nixpkgs/pkgs/applications/science/biology
Sergei Trofimovich 90a5d1b931 megahit: fir gcc-13 build failure
Without the change build fails on `master` against `gcc-13` as
https://hydra.nixos.org/build/247673319:

    In file included from /build/source/src/main_local_assemble.cpp:27:
    /build/source/src/localasm/local_assemble.h:31:3: error: 'uint32_t' does not name a type
       31 |   uint32_t kmin{11};
          |   ^~~~~~~~
    /build/source/src/localasm/local_assemble.h:1:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
      +++ |+#include <cstdint>
2024-02-10 10:26:43 +00:00
..
angsd angsd: pull patch pending upstream inclusion for parallel build fix 2023-08-20 08:50:53 +01:00
ants ants: 2.5.0 -> 2.5.1 2024-01-26 01:12:12 +01:00
aragorn aragorn: fix format 2023-06-08 18:42:29 +09:00
astral
bamtools bamtools: init at 2.5.2 2023-08-18 00:17:15 +09:00
bayescan
bcftools bcftools: 1.18 -> 1.19 2023-12-13 06:48:21 +00:00
bedops
bedtools bedtools: 2.31.0 -> 2.31.1 2023-11-09 06:18:08 +00:00
bftools
bioawk bioawk: init at unstable-2017-09-11 2023-08-18 00:36:09 +09:00
blast blast-bin: add sourceProvenance to meta 2023-10-07 10:12:24 +09:00
bowtie
bowtie2 bowtie2: 2.5.2 -> 2.5.3 2024-01-18 01:41:31 +00:00
bppsuite bppsuite: fix homepage 2023-06-15 12:18:11 -04:00
bwa bwa: add runHook 2023-05-15 16:13:49 +09:00
bwa-mem2 bwa-mem2: init at version 2.2.1 2023-08-23 15:02:06 -07:00
cd-hit
clustal-omega
cmtk cmtk: fix format 2023-07-11 17:50:47 +09:00
conglomerate
dcm2niix
deeptools deeptools: fix build 2024-01-28 12:17:37 -08:00
delly delly: 1.1.8 -> 1.2.6 2023-12-22 18:36:25 +00:00
diamond diamond: 2.1.7 -> 2.1.8 2023-06-25 04:35:30 +00:00
dssp dssp: 4.4.4.1 -> 4.4.5 2023-11-24 22:34:06 +09:00
ecopcr
eggnog-mapper eggnog-mapper: 2.1.10 -> 2.1.12 2024-01-18 19:17:47 +00:00
emboss
est-sfs
exonerate
EZminc
fastp fastp: 0.23.3 -> 0.23.4 2023-06-04 03:21:21 +00:00
febio-studio
flywheel-cli treewide: s_targetPlatform_hostPlatform_ in non-compiler packages 2023-11-17 08:07:34 +00:00
freebayes
gatk gatk: 4.4.0.0 -> 4.5.0.0 2023-12-15 04:20:42 +00:00
genmap
hh-suite hh-suite: fix build on GCC 13 2024-02-08 21:54:47 +00:00
hisat2
hmmer hmmer: add changelog to meta 2023-09-24 04:24:00 +00:00
igv igv: use jdk17 instead of jdk11 (#285521) 2024-02-01 14:42:34 +01:00
inormalize inormalize: fix build on darwin 2024-01-21 23:26:55 +01:00
iqtree iqtree: 2.2.2.6 -> 2.2.2.7 2023-08-25 12:25:13 +00:00
itsx
iv
jbrowse jbrowse: init at 2.5.0 2023-05-12 11:24:26 -07:00
kalign kalign: 3.3.5 -> 3.4.0 2023-12-11 06:26:11 +00:00
kallisto kallisto: 0.50.0 -> 0.50.1 2023-11-02 11:02:00 +00:00
kent perlPackages.BioBigFile: Addressing reviewer change 2023-11-21 23:16:39 +01:00
kssd kssd: enable aarch64-linux support & tests 2023-11-03 19:34:28 +09:00
