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

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merged 6 commits into from Nov 26, 2020

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@SuperSandro2000
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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

Motivation for this change

#100814

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
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.
@SuperSandro2000 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 SuperSandro2000 changed the title deeptools,tebreak: Remove pytest cause there are no tests deeptools,tebreak: Do import test Oct 30, 2020
@ofborg ofborg bot requested a review from jbedo Oct 30, 2020
@SuperSandro2000 SuperSandro2000 changed the title deeptools,tebreak: Do import test deeptools,tebreak,python38Packages.cnvkit,python3Packages.HTSeq: Do import test Oct 30, 2020
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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

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.

@ofborg ofborg bot requested a review from unode Oct 30, 2020
@Mic92
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@Mic92 Mic92 commented Oct 30, 2020

The PR is merged now.

@unode
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@unode unode commented Oct 30, 2020

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

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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

@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.

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@FRidh FRidh commented Oct 30, 2020

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.

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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

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.

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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

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.

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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

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

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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

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...

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@SuperSandro2000 SuperSandro2000 commented Oct 30, 2020

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

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

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@SuperSandro2000 SuperSandro2000 commented Oct 31, 2020

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

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@SuperSandro2000 SuperSandro2000 commented Oct 31, 2020

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

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@unode unode commented Oct 31, 2020

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
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@unode unode commented Oct 31, 2020

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

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@jonringer jonringer left a comment

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

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@SuperSandro2000 SuperSandro2000 commented Nov 25, 2020

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

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@SuperSandro2000 SuperSandro2000 commented Nov 25, 2020

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 SuperSandro2000 merged commit c2d728f into NixOS:master Nov 26, 2020
19 checks passed
@SuperSandro2000 SuperSandro2000 deleted the patch-2 branch Nov 26, 2020
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5 participants