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
