** Description changed: + [Impact] + + * The package of metaphlan2 is uninstallable in bionic. + + * The "_metaphlan2.py" file contains Python 3 source but the "postinst" + script runs "pycompile" on the Python source files. However, "pycompile" + only supports Python version 2. The print() function in "_metaphlan2.py" + can be imported from the "__future__" library, but Python 2 does not + support function annotations: These are optional in Python 3, and are + removed from the function definitions in "_metaphlan2.py" by the patch. + + [Test Case] + + * Try to install the package. + + [Regression Potential] + + * This patch is already applied in Debian since ~ 10 months and in Ubuntu + since Cosmic without any problem. + + ============================================= + Already reported by me and Fixed by Andreas Tille in the Debian-Med team. Python3 syntax is used in _metaphlan2.py, but "pycompile" run by the "postinst" script only supports Python2. Fixed by adding "print()" and removing function annotations: /usr/share/metaphlan2# diff -Naur _metaphlan2.py.dist _metaphlan2.py --- _metaphlan2.py.dist 2018-02-07 10:43:00.000000000 +0000 +++ _metaphlan2.py 2018-06-15 16:09:30.056981110 +0100 @@ -3,7 +3,7 @@ - # This module defines the functions which run MetaPhlAn2 on - # single and paired fastq data. - + # This module defines the functions which run MetaPhlAn2 on + # single and paired fastq data. + - +from __future__ import print_function - import subprocess as sb - from q2_types.per_sample_sequences import SingleLanePerSampleSingleEndFastqDirFmt - from q2_types.per_sample_sequences import SingleLanePerSamplePairedEndFastqDirFmt + import subprocess as sb + from q2_types.per_sample_sequences import SingleLanePerSampleSingleEndFastqDirFmt + from q2_types.per_sample_sequences import SingleLanePerSamplePairedEndFastqDirFmt @@ -24,8 +24,7 @@ - sb.run(cmd, check=True) - - + sb.run(cmd, check=True) + -def profile_single_fastq(raw_data: SingleLanePerSampleSingleEndFastqDirFmt, - nproc: int=1) -> biom.Table: +def profile_single_fastq(raw_data, nproc=1): - output_biom = None - - with tempfile.TemporaryDirectory() as tmp_dir: + output_biom = None + + with tempfile.TemporaryDirectory() as tmp_dir: @@ -36,8 +35,7 @@ - return output_biom - - + return output_biom + -def profile_paired_fastq(raw_data: SingleLanePerSamplePairedEndFastqDirFmt, - nproc: int=1) -> biom.Table: +def profile_paired_fastq(raw_data, nproc=1): - output_biom = None - - with tempfile.TemporaryDirectory() as tmp_dir: + output_biom = None + + with tempfile.TemporaryDirectory() as tmp_dir: ProblemType: Package DistroRelease: Ubuntu 18.04 Package: metaphlan2 2.7.5-1 [modified: usr/share/metaphlan2/_metaphlan2.py] ProcVersionSignature: Ubuntu 4.15.0-23.25-generic 4.15.18 Uname: Linux 4.15.0-23-generic x86_64 NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair ApportVersion: 2.20.9-0ubuntu7.2 Architecture: amd64 Date: Fri Jun 15 15:07:54 2018 ErrorMessage: installed metaphlan2 package post-installation script subprocess returned error exit status 101 PackageArchitecture: all Python3Details: /usr/bin/python3.6, Python 3.6.5, python3-minimal, 3.6.5-3 PythonDetails: /usr/bin/python2.7, Python 2.7.15rc1, python-minimal, 2.7.15~rc1-1 RelatedPackageVersions: - dpkg 1.19.0.5ubuntu2 - apt 1.6.1 + dpkg 1.19.0.5ubuntu2 + apt 1.6.1 SourcePackage: metaphlan2 Title: package metaphlan2 2.7.5-1 [modified: usr/share/metaphlan2/_metaphlan2.py] failed to install/upgrade: installed metaphlan2 package post-installation script subprocess returned error exit status 101 UpgradeStatus: No upgrade log present (probably fresh install)
** Summary changed: - package metaphlan2 2.7.5-1 [modified: usr/share/metaphlan2/_metaphlan2.py] failed to install/upgrade: installed metaphlan2 package post-installation script subprocess returned error exit status 101 + metaphlan2 is uninstallable in bionic ** Summary changed: - metaphlan2 is uninstallable in bionic + metaphlan2 is