diff options
196 files changed, 352 insertions, 26 deletions
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py index 99075ec0b0..3d09e6a104 100644 --- a/var/spack/repos/builtin/packages/r-a4/package.py +++ b/var/spack/repos/builtin/packages/r-a4/package.py @@ -14,6 +14,7 @@ class RA4(RPackage): bioc = "a4" + version("1.46.0", commit="1b8f1300025fb0940e7f24cff7ffec9fca02d0e4") version("1.44.0", commit="5b0fc5a9971d8f3688ad1f88a4f5ee1498e91633") version("1.42.0", commit="fc26809e2bce7cd50d99d6f6dd5f85c38342fdea") version("1.38.0", commit="5b7a9087bab10c55e24707e96e48046995236c94") diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py index 8291f918c7..68d1458cc6 100644 --- a/var/spack/repos/builtin/packages/r-a4base/package.py +++ b/var/spack/repos/builtin/packages/r-a4base/package.py @@ -14,6 +14,7 @@ class RA4base(RPackage): bioc = "a4Base" + version("1.46.0", commit="be70ae723bb6031cdf9540d62dc6113761074e88") version("1.44.0", commit="9ae69e03118c7b14df0e6c9e3b25362b09f25bbe") version("1.42.0", commit="d7296e2792020e9c5b1c19101104326ee8bebfe6") version("1.38.0", commit="4add242fa9c62795aca5b0dfca34a43484c5aa82") diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py index 8de2c13eab..41c53d79c1 100644 --- a/var/spack/repos/builtin/packages/r-a4classif/package.py +++ b/var/spack/repos/builtin/packages/r-a4classif/package.py @@ -15,6 +15,7 @@ class RA4classif(RPackage): bioc = "a4Classif" + version("1.46.0", commit="96794183a76ab7da7a1863ccd421640254447af5") version("1.44.0", commit="df0fce781f9bc480a1159d958c9a63c314a9ed01") version("1.42.0", commit="820854a7ca9ed0c295479a25b7e3375c6d01d0b5") version("1.38.0", commit="c4d058813efb835774813b2d69c52912162f8e75") diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py index 09e2cc4f93..4bb4de584a 100644 --- a/var/spack/repos/builtin/packages/r-a4core/package.py +++ b/var/spack/repos/builtin/packages/r-a4core/package.py @@ -14,6 +14,7 @@ class RA4core(RPackage): bioc = "a4Core" + version("1.46.0", commit="8999fe146be6d04ae36c725d2b6324a6ce8ceb83") version("1.44.0", commit="61a7f3a51a41af615bfd4c22984e4c4a82874e8c") version("1.42.0", commit="6985950b72c2a0f20ec44fe2067d8864e004bfaa") version("1.38.0", commit="a027dcd3486c64950815ec7c7271f1f65ba3d8a1") diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py index 065595179b..131f0c79ee 100644 --- a/var/spack/repos/builtin/packages/r-a4preproc/package.py +++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py @@ -14,6 +14,7 @@ class RA4preproc(RPackage): bioc = "a4Preproc" + version("1.46.0", commit="8463958692c73fd655a6dfec39ea99c915513719") version("1.44.0", commit="252381265b96b83803a93e0c2014dd6b0574e57f") version("1.42.0", commit="773a91e884d2ada16fe9cf57d5ed53c0155e3fa2") version("1.38.0", commit="c93c223bd531bff090531a109b51f8dcd710d0cb") diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py index 1db0033d3e..2470d3b7ec 100644 --- a/var/spack/repos/builtin/packages/r-a4reporting/package.py +++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py @@ -14,6 +14,7 @@ class RA4reporting(RPackage): bioc = "a4Reporting" + version("1.46.0", commit="00b82d25bef4d518ae92f615d3a6f7931c0618dc") version("1.44.0", commit="bfe83507daf53e2e327474ea3012f0dc920efac1") version("1.42.0", commit="b0d715b9cdac80bc412f0a9a6b33941c4a7582bb") version("1.38.0", commit="cd3cf244e7a299b2485684ed15519cbbda1c590f") diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py index c7e4e10211..1e448c8896 100644 --- a/var/spack/repos/builtin/packages/r-absseq/package.py +++ b/var/spack/repos/builtin/packages/r-absseq/package.py @@ -17,6 +17,7 @@ class RAbsseq(RPackage): bioc = "ABSSeq" + version("1.52.0", commit="07038c047775e17d5d29909927d2143efb63e9cb") version("1.50.0", commit="4f384d04ebaae6ea0b56e5cff9a9dcdcb6c8afb0") version("1.48.0", commit="b237c967d44d075ca306c35e92df8b66a60ce72d") version("1.44.0", commit="c202b4a059021ed1228ccee7303c69b0aa4ca1ee") diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py