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SPAdes: 3.15.2 -> 3.15.3#134133

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bobby285271 merged 1 commit intoNixOS:masterfrom
Kranzes:auto-update/SPAdes
Sep 16, 2021
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SPAdes: 3.15.2 -> 3.15.3#134133
bobby285271 merged 1 commit intoNixOS:masterfrom
Kranzes:auto-update/SPAdes

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@Kranzes Kranzes commented Aug 15, 2021

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/SPAdes/versions.

meta.description for SPAdes is: "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"

meta.homepage for SPAdes is: "http://cab.spbu.ru/software/spades/"

meta.changelog for SPAdes is: ""

Updates performed
  • Version update
To inspect upstream changes
Impact
Checks done (click to expand)
  • built on NixOS
  • The tests defined in passthru.tests, if any, passed
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-gbuilder passed the binary check.
  • Warning: no invocation of /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-bwa had a zero exit code or showed the expected version
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/coronaspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/truspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/plasmidspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades_init.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/metaplasmidspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-convert-bin-to-fasta passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/mag-improve passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/cds-subgraphs passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/rnaspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/metaviralspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades.py passed the binary check.
  • Warning: no invocation of /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-corrector-core had a zero exit code or showed the expected version
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-read-filter passed the binary check.
  • Warning: no invocation of /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-hammer had a zero exit code or showed the expected version
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-kmer-estimating passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-gsimplifier passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-gmapper passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-kmercount passed the binary check.
  • Warning: no invocation of /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-core had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-truseq-scfcorrection had a zero exit code or showed the expected version
  • Warning: no invocation of /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spades-ionhammer had a zero exit code or showed the expected version
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/rnaviralspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/metaspades.py passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/spaligner passed the binary check.
  • /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin/cds-mapping-stats passed the binary check.
  • 13 of 27 passed binary check by having a zero exit code.
  • 13 of 27 passed binary check by having the new version present in output.
  • found 3.15.3 with grep in /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3
  • found 3.15.3 in filename of file in /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3
Rebuild report (if merged into master) (click to expand) 
1 total rebuild path(s)

1 package rebuild(s)

0 x86_64-linux rebuild(s)
0 i686-linux rebuild(s)
0 x86_64-darwin rebuild(s)
0 aarch64-linux rebuild(s)


First fifty rebuilds by attrpath
SPAdes
Instructions to test this update (click to expand)

Build yourself:

nix-build -A SPAdes https://github.com/Kranzes/nixpkgs/archive/9f5b3fafa034e6434b136374f5b72567d24eea23.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:

ls -la /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3
ls -la /nix/store/n12yy8q275lqic9vanqkz0ipb1rjnxjx-SPAdes-3.15.3/bin

Pre-merge build results

We have automatically built all packages that will get rebuilt due to
this change.

This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.

Result of nixpkgs-review run on x86_64-linux 1

1 package built:
  • SPAdes
Maintainer pings

cc @bzizou for testing.

@ofborg ofborg bot requested a review from bzizou August 15, 2021 08:34
@ofborg ofborg bot added 10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-darwin: 1 This PR causes 1 package to rebuild on Darwin. 10.rebuild-linux: 1-10 This PR causes between 1 and 10 packages to rebuild on Linux. 10.rebuild-linux: 1 This PR causes 1 package to rebuild on Linux. labels Aug 15, 2021
@Kranzes
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Kranzes commented Sep 12, 2021

@SuperSandro2000 and this is the last one <3

@bobby285271
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bobby285271 commented Sep 16, 2021

Result of nixpkgs-review pr 134133 run on x86_64-linux 1

1 package built:
  • SPAdes

@bobby285271 bobby285271 merged commit 12d38c5 into NixOS:master Sep 16, 2021
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@bzizou bzizou bzizou approved these changes

@fufexan fufexan fufexan approved these changes

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10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-darwin: 1 This PR causes 1 package to rebuild on Darwin. 10.rebuild-linux: 1-10 This PR causes between 1 and 10 packages to rebuild on Linux. 10.rebuild-linux: 1 This PR causes 1 package to rebuild on Linux.

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@Kranzes @bobby285271 @bzizou @fufexan