it is something obvious that I am completely missing. > > Thanks in advance > -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: [email protected] Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