index 655a9d4a1a..e47a9542e3 100644 --- a/var/spack/repos/builtin/packages/r-acde/package.py +++ b/var/spack/repos/builtin/packages/r-acde/package.py @@ -22,6 +22,7 @@ class RAcde(RPackage): bioc = "acde" + version("1.28.0", commit="0edccca7be2475fa2ae3b3c36d0d64924c37b3c0") version("1.26.0", commit="dfef9a435062e948efd5eda22942a0d500baa992") version("1.24.0", commit="0c3c4d47af7eaff37420032ea5245743a65124cf") version("1.20.0", commit="cefb4f2e2b0ef3c5f51944c0ece7a71294020350") diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py index 10e718e262..5006e073bc 100644 --- a/var/spack/repos/builtin/packages/r-acgh/package.py +++ b/var/spack/repos/builtin/packages/r-acgh/package.py @@ -16,6 +16,7 @@ class RAcgh(RPackage): bioc = "aCGH" + version("1.76.0", commit="c6068522854ed0b1c3feb006619ef25590f70ad6") version("1.74.0", commit="e7ba380af0da138788eb6c86f5dbe453269c0810") version("1.72.0", commit="b5d4022ac487125194d3913f1b8c2948db6e2792") version("1.68.0", commit="91f41a3917ddce43eb05e11c90eb99c467ba2247") diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py index c085078f13..53aff8f8d1 100644 --- a/var/spack/repos/builtin/packages/r-acme/package.py +++ b/var/spack/repos/builtin/packages/r-acme/package.py @@ -21,6 +21,7 @@ class RAcme(RPackage): bioc = "ACME" + version("2.54.0", commit="8d39d9d6623adf427f5eba308790e1de01213870") version("2.52.0", commit="14a97c722d0201654af9e583e7e462b458c28a77") version("2.50.0", commit="d55a19a8c091e8ea5fd35041520107a7f7603e14") version("2.46.0", commit="68f45c9f7d34c28adf6a0fc4245fdf63881109de") diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py index 8d65deccbb..5c31fb8df6 100644 --- a/var/spack/repos/builtin/packages/r-adsplit/package.py +++ b/var/spack/repos/builtin/packages/r-adsplit/package.py @@ -16,6 +16,7 @@ class RAdsplit(RPackage): bioc = "adSplit" + version("1.68.0", commit="705977b5e1cb7dd69793cc673fa215baaba42af5") version("1.66.0", commit="64580a6f7a9bc6b16334267c90df48fbb839cc16") version("1.64.0", commit="32f150eb51c66b867301dceeb527de5b97f9f490") version("1.60.0", commit="de5abccfe652cbc5b5f49fb6ed77cdd15cc760cd") diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py index 744bcbbe63..5e839e4853 100644 --- a/var/spack/repos/builtin/packages/r-affxparser/package.py +++ b/var/spack/repos/builtin/packages/r-affxparser/package.py @@ -20,6 +20,7 @@ class RAffxparser(RPackage): bioc = "affxparser" + version("1.70.0", commit="28f94cd3477e9500942be89cbcb5cad1bbb369fe") version("1.68.1", commit="821a01a2df18115a3b7864b3f45418255b7123eb") version("1.66.0", commit="2ea72d4c924ac14bdd807b23563c8501c226ce3a") version("1.62.0", commit="b3e988e5c136c3f1a064e1da13730b403c8704c0") diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py index e94ff7961f..7d57bb42e0 100644 --- a/var/spack/repos/builtin/packages/r-affy/package.py +++ b/var/spack/repos/builtin/packages/r-affy/package.py @@ -15,6 +15,7 @@ class RAffy(RPackage): bioc = "affy" + version("1.76.0", commit="3bb309388d5d6402c356d4a5270ee83c5b88942f") version("1.74.0", commit="2266c4a46eda7e5b64f7f3e17e8b61e7b85579ff") version("1.72.0", commit="3750b4eb8e5224b19100f6c881b67e568d8968a2") version("1.68.0", commit="1664399610c9aa519399445a2ef8bb9ea2233eac") diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py index 0cb8adb924..b3c58970dd 100644 --- a/var/spack/repos/builtin/packages/r-affycomp/package.py +++ b/var/spack/repos/builtin/packages/r-affycomp/package.py @@ -14,6 +14,7 @@ class RAffycomp(RPackage): bioc = "affycomp" + version("1.74.0", commit="1160d6395f23085456938ba2bd38fb45597fc92f") version("1.72.0", commit="c52baea98b80abd4a99380ac9d4b68ef91869d40") version("1.70.0", commit="487f6775975092475581a6c02ddb27590559cf07") version("1.66.0", commit="388d01af8b1e6ab11051407f77d0206512df8424") diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py