deeptools,tebreak,python3Packages.cnvkit,python3Packages.HTSeq: Fix test #102140

SuperSandro2000 · 2020-10-30T08:42:32Z

Motivation for this change

writing manifest file 'deepTools.egg-info/SOURCES.txt'
running build_ext
Matplotlib created a temporary config/cache directory at /build/matplotlib-qzbkbnui because the default path (/homeless-shelter/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
Finished executing setuptoolsCheckPhase
pytestcachePhase
copying 1 paths...
copying path '/nix/store/n60jc9dap8acc3f28j154779am5rpsnd-deepTools-3.5.0'

Things done

SuperSandro2000 · 2020-10-30T09:47:09Z

Result of nixpkgs-review pr 102140 run on x86_64-linux 1

7 packages failed to build:

deeptools
python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python38Packages.HTSeq
python38Packages.cnvkit
tebreak

Building currently fails because tests in pysam fail which should be resolved with #100814.

Mic92 · 2020-10-30T15:45:24Z

The PR is merged now.

unode · 2020-10-30T16:13:36Z

@SuperSandro2000 instead of disabling tests altogether, can we disable only the failing ones?

SuperSandro2000 · 2020-10-30T18:29:16Z

@SuperSandro2000 instead of disabling tests altogether, can we disable only the failing ones?

If I did no mistake they all have zero tests indicated by Ran 0 tests in 0.000s.

FRidh · 2020-10-30T18:33:56Z

If I did no mistake they all have zero tests indicated by Ran 0 tests in 0.000s.

That depends on how the tests should be run. buildPythonPackage has a default runner, but the default is often not sufficient. Check the source / sdist for tests.

SuperSandro2000 · 2020-10-30T19:00:26Z

That depends on how the tests should be run. buildPythonPackage has a default runner, but the default is often not sufficient. Check the source / sdist for tests.

The pypi tar balls often don't contain tests. I switch to the GitHub ones.

We should really pay more attention to this in the future when updating/adding packages.

SuperSandro2000 · 2020-10-30T20:13:57Z

Result of nixpkgs-review pr 102140 run on x86_64-darwin 1

7 packages marked as broken and skipped:

deeptools
python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python38Packages.HTSeq
python38Packages.cnvkit
tebreak

Failed because xmlsec failed to build.

Edit: patching xmlsec to be reproducible and build in sandbox.

SuperSandro2000 · 2020-10-30T23:20:06Z

Result of nixpkgs-review pr 102140 run on x86_64-linux 1

1 package marked as broken and skipped:

kmymoney

5 packages failed to build:

python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python38Packages.HTSeq
python38Packages.cnvkit

8 packages built:

deeptools
gnucash
lasso
matrix-synapse
python37Packages.pysaml2
python38Packages.pysaml2
tebreak
xmlsec

SuperSandro2000 · 2020-10-30T23:30:51Z

Result of nixpkgs-review pr 102140 run on x86_64-linux 1

1 package marked as broken and skipped:

kmymoney

5 packages failed to build:

python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python38Packages.HTSeq
python38Packages.cnvkit

9 packages built:

aqbanking
deeptools
gnucash
lasso
matrix-synapse
python37Packages.pysaml2
python38Packages.pysaml2
tebreak
xmlsec

I just build this locally...

SuperSandro2000 · 2020-10-30T23:58:31Z

Result of nixpkgs-review pr 102140 run on x86_64-linux 1

1 package marked as broken and skipped:

kmymoney

4 packages failed to build:

python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python38Packages.HTSeq

10 packages built:

aqbanking
deeptools
gnucash
lasso
matrix-synapse
python37Packages.pysaml2
python38Packages.cnvkit
python38Packages.pysaml2
tebreak
xmlsec

Only 3 more tries and this should build.

