Arch Linux User Repository

anyways i have updated PKGBUILD with new checksum.

Looks like the upstream changed the tag somehow. I downloaded https://github.com/ncbi/sra-tools/archive/refs/tags/3.3.0.tar.gz and its sha256 was 3bfa26c5499a94d3b2a98eb65113bbb902f51dadef767c7c7247fc0175885a9a.

That's odd. Our build server did build the package successfully with PKGBUILD and didn't encounter any checksum issues as per the build log https://build.bioarchlinux.org/api/pkg/sra-tools/log/1764850169

Looks like the checksum verification is failing for 3.3.0.

@luka5 @leuko thanks for your suggestions. the updated PKGBUILDS builds packages just fine on our project's, BioArchlinux, build server. it would be better if you use Bioarchlinux repo for installing packages. AUR serves as backup to push updated PKGBUILDS whenever a package is successfully built.

@leuko coreutils changed the behavor of mv -n also known as mv --no-clobber in v9.2 from silently doing nothing to failing. In v9.3 they introduced --update=none which works as -n before. The NEWs says:

** New features

  cp and mv now support --update=none to always skip existing files
  in the destination, while not affecting the exit status.
  This is equivalent to the --no-clobber behavior from before v9.2.

To achieve the same behavior as before, one would need to change -n to --update=none.

Error during building of sra-tools (the second part of build()):

...
/bin/sh: line 1: cd: /home/u/.cache/pikaur/build/sra-tools/src/sra-tools-3.0.3/build1/obj/ngs/ngs-java/javadoc/ngs-doc: No such file or directory

This is addressed in https://github.com/ncbi/sra-tools/pull/772/files and can be fixed (until the next release) using:

prepare(){
  ...
  sed -i 's|NGS_JAVADOC_DIR ${TARGDIR}/obj|NGS_JAVADOC_DIR ${TARGDIR}|g' ngs/ngs-java/CMakeLists.txt
}

There is another error in package():

mv: not replacing '....cache/pikaur/build/sra-tools/pkg/sra-tools/usr/bin/abi-dump'

The lines that remove the unnecessary suffixes seems to error out. I fixed them using:

  # Fix filenames: remove $pkgver suffix from end of binaries
  for filename in "$pkgdir"/usr/bin/*$pkgver; do
    mv $filename ${filename%.$pkgver}
  done

  # Fix filenames: remove -orig suffix from end of binaries
  for filename in "$pkgdir"/usr/bin/*-orig; do
    mv $filename ${filename%-orig}
  done

Error: Failed to commit transaction: failed retrieving file 'perl-file-copy-recursive-0.44-2-any.pkg.tar.xz' from ct.mirror.garr.it : Connection timed out after 30000 milliseconds

'/usr/bin/kget -> kget.2' is conflicted with Extra/kget at <https://www.archlinux.org/packages/extra/x86_64/kget/>.

Would you rename the one in sra-tools ?

pkgbuild fails because the installer is not capable of accessing https:

Running 43 test cases...

*** No errors detected ++++++++++++++++++++++++++++++++++++++++++++++++++++++ Run /tmp/trizen-moritz/ncbi-vdb/src/build_dir/ncbi-vdb/linux/gcc/x86_64/rel/test-bin/test-ngs_sra Running 67 test cases... 2018-12-19T15:20:16 test-ngs_sra.1.0.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2018-12-19T15:20:16 test-ngs_sra.1.0.0 int: file not open while identifying file within network system module - cannot KSocketGetRemoteEndpoint 2018-12-19T15:20:16 test-ngs_sra.1.0.0 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing unknown IP from '10.5.117.40' 2018-12-19T15:20:16 test-ngs_sra.1.0.0 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.27) from '10.5.117.40' 2018-12-19T15:20:16 test-ngs_sra.1.0.0 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/000000/SRR000001' /tmp/trizen-moritz/ncbi-vdb/src/ncbi-vdb-2.9.3/test/ngs/ngstest_sra.cpp(97): last checkpoint before exception "NGS_ReadCollectionMake(SRR000001) failed" ...