| 2018-06-15 15:59:41 |
Tony Travis |
bug |
|
|
added bug |
| 2018-07-25 22:56:04 |
Launchpad Janitor |
metaphlan2 (Ubuntu): status |
New |
Confirmed |
|
| 2019-04-24 14:45:41 |
Dylan Aïssi |
metaphlan2 (Ubuntu): assignee |
|
Dylan Aïssi (daissi) |
|
| 2019-04-24 19:34:23 |
Graham Inggs |
metaphlan2 (Ubuntu): status |
Confirmed |
Fix Released |
|
| 2019-04-24 19:34:26 |
Dylan Aïssi |
attachment added |
|
metaphlan2_2.7.5-1ubuntu1.debdiff https://bugs.launchpad.net/ubuntu/+source/metaphlan2/+bug/1777165/+attachment/5258731/+files/metaphlan2_2.7.5-1ubuntu1.debdiff |
|
| 2019-04-24 19:34:30 |
Graham Inggs |
nominated for series |
|
Ubuntu Bionic |
|
| 2019-04-24 19:34:30 |
Graham Inggs |
bug task added |
|
metaphlan2 (Ubuntu Bionic) |
|
| 2019-04-24 19:34:56 |
Graham Inggs |
metaphlan2 (Ubuntu Bionic): status |
New |
Confirmed |
|
| 2019-04-24 19:35:16 |
Graham Inggs |
metaphlan2 (Ubuntu Bionic): assignee |
|
Dylan Aïssi (daissi) |
|
| 2019-04-24 19:35:22 |
Graham Inggs |
metaphlan2 (Ubuntu): assignee |
Dylan Aïssi (daissi) |
|
|
| 2019-04-24 19:56:31 |
Dylan Aïssi |
description |
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) |
[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.
-
+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) |
|
| 2019-04-24 19:56:52 |
Dylan Aïssi |
summary |
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 |
|
| 2019-04-24 19:57:15 |
Dylan Aïssi |
summary |
metaphlan2 is uninstallable in bionic |
metaphlan2 is not installable in bionic |
|
| 2019-04-24 19:57:28 |
Dylan Aïssi |
description |
[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.
-
+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) |
[Impact]
* 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.
[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.
-
+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) |
|
| 2019-04-24 20:02:11 |
Graham Inggs |
summary |
metaphlan2 is not installable in bionic |
[SRU] metaphlan2 is not installable in bionic |
|
| 2019-04-24 20:15:02 |
Graham Inggs |
metaphlan2 (Ubuntu Bionic): status |
Confirmed |
In Progress |
|
| 2019-05-15 13:20:53 |
Robie Basak |
metaphlan2 (Ubuntu Bionic): status |
In Progress |
Fix Committed |
|
| 2019-05-15 13:20:54 |
Robie Basak |
bug |
|
|
added subscriber Ubuntu Stable Release Updates Team |
| 2019-05-15 13:20:57 |
Robie Basak |
bug |
|
|
added subscriber SRU Verification |
| 2019-05-15 13:21:01 |
Robie Basak |
tags |
amd64 apport-package bionic |
amd64 apport-package bionic verification-needed verification-needed-bionic |
|
| 2019-05-18 20:29:34 |
Dylan Aïssi |
tags |
amd64 apport-package bionic verification-needed verification-needed-bionic |
amd64 apport-package bionic verification-done verification-done-bionic |
|
| 2019-05-23 08:47:33 |
Launchpad Janitor |
metaphlan2 (Ubuntu Bionic): status |
Fix Committed |
Fix Released |
|
| 2019-05-23 08:47:38 |
Łukasz Zemczak |
removed subscriber Ubuntu Stable Release Updates Team |
|
|
|