SuperSandro2000 · 2020-10-31T02:15:01Z

Result of nixpkgs-review pr 102140 run on x86_64-darwin 1

9 packages marked as broken and skipped:

bareos
deeptools
krunner-pass
python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python38Packages.HTSeq
python38Packages.cnvkit
tebreak

1 package failed to build:

python37Packages.pysaml2

5 packages built:

matrix-synapse
oathToolkit
passExtensions.pass-otp
python38Packages.pysaml2
xmlsec

SuperSandro2000 · 2020-10-31T12:28:09Z

Result of nixpkgs-review pr 102140 run on x86_64-darwin 1

7 packages built:

matrix-synapse
oathToolkit
pass-otp
passExtensions.pass-otp
python37Packages.pysaml2
python38Packages.pysaml2
xmlsec

SuperSandro2000 · 2020-10-31T12:45:50Z

Result of nixpkgs-review pr 102140 run on x86_64-linux 1

1 package marked as broken and skipped:

kmymoney

14 packages built:

aqbanking
deeptools
gnucash
lasso
matrix-synapse
python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python37Packages.pysaml2
python38Packages.HTSeq
python38Packages.cnvkit
python38Packages.pysaml2
tebreak
xmlsec

unode · 2020-10-31T18:52:47Z

1 package failed to build:

kmymoney

builder for '/nix/store/3dmc2ghin4lciidqpx1835j8s0b549as-kdiagram-2.6.0.drv' failed with exit code 2; last 10 log lines:
                   from /nix/store/gnbsmzcp9n66vssz1sfv2yw26fd9xkb5-qtbase-5.15.0-dev/include/QtWidgets/qabstractscrollarea.h:44,
                   from /nix/store/gnbsmzcp9n66vssz1sfv2yw26fd9xkb5-qtbase-5.15.0-dev/include/QtWidgets/qabstractitemview.h:44,
                   from /nix/store/gnbsmzcp9n66vssz1sfv2yw26fd9xkb5-qtbase-5.15.0-dev/include/QtWidgets/QAbstractItemView:1,
                   from /build/kdiagram-2.6.0/src/KGantt/kganttlegend.h:23,
                   from /build/kdiagram-2.6.0/src/KGantt/kganttlegend.cpp:20:
  /nix/store/gnbsmzcp9n66vssz1sfv2yw26fd9xkb5-qtbase-5.15.0-dev/include/QtGui/qfontmetrics.h:106:9: note: declared here
    106 |     int width(const QString &, int len = -1) const;
        |         ^~~~~
  make[1]: *** [CMakeFiles/Makefile2:1943: src/KGantt/CMakeFiles/KGantt.dir/all] Error 2
  make: *** [Makefile:149: all] Error 2
builder for '/nix/store/845mhhmpx3nljs0q8hqh29v0ywvng8sv-qtwebkit-5.212.0-alpha4.drv' failed with exit code 2; last 10 log lines:
  [ 67%] Building CXX object Source/WebCore/CMakeFiles/WebCore.dir/__/__/DerivedSources/WebCore/UserAgentStyleSheetsData.cpp.o
  [ 67%] Building CXX object Source/WebCore/CMakeFiles/WebCore.dir/__/__/DerivedSources/WebCore/PlugInsResourcesData.cpp.o
  [ 67%] Building CXX object Source/WebCore/CMakeFiles/WebCore.dir/__/__/DerivedSources/WebCore/CSSGrammar.cpp.o
  /build/source/build/DerivedSources/WebCore/CSSGrammar.cpp:160:10: fatal error: CSSGrammar.hpp: No such file or directory
    160 | #include "CSSGrammar.hpp"
        |          ^~~~~~~~~~~~~~~~
  compilation terminated.
  make[2]: *** [Source/WebCore/CMakeFiles/WebCore.dir/build.make:28188: Source/WebCore/CMakeFiles/WebCore.dir/__/__/DerivedSources/WebCore/CSSGrammar.cpp.o] Error 1
  make[1]: *** [CMakeFiles/Makefile2:1629: Source/WebCore/CMakeFiles/WebCore.dir/all] Error 2
  make: *** [Makefile:182: all] Error 2