last last: 1519 -> 1540 2024-02-06 06:07:25 +00:00
macs2 macs2: 2.2.8 -> 2.2.9.1 2023-08-11 14:45:45 -07:00
macse
mafft
manta
megahit megahit: fir gcc-13 build failure 2024-02-10 10:26:43 +00:00
meme-suite
messer-slim messer-slim: 4.0.1 -> 4.1 2023-12-16 20:13:33 +00:00
migrate
minc-tools
minc-widgets
minia
minimap2 minimap2: 2.25 -> 2.26 2023-05-03 19:38:48 +00:00
mmseqs2 mmseqs2: 14-7e284 -> 15-6f452 2023-11-01 09:19:34 +00:00
mni_autoreg
mrbayes
mrtrix mrtrix: unstable-2021-11-25 -> 3.0.4 2023-09-06 12:11:38 -04:00
muscle treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases 2023-08-03 16:32:03 +00:00
N3 n3: fix build on darwin 2024-01-21 23:22:54 +01:00
nest nest-mpi: 3.5 -> 3.6 2023-09-30 18:54:13 +00:00
neuron neuron-mpi: 8.2.2 -> 8.2.3 2023-09-23 02:33:53 +00:00
niftyreg
niftyseg
obitools treewide: replace lib/${python.libPrefix}/site-packages with its shorthand ${python.sitePackages} 2024-01-30 19:56:57 +01:00
octopus various packages: pin boost179 2023-07-22 16:54:22 +02:00
paml paml: refactor 2023-07-14 15:08:14 +09:00
picard-tools picard-tools: 3.1.0 -> 3.1.1 2023-11-15 14:35:32 +00:00
platypus
plink-ng
poretools poretools: mark as broken 2023-12-11 04:28:39 +00:00
prodigal
quast treewide: change pythonForBuild to pythonOnBuildForHost 2023-11-05 17:42:12 -08:00
raxml raxml: 8.2.12 -> 8.2.13 2023-10-16 22:16:12 +00:00
repseek
sambamba sambamba: 1.0.0 -> 1.0.1 2023-08-25 06:20:00 +00:00
samblaster
samtools samtools: 1.19 -> 1.19.2 2024-01-28 12:24:10 -08:00
seaview
seqkit seqkit: 2.6.1 -> 2.7.0 2024-02-01 04:24:02 +00:00
seqtk seqtk: 1.3 -> 1.4 2023-05-28 06:48:51 +00:00
snpeff
somatic-sniper
sortmerna treewide: replace -DCMAKE_BUILD_TYPE in cmakeFlags with cmakeBuildType 2023-09-08 14:18:26 +00:00
spades SPAdes: fix build 2024-01-20 15:28:48 -03:00
sratoolkit treewide: remove unneeded dots and slashes in sourceRoots 2023-08-12 08:29:56 +00:00
stacks stacks: 2.65 -> 2.66 2024-01-24 07:54:36 +00:00
star treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases 2023-08-03 16:32:03 +00:00
strelka strelka: add aarch64-linux support 2023-12-11 13:37:17 +01:00
subread subread: 2.0.5 -> 2.0.6 2023-05-10 22:30:35 +10:00
sumatools
svaba
tandem-aligner treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases 2023-08-03 16:32:03 +00:00
tebreak
treemix
trf
trimal treewide: remove execute bit for non-executable *.nix files 2023-10-20 19:55:39 +02:00
trimmomatic trimmomatic: make deterministic and clean up 2024-01-04 21:45:11 +01:00
truvari truvari: 4.0.0 -> 4.1.0 2023-10-07 01:30:27 +09:00
varscan
vcftools treewide: remove execute bit for non-executable *.nix files 2023-10-20 19:55:39 +02:00
veryfasttree veryfasttree: 4.0.2 -> 4.0.3 2023-09-12 06:13:28 +00:00
whisper whisper: enable parallel building 2024-01-25 19:27:12 +00:00
xenomapper