not installable in bionic ** Description changed: [Impact] - * The package of metaphlan2 is uninstallable in bionic. + * The package of metaphlan2 is not installable in bionic. - * The "_metaphlan2.py" file contains Python 3 source but the "postinst" - script runs "pycompile" on the Python source files. However, "pycompile" - only supports Python version 2. The print() function in "_metaphlan2.py" - can be imported from the "__future__" library, but Python 2 does not - support function annotations: These are optional in Python 3, and are - removed from the function definitions in "_metaphlan2.py" by the patch. + * The "_metaphlan2.py" file contains Python 3 source but the "postinst" + script runs "pycompile" on the Python source files. However, "pycompile" + only supports Python version 2. The print() function in "_metaphlan2.py" + can be imported from the "__future__" library, but Python 2 does not + support function annotations: These are optional in Python 3, and are + removed from the function definitions in "_metaphlan2.py" by the patch. [Test Case] - * Try to install the package. + * Try to install the package. [Regression Potential] - * This patch is already applied in Debian since ~ 10 months and in Ubuntu - since Cosmic without any problem. + * This patch is already applied in Debian since ~ 10 months and in Ubuntu + since Cosmic without any problem. ============================================= Already reported by me and Fixed by Andreas Tille in the Debian-Med team. Python3 syntax is used in _metaphlan2.py, but "pycompile" run by the "postinst" script only supports Python2. Fixed by adding "print()" and removing function annotations: /usr/share/metaphlan2# diff -Naur _metaphlan2.py.dist _metaphlan2.py --- _metaphlan2.py.dist 2018-02-07 10:43:00.000000000 +0000 +++ _metaphlan2.py 2018-06-15 16:09:30.056981110 +0100 @@ -3,7 +3,7 @@ # This module defines the functions which run MetaPhlAn2 on # single and paired fastq data. - +from __future__ import print_function import subprocess as sb from q2_types.per_sample_sequences import SingleLanePerSampleSingleEndFastqDirFmt from q2_types.per_sample_sequences import SingleLanePerSamplePairedEndFastqDirFmt @@ -24,8 +24,7 @@ sb.run(cmd, check=True) -def profile_single_fastq(raw_data: SingleLanePerSampleSingleEndFastqDirFmt, - nproc: int=1) -> biom.Table: +def profile_single_fastq(raw_data, nproc=1): output_biom = None with tempfile.TemporaryDirectory() as tmp_dir: @@ -36,8 +35,7 @@ return output_biom -def profile_paired_fastq(raw_data: SingleLanePerSamplePairedEndFastqDirFmt, - nproc: int=1) -> biom.Table: +def profile_paired_fastq(raw_data, nproc=1): output_biom = None with tempfile.TemporaryDirectory() as tmp_dir: ProblemType: Package DistroRelease: Ubuntu 18.04 Package: metaphlan2 2.7.5-1 [modified: usr/share/metaphlan2/_metaphlan2.py] ProcVersionSignature: Ubuntu 4.15.0-23.25-generic 4.15.18 Uname: Linux 4.15.0-23-generic x86_64 NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair ApportVersion: 2.20.9-0ubuntu7.2 Architecture: amd64 Date: Fri Jun 15 15:07:54 2018 ErrorMessage: installed metaphlan2 package post-installation script subprocess returned error exit status 101 PackageArchitecture: all Python3Details: /usr/bin/python3.6, Python 3.6.5, python3-minimal, 3.6.5-3 PythonDetails: /usr/bin/python2.7, Python 2.7.15rc1, python-minimal, 2.7.15~rc1-1 RelatedPackageVersions: dpkg 1.19.0.5ubuntu2 apt 1.6.1 SourcePackage: metaphlan2 Title: package metaphlan2 2.7.5-1 [modified: usr/share/metaphlan2/_metaphlan2.py] failed to install/upgrade: installed metaphlan2 package post-installation script subprocess returned error exit status 101 UpgradeStatus: No upgrade log present (probably fresh install) -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1777165 Title: [SRU] metaphlan2 is not installable in bionic To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/metaphlan2/+bug/1777165/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