13 packages built:

deeptools
gnucash
lasso
matrix-synapse
python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python37Packages.pysaml2
python38Packages.HTSeq
python38Packages.cnvkit
python38Packages.pysaml2
tebreak
xmlsec

The build failure seems unrelated to this pull request so LGTM on x86_64-linux

unode · 2020-10-31T20:29:18Z

Result of nixpkgs-review pr 102140 1

1 package failed to build:

- kmymoney

13 packages built:

- deeptools
- gnucash
- lasso
- matrix-synapse
- python27Packages.HTSeq
- python37Packages.HTSeq
- python37Packages.cnvkit
- python37Packages.pysaml2
- python38Packages.HTSeq
- python38Packages.cnvkit
- python38Packages.pysaml2
- tebreak
- xmlsec

jonringer

diff LGTM

https://github.com/NixOS/nixpkgs/pull/102140
1 package marked as broken and skipped:
kmymoney

13 packages built:
deeptools gnucash lasso matrix-synapse python27Packages.HTSeq python37Packages.HTSeq python37Packages.cnvkit python37Packages.pysaml2 python38Packages.HTSeq python38Packages.cnvkit python38Packages.pysaml2 tebreak xmlsec

SuperSandro2000 · 2020-11-25T21:33:55Z

Result of nixpkgs-review pr 102140 run on x86_64-linux 1

14 packages built:

aqbanking
deeptools
gnucash
kmymoney
lasso
matrix-synapse
python37Packages.HTSeq
python37Packages.cnvkit
python37Packages.pysaml2
python38Packages.HTSeq
python38Packages.cnvkit
python38Packages.pysaml2
tebreak
xmlsec

SuperSandro2000 · 2020-11-25T23:59:43Z

Result of nixpkgs-review pr 102140 run on x86_64-darwin 1

9 packages marked as broken and skipped:

bareos
deeptools
krunner-pass
python27Packages.HTSeq
python37Packages.HTSeq
python37Packages.cnvkit
python38Packages.HTSeq
python38Packages.cnvkit
tebreak

6 packages built:

matrix-synapse
oathToolkit
passExtensions.pass-otp
python37Packages.pysaml2
python38Packages.pysaml2
xmlsec

SuperSandro2000 changed the title ~~deeptools: Remove pytest cause there are no tests~~ deeptools,tebreak: Remove pytest cause there are no tests Oct 30, 2020

SuperSandro2000 force-pushed the patch-2 branch from f390ce4 to ff9c6fa Compare October 30, 2020 08:47

SuperSandro2000 requested review from FRidh and jonringer as code owners October 30, 2020 08:47

SuperSandro2000 changed the title ~~deeptools,tebreak: Remove pytest cause there are no tests~~ deeptools,tebreak: Do import test Oct 30, 2020

SuperSandro2000 force-pushed the patch-2 branch from ff9c6fa to 94dcd5a Compare October 30, 2020 08:48

ofborg bot added 10.rebuild-darwin: 1-10 10.rebuild-darwin: 1 10.rebuild-linux: 1-10 10.rebuild-linux: 1 labels Oct 30, 2020

ofborg bot requested a review from jbedo October 30, 2020 09:07

ofborg bot removed 10.rebuild-darwin: 1 10.rebuild-linux: 1 labels Oct 30, 2020

SuperSandro2000 force-pushed the patch-2 branch from 94dcd5a to d4e0df3 Compare October 30, 2020 09:39

SuperSandro2000 changed the title ~~deeptools,tebreak: Do import test~~ deeptools,tebreak,python38Packages.cnvkit,python3Packages.HTSeq: Do import test Oct 30, 2020

ofborg bot added the 6.topic: python label Oct 30, 2020

ofborg bot requested a review from unode October 30, 2020 09:50

SuperSandro2000 force-pushed the patch-2 branch from d4e0df3 to 39a8cea Compare October 30, 2020 11:09

SuperSandro2000 force-pushed the patch-2 branch from 39a8cea to 3df68d3 Compare October 30, 2020 18:30

SuperSandro2000 mentioned this pull request Oct 30, 2020

xmlsec: fix build in darwin sandbox, make tests (more) reproducible #102188

Closed

10 tasks

SuperSandro2000 force-pushed the patch-2 branch from 3df68d3 to 3762141 Compare October 30, 2020 22:42

ofborg bot added 10.rebuild-darwin: 11-100 10.rebuild-linux: 11-100 labels Oct 30, 2020

ofborg bot removed 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Oct 30, 2020

SuperSandro2000 force-pushed the patch-2 branch from 3762141 to 9c029bb Compare October 30, 2020 23:24

SuperSandro2000 force-pushed the patch-2 branch from 9c029bb to 3faa754 Compare October 30, 2020 23:53

SuperSandro2000 force-pushed the patch-2 branch from 3faa754 to 40f5bc7 Compare October 31, 2020 01:24

SuperSandro2000 changed the title ~~deeptools,tebreak,python38Packages.cnvkit,python3Packages.HTSeq: Do import test~~ deeptools,tebreak,python3Packages.cnvkit,python3Packages.HTSeq: Fix test Oct 31, 2020

SuperSandro2000 force-pushed the patch-2 branch from 40f5bc7 to 911f0bc Compare October 31, 2020 01:32

jonringer approved these changes Nov 1, 2020

View reviewed changes

SuperSandro2000 added 6 commits November 25, 2020 21:36

xmlsec: fix build in darwin sandbox, make tests (more) reproducible

169637a

deeptools: Fix tests

5f29976

tebreak: Fix tests

e166f22

pythonPackages.cnvkit: Fix tests

0cbabf1

python3Packages.HTSeq: Fix tests

a163fde

pythonPackages.pysaml2: Make tests pass in darwin sandbox

84f0c4b

SuperSandro2000 force-pushed the patch-2 branch from a497e9a to 84f0c4b Compare November 25, 2020 20:37

SuperSandro2000 merged commit c2d728f into NixOS:master Nov 26, 2020

SuperSandro2000 deleted the patch-2 branch November 26, 2020 00:00

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

deeptools,tebreak,python3Packages.cnvkit,python3Packages.HTSeq: Fix test #102140

deeptools,tebreak,python3Packages.cnvkit,python3Packages.HTSeq: Fix test #102140

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 30, 2020 •

edited

Mic92 commented Oct 30, 2020

unode commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020

FRidh commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 31, 2020

SuperSandro2000 commented Oct 31, 2020

SuperSandro2000 commented Oct 31, 2020

unode commented Oct 31, 2020

unode commented Oct 31, 2020

jonringer left a comment

SuperSandro2000 commented Nov 25, 2020

SuperSandro2000 commented Nov 25, 2020

deeptools,tebreak,python3Packages.cnvkit,python3Packages.HTSeq: Fix test #102140

deeptools,tebreak,python3Packages.cnvkit,python3Packages.HTSeq: Fix test #102140

Conversation

SuperSandro2000 commented Oct 30, 2020 • edited

Motivation for this change

Things done

SuperSandro2000 commented Oct 30, 2020 • edited

Mic92 commented Oct 30, 2020

unode commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020

FRidh commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020 • edited

SuperSandro2000 commented Oct 30, 2020

SuperSandro2000 commented Oct 30, 2020 • edited

SuperSandro2000 commented Oct 30, 2020 • edited

SuperSandro2000 commented Oct 31, 2020

SuperSandro2000 commented Oct 31, 2020

SuperSandro2000 commented Oct 31, 2020

unode commented Oct 31, 2020

unode commented Oct 31, 2020

jonringer left a comment

Choose a reason for hiding this comment

SuperSandro2000 commented Nov 25, 2020

SuperSandro2000 commented Nov 25, 2020

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 30, 2020 •

edited

SuperSandro2000 commented Oct 30, 2020 •

edited