index 3268041076..edb7d9f308 100644 --- a/var/spack/repos/builtin/packages/r-affycompatible/package.py +++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py @@ -18,6 +18,7 @@ class RAffycompatible(RPackage): bioc = "AffyCompatible" + version("1.58.0", commit="6508e72736371d353ec5f02d30caf8ffe39b342a") version("1.56.0", commit="37ea4bb885c791fb989f40092f3d0d2c57d35641") version("1.54.0", commit="fde7d86ccdb03c13c4838c18ac25477ffe6e0fe5") version("1.50.0", commit="3b12d12bd6d1a9f0d45e012817231d137d47089e") diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py index 1265d709bb..4e85fbe081 100644 --- a/var/spack/repos/builtin/packages/r-affycontam/package.py +++ b/var/spack/repos/builtin/packages/r-affycontam/package.py @@ -14,6 +14,7 @@ class RAffycontam(RPackage): bioc = "affyContam" + version("1.56.0", commit="e2b8a4fba1648255eadce954a848f2dd8e22bcb3") version("1.54.0", commit="c5208b48b8881983ff53a4713244327e8ad13b78") version("1.52.0", commit="47c1d86da330f157d3ece0e26b0657d66a5ca0c9") version("1.48.0", commit="88387a2ad4be4234d36710c65f2ca3a5b06b67da") diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py index c0c86de44b..bc7a174684 100644 --- a/var/spack/repos/builtin/packages/r-affycoretools/package.py +++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py @@ -15,6 +15,7 @@ class RAffycoretools(RPackage): bioc = "affycoretools" + version("1.70.0", commit="f09a788aa83e1e052a7c5f148a451a99fe9c9c96") version("1.68.1", commit="69546b1fe5edd71eca130d53d33f0fb0fcf62c97") version("1.66.0", commit="6bf769d70e196634097f465ed2fa85cce5312a6d") version("1.62.0", commit="c9779e4da648fd174c9bd575c6020be1c03047c4") diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py index c270226a65..d2da968049 100644 --- a/var/spack/repos/builtin/packages/r-affydata/package.py +++ b/var/spack/repos/builtin/packages/r-affydata/package.py @@ -15,6 +15,7 @@ class RAffydata(RPackage): bioc = "affydata" + version("1.46.0", commit="870745b886df9f1fbbd6130d266c0ef96f3afa66") version("1.44.0", commit="f18304a356cee8cd7297bab362b13c40e50439df") version("1.42.0", commit="4b54c1206bedd27ff9be32affc999a279f4e96f0") version("1.38.0", commit="b5e843b2514789d0d87bea44d762c89a95314ee7") diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py index 4603fcb16b..ff83536dde 100644 --- a/var/spack/repos/builtin/packages/r-affyilm/package.py +++ b/var/spack/repos/builtin/packages/r-affyilm/package.py @@ -16,6 +16,7 @@ class RAffyilm(RPackage): bioc = "affyILM" + version("1.50.0", commit="185cd8e4712a3378ce7a156d4940224bbb2c4122") version("1.48.0", commit="4603a4c4d6c2330a8a56a7bb657dc56c51a9393a") version("1.46.0", commit="67ffbfa6c881ed83d15604bf4463fe5dba81036b") version("1.42.0", commit="b97b29786b866de38802ebbb995169be91e90942") diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py index 076bc86f11..eb66279855 100644 --- a/var/spack/repos/builtin/packages/r-affyio/package.py +++ b/var/spack/repos/builtin/packages/r-affyio/package.py @@ -15,6 +15,7 @@ class RAffyio(RPackage): bioc = "affyio" + version("1.68.0", commit="33080c5eeb14c0ca40f0d231706af4e0c2c1ef8b") version("1.66.0", commit="3a0b90704fc46cddd99a72b985a6bdb348f69b50") version("1.64.0", commit="aa7ce48f3f4110431f6f488d45961fde4019ffb0") version("1.60.0", commit="ee20528b32700e99768da48143d6d45c9a7bbe91") diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py index 91191386b6..2798c7d320 100644 --- a/var/spack/repos/builtin/packages/r-affyplm/package.py +++ b/var/spack/repos/builtin/packages/r-affyplm/package.py @@ -17,6 +17,7 @@ class RAffyplm(RPackage): bioc = "affyPLM" + version("1.74.0", commit="5f76ef92e69deabc19c5395eaec4adb85c66b63d") version("1.72.0", commit="394c0a8e213f188d0b1d01e20516df8bf1bc5c09") version("1.70.0", commit="64abfec92b347aa340b54a8c7b2fbd524fe9c312") version("1.66.0", commit="f0780c3d0e9dccaff83861b98beb5c1d324c4399") diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py index 0d97b485ca..28003c9979 100644 --- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py +++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py @@ -18,6 +18,7 @@ class RAffyrnadegradation(RPackage): bioc = "AffyRNADegradation" + version("1.44.0", commit="63881f41fc67cc7322b189446dcffb4e1060e303") version("1.42.0", commit="5775f41f538b3c8ee4d07d38cec1b49c548cebe6") version("1.40.0", commit="8539a91ee464d692a267bb17c91dc1ef9a231f41") version("1.36.0", commit="89662b93076659db2967a526899184c12c156bc5") diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py index beb885af15..9a5333f601 100644 --- a/var/spack/repos/builtin/packages/r-agdex/package.py +++ b/var/spack/repos/builtin/packages/r-agdex/package.py @@ -14,6 +14,7 @@ class RAgdex(RPackage): bioc = "AGDEX" + version("1.46.0", commit="d7c38e8bdcaa7b0261117c605e7f61e2b07e8316") version("1.44.0", commit="9d3eb90eaf7bf093c7fa73facb3df89506a85185") version("1.42.0", commit="175cf1b384b0942103d841b1feb9e4f7d141ba06") version("1.38.0", commit="7e2c1f5f27ccbea6a7157f5122212e40408b74da") diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py index fcb6cc1fbf..b8ebae3c67 100644 --- a/var/spack/repos/builtin/packages/r-agilp/package.py +++ b/var/spack/repos/builtin/packages/r-agilp/package.py @@ -13,6 +13,7 @@ class RAgilp(RPackage): bioc = "agilp" + version("3.30.0", commit="a2c898dc901ccdda4b8582caff079ab20b1bfc28") version("3.28.0", commit="2c6dfccc76473b5bef13b75fa59adf46b3381f55") version("3.26.0", commit="3170fe2b1cc459d5e2ca7f61a127aac17cd66a96") version("3.22.0", commit="7d089d576752e0526f15a1007e94436089954313") diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py index 9a1f616266..f6e6aca334 100644 --- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py +++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py @@ -14,6 +14,7 @@ class RAgimicrorna(RPackage): bioc = "AgiMicroRna" + version("2.48.0", commit="4c163b1b730150a3a60a3815bd8c08fa04d71fc1") version("2.46.0", commit="8c6d73e1c3f1f9cc019bdb219b19e6179bb1efe4") version("2.44.0", commit="8b308baa3b1b0afc0855ea263630a288689e3864") version("2.40.0", commit="cfa4acb2215da44767ab3a45845bcd587c309e74") diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py index cad30b0940..2bc542f414 100644 --- a/var/spack/repos/builtin/packages/r-aims/package.py +++ b/var/spack/repos/builtin/packages/r-aims/package.py @@ -17,6 +17,7 @@ class RAims(RPackage): bioc = "AIMS" + version("1.30.0", commit="2ab61159c5aa0902cc33fc1502f7853b66912cce") version("1.28.0", commit="84608df638b5694c08158ed77ad2c8a64c4e594b") version("1.26.0", commit="5dcf60eb4cdcf563ea848482c9c488f465c27bbd") version("1.22.0", commit="34a38978b24377abb864eff7683bb36344ff171d") diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py index ff4d070d4a..259aec76b6 100644 --- a/var/spack/repos/builtin/packages/r-aldex2/package.py +++ b/var/spack/repos/builtin/packages/r-aldex2/package.py @@ -23,6 +23,7 @@ class RAldex2(RPackage): bioc = "ALDEx2" + version("1.30.0", commit="cb6670515a8722f9cfedac12a8c2747a5298ee46") version("1.28.1", commit="f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6") version("1.26.0", commit="0876a2eac08d3f1c01df7414d97d391c80182ada") version("1.22.0", commit="ac7f0ab3f094ec52713da7620a27058b14c7181d") diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py index 4f91c95546..ec6e85bf7c 100644 --- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py +++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py @@ -14,6 +14,7 @@ class RAllelicimbalance(RPackage): bioc = "AllelicImbalance" + version("1.36.0", commit="cb4910c1fd58cc4272c21251a8f120990e1aa431") version("1.34.0", commit="290708ccc4ceae1fbb9e9257cb254916449d389b") version("1.32.0", commit="428ab8c96bb15fab45e4084da25f98b01b9d60b6") version("1.28.0", commit="ac5d13c9ee0935bf9500ee542792644e752a1fde") diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py index 5749ff9f73..9625c58160 100644 --- a/var/spack/repos/builtin/packages/r-alpine/package.py +++ b/var/spack/repos/builtin/packages/r-alpine/package.py @@ -14,6 +14,7 @@ class RAlpine(RPackage): bioc = "alpine" + version("1.24.0", commit="7e734d49881761cafaacea096ce757531b6bd522") version("1.22.0", commit="6107a82962f07e0434e93f261cd375eaaa171d91") version("1.20.0", commit="9348ef14128aa6be10cca1987736ddbc385df7e9") version("1.16.0", commit="aee397774ac6cd17ad45dc05be14c526647f3c13") diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py index dad3870c21..db2c5fc1b1 100644 --- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py +++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py @@ -13,6 +13,7 @@ class RAltcdfenvs(RPackage): bioc = "altcdfenvs" + version("2.60.0", commit="0bc0b4493b8e9fe2eb47fb8e9377123ce8f472bb") version("2.58.0", commit="08255a777ffa1e1414d3dd3062d95bfdd3dfd47c") version("2.56.0", commit="941e00b97a33662a8230991e387070324b2e76bf") version("2.52.0", commit="21329abf82eae26f84b7c0270e81c8e089c548ce") diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py index 35233d51a0..e748cdd16b 100644 --- a/var/spack/repos/builtin/packages/r-anaquin/package.py +++ b/var/spack/repos/builtin/packages/r-anaquin/package.py @@ -17,6 +17,7 @@ class RAnaquin(RPackage): bioc = "Anaquin" + version("2.22.0", commit="d848a9bd7bf9d1d62202cc477300bf1a65b3e36c") version("2.20.0", commit="61598dd3430b09b57f31d7d550ea95126a2d73c8") version("2.18.0", commit="c8e3df3e299c32daac0dda23cea59a18673d886b") version("2.14.0", commit="d0a34c931a0e72080bff91dacb37dbbe26b45386") diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py index 1b0d49048b..4c62741bb3 100644 --- a/var/spack/repos/builtin/packages/r-aneufinder/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py @@ -15,6 +15,7 @@ class RAneufinder(RPackage): bioc = "AneuFinder" + version("1.26.0", commit="7cd59a1e24c6512f2e4fcbe2c53a0d3cd2d06217") version("1.24.0", commit="4c6906eee514eba3e8ac159654a6953e37a99bba") version("1.22.0", commit="ea0beb3d827c2dd4bc56708a839a93c55304918b") version("1.18.0", commit="76ec9af947f97212084ca478e8e82f9e0eb79de9") diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py index ea147a4775..8b784c8512 100644 --- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py +++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py @@ -14,6 +14,7 @@ class RAneufinderdata(RPackage): bioc = "AneuFinderData" + version("1.26.0", commit="4b810599b62a3fb39239bfd98ed960c93989e86b") version("1.24.0", commit="cf6f3852702aab28e3170fc56b695d00b7389666") version("1.22.0", commit="ae8eec3b0afdc351dc447aad2024df5b2c75e56b") version("1.18.0", commit="1bf1657b28fc8c1425e611980a692da952ce3d1e") diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py index 32b9f63d67..7aaad6660c 100644 --- a/var/spack/repos/builtin/packages/r-annaffy/package.py +++ b/var/spack/repos/builtin/packages/r-annaffy/package.py @@ -16,6 +16,7 @@ class RAnnaffy(RPackage): bioc = "annaffy" + version("1.70.0", commit="c99e81259adb39b5d8e954fd7afe7f93675229bc") version("1.68.0", commit="fa930c0bbdca9828a130ab06d86c65d451380830") version("1.66.0", commit="aa1afa1509754128d27508228c1f39f51a8da043") version("1.62.0", commit="ad9c37e0e7e45e0f35c208ce528ba48000b37432") diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py index 0c20c2fe59..34639af484 100644 --- a/var/spack/repos/builtin/packages/r-annotate/package.py +++ b/var/spack/repos/builtin/packages/r-annotate/package.py @@ -13,6 +13,7 @@ class RAnnotate(RPackage): bioc = "annotate" + version("1.76.0", commit="0181d5c41d594e36be06adb6a02302db0ad2c507") version("1.74.0", commit="200c71743417792880f8171d59b2ac0ddd3902a8") version("1.72.0", commit="67ac76a9ff6d60dc1620763d3aa98aef39443110") version("1.68.0", commit="98cdb12c612b3f3fc06329a89a1ffb0a92b555c0") diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py index 04a2faf0e0..67796d367f 100644 --- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py +++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py @@ -14,6 +14,7 @@ class RAnnotationdbi(RPackage): bioc = "AnnotationDbi" + version("1.60.0", commit="cd61bd1b1538e2f1f411fd7087820749ecf39da8") version("1.58.0", commit="05fcf7a28a6b15b195da23474d7ba89bd0cfd891") version("1.56.2", commit="13fdc4a93852199ca6ec120a2fe1078f9f445f67") version("1.52.0", commit="c4e0ca9bd65362ae9cad6a98d90f54267b0ae838") diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py index 1044dc9819..246079e9fd 100644 --- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py +++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py @@ -15,6 +15,7 @@ class RAnnotationfilter(RPackage): bioc = "AnnotationFilter" + version("1.22.0", commit="c9fea4a829ce9419b6e0af987915b2d469358597") version("1.20.0", commit="2818aff6502fd6fe819521cd8d97695ef6f9198e") version("1.18.0", commit="60a9b666d7362d7ed5c357fd4a5d2744d8598c20") version("1.14.0", commit="6ee3a13ed93a535ed452cbc8c118151a2cbb732c") diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py index cab4169145..de79e0586b 100644 --- a/var/spack/repos/builtin/packages/r-annotationforge/package.py +++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py @@ -14,6 +14,7 @@ class RAnnotationforge(RPackage): bioc = "AnnotationForge" + version("1.40.0", commit="f77d3a942eb6b18c18888b7af3f0e652596cf19f") version("1.38.1", commit="2dcedf353bc57bf80818e6adb1f7129c21886f6b") version("1.38.0", commit="1f77750562ea3a01f0f1a46c299184fc31196ffd") version("1.36.0", commit="523b5f0c3ffb77e59e1568e5f36a5a470bfeeae5") diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py index aa9f457af0..d67dec6b80 100644 --- a/var/spack/repos/builtin/packages/r-annotationhub/package.py +++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py @@ -20,6 +20,7 @@ class RAnnotationhub(RPackage): bioc = "AnnotationHub" + version("3.6.0", commit="3315a73b7803a92412ed18209dd37b378195b86f") version("3.4.0", commit="e74e54ca44f50c2c15c60f8620e3d1721f8f5b6d") version("3.2.1", commit="ad1dfe86f0b0ea4711cc9cdb89e073e8794ec9aa") version("2.22.0", commit="3ab7dceebbc31ac14ca931f66c662cf9538b7d0a") diff --git a/var/spack/repos/builtin/packages/r-aroma-light/package.py b/var/spack/repos/builtin/packages/r-aroma-light/package.py index 8d65bfea57..bcf1315321 100644 --- a/var/spack/repos/builtin/packages/r-aroma-light/package.py +++ b/var/spack/repos/builtin/packages/r-aroma-light/package.py @@ -16,6 +16,7 @@ class RAromaLight(RPackage): bioc = "aroma.light" + version("3.28.0", commit="7749dd7033e9885ec2546a5cac0562bac2fea04d") version("3.26.0", commit="7ead7517a77bc8b4b4b42aace69957a17e8fe016") version("3.24.0", commit="3ff48b8f546acc9803b3c652363cac78d3b81ae5") version("3.20.0", commit="02cde7fa166259bce73c396a87dca2ecc8249c39") diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py index 918459d049..9f32603a7e 100644 --- a/var/spack/repos/builtin/packages/r-bamsignals/package.py +++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py @@ -16,6 +16,7 @@ class RBamsignals(RPackage): bioc = "bamsignals" + version("1.30.0", commit="aac37dffd6f6876b4626866e3d40bb7af75620fe") version("1.28.0", commit="27b70be6f73747d9d32054da043f4a37ea55b917") version("1.26.0", commit="d57643441d04f77db0907637dc9e7cd5bed5842f") version("1.22.0", commit="5f533969c84212406bcb3ebf725ebb6d77e9947a") diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py index 6d44251654..d63237052d 100644 --- a/var/spack/repos/builtin/packages/r-beachmat/package.py +++ b/var/spack/repos/builtin/packages/r-beachmat/package.py @@ -17,6 +17,7 @@ class RBeachmat(RPackage): bioc = "beachmat" + version("2.14.0", commit="5a4b85f4a22f3447f12d03157ab95de73f6137c6") version("2.12.0", commit="3e6af145bdcdf0a0b722d8256ba1a38b8a36b2f5") version("2.10.0", commit="b7cc532d4a5b26d9073135cc9945258ea08e5079") version("2.6.4", commit="7d9dc6379017d723dda3e8dc9fd1f6de7fd33cdb") diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py index 8c70568a68..dbb1f93ecc 100644 --- a/var/spack/repos/builtin/packages/r-biobase/package.py +++ b/var/spack/repos/builtin/packages/r-biobase/package.py @@ -14,6 +14,7 @@ class RBiobase(RPackage): bioc = "Biobase" + version("2.58.0", commit="767f2f33f158f233616178e12ce08cdb03d2a5a2") version("2.56.0", commit="3b2dd91b333677c2f27257c7624014a55e73c52b") version("2.54.0", commit="8215d76ce44899e6d10fe8a2f503821a94ef6b40") version("2.50.0", commit="9927f90d0676382f2f99e099d8d2c8e2e6f1b4de") diff --git a/var/spack/repos/builtin/packages/r-biocfilecache/package.py b/var/spack/repos/builtin/packages/r-biocfilecache/package.py index 32b253a9fd..a7cfb55cb1 100644 --- a/var/spack/repos/builtin/packages/r-biocfilecache/package.py +++ b/var/spack/repos/builtin/packages/r-biocfilecache/package.py @@ -16,6 +16,7 @@ class RBiocfilecache(RPackage): bioc = "BiocFileCache" + version("2.6.0", commit="f5b8368c1402b15e8db8eab59217f1176e902e6f") version("2.4.0", commit="2c00eee40d95fddad223f115f959b09e1a14f75d") version("2.2.1", commit="cc912123408803193bf37395f4d18baa8dcd6f47") version("1.14.0", commit="cdcde4b59ae73dda12aa225948dbd0a058d9be6d") diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py index 758593b153..a6e6f09d4f 100644 --- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py @@ -13,6 +13,7 @@ class RBiocgenerics(RPackage): bioc = "BiocGenerics" + version("0.44.0", commit="d7cd9c19958bd8d4573d980494188fa15ab16e45") version("0.42.0", commit="3582d47b836387afc08157f3d6a5013fd64334ed") version("0.40.0", commit="0bc1e0ed4d20c7101cd782a14f6373e27478acfc") version("0.36.0", commit="0d5d169d7d64d648a22f9043837c93bc784e71ed") diff --git a/var/spack/repos/builtin/packages/r-biocio/package.py b/var/spack/repos/builtin/packages/r-biocio/package.py index 8a48770230..dbef28f512 100644 --- a/var/spack/repos/builtin/packages/r-biocio/package.py +++ b/var/spack/repos/builtin/packages/r-biocio/package.py @@ -22,9 +22,11 @@ class RBiocio(RPackage): bioc = "BiocIO" + version("1.8.0", commit="4a719fa41e014b7b948f7b245e581ede6a04eda1") version("1.6.0", commit="60c8aa1a961e43bf0ee5d563a6d9fcec84f7f8f8") version("1.4.0", commit="c335932526a38c75dbfa4970c1d90b8a21466d37") depends_on("r@4.0.0:", type=("build", "run")) + depends_on("r@4.0:", type=("build", "run"), when="@1.8.0:") depends_on("r-biocgenerics", type=("build", "run")) depends_on("r-s4vectors", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-biocneighbors/package.py b/var/spack/repos/builtin/packages/r-biocneighbors/package.py index 1ce09e75bf..3239d3a787 100644 --- a/var/spack/repos/builtin/packages/r-biocneighbors/package.py +++ b/var/spack/repos/builtin/packages/r-biocneighbors/package.py @@ -21,6 +21,7 @@ class RBiocneighbors(RPackage): bioc = "BiocNeighbors" + version("1.16.0", commit="3b227beead424314aab5ef847222f8f4243c684f") version("1.14.0", commit="670a1bd4d82636d28fbff50cea2157e16bb1a858") version("1.12.0", commit="3c8a290f75adc944b408e6e77a36f3a0c1509c4c") version("1.8.2", commit="889bc91f8cb45d210b47ae5c0b9cfb86fb071ca2") diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py index 0a315307a9..42f8e23529 100644 --- a/var/spack/repos/builtin/packages/r-biocparallel/package.py +++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py @@ -15,6 +15,7 @@ class RBiocparallel(RPackage): bioc = "BiocParallel" + version("1.32.1", commit="6c85dbad596a74a6d3022173a4a11c6b81a4a2c2") version("1.30.4", commit="1229ebe9f6d8305f9f61e562464f83f9ba86e699") version("1.30.2", commit="e7e109f7a94dbfbc50f926be030c7ad8c1a053db") version("1.28.3", commit="2f9d88ad83659939e7911d49c2d24d2cd599c7cc") @@ -30,3 +31,4 @@ class RBiocparallel(RPackage): depends_on("r-snow", type=("build", "run")) depends_on("r-codetools", type=("build", "run"), when="@1.30.4:") depends_on("r-bh", type=("build", "run"), when="@1.12.0:") + depends_on("r-cpp11", type=("build", "run"), when="@1.32.1:") diff --git a/var/spack/repos/builtin/packages/r-biocsingular/package.py b/var/spack/repos/builtin/packages/r-biocsingular/package.py index f243753aef..30e220d638 100644 --- a/var/spack/repos/builtin/packages/r-biocsingular/package.py +++ b/var/spack/repos/builtin/packages/r-biocsingular/package.py @@ -17,6 +17,7 @@ class RBiocsingular(RPackage): bioc = "BiocSingular" + version("1.14.0", commit="6dc42b30110e498f6694f18037f991c1006c71b7") version("1.12.0", commit="7d1b8f4954e9e6f2c30a5111cdab9aabc8bcc3a6") version("1.10.0", commit="6615ae8cb124aba6507447c1081bd2eba655e57d") version("1.6.0", commit="11baf1080d6f791439cd5d97357589d6451643d9") diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py index 3f7806c856..25a3aed9b8 100644 --- a/var/spack/repos/builtin/packages/r-biocstyle/package.py +++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py @@ -14,6 +14,7 @@ class RBiocstyle(RPackage): bioc = "BiocStyle" + version("2.26.0", commit="add035498bdce76d71a0afa22a063c2d8e5588bc") version("2.24.0", commit="53095b534b7e6c80a33a67b5f2db0db8f00db902") version("2.22.0", commit="86250b637afa3a3463fac939b99c0402b47876ea") version("2.18.1", commit="956f0654e8e18882ba09305742401128c9c7d47d") diff --git a/var/spack/repos/builtin/packages/r-biocversion/package.py b/var/spack/repos/builtin/packages/r-biocversion/package.py index 0cb2d029c3..8b4d28f78a 100644 --- a/var/spack/repos/builtin/packages/r-biocversion/package.py +++ b/var/spack/repos/builtin/packages/r-biocversion/package.py @@ -14,6 +14,7 @@ class RBiocversion(RPackage): bioc = "BiocVersion" + version("3.16.0", commit="c681e06fe30ea6815f958c1a3c74c090863680ba") version("3.15.2", commit="818ab03b6a3551993b712e3702126040f9fb7600") version("3.14.0", commit="aa56d93d0ea5dcdbf301f120502981740fd91e1e") version("3.12.0", commit="23b971963c6b73550a7e330dab5a046d58ce0223") diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py index ea6974e11e..59a558e8df 100644 --- a/var/spack/repos/builtin/packages/r-biomart/package.py +++ b/var/spack/repos/builtin/packages/r-biomart/package.py @@ -24,6 +24,7 @@ class RBiomart(RPackage): bioc = "biomaRt" + version("2.54.0", commit="4fb88fb56c684d5678f8288ba05db193e4881758") version("2.52.0", commit="cf4932ac02686da45ea36ff5137fa63cead8860b") version("2.50.3", commit="83a519ac13d73dc545cb6aafde5f4b5001e9e08f") version("2.46.2", commit="90d6abfdfa04259006f7b47efb10271ada76aec1") diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py index e4c8f0748e..70f0d6f1fe 100644 --- a/var/spack/repos/builtin/packages/r-biomformat/package.py +++ b/var/spack/repos/builtin/packages/r-biomformat/package.py @@ -21,6 +21,7 @@ class RBiomformat(RPackage): bioc = "biomformat" + version("1.26.0", commit="f851ba2428b57769f6fbb287874bad0dc84dd69c") version("1.24.0", commit="4e14692dbcc34c3bd51defd74c728df5de9d0829") version("1.22.0", commit="ab7c6411a038fec010baa72e663f362fd972cb34") version("1.18.0", commit="dc18859c139f4d76805adb6f01e199573cdd5a8b") diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py index b4fa9866a0..9b981f1892 100644 --- a/var/spack/repos/builtin/packages/r-biostrings/package.py +++ b/var/spack/repos/builtin/packages/r-biostrings/package.py @@ -15,6 +15,7 @@ class RBiostrings(RPackage): bioc = "Biostrings" + version("2.66.0", commit="3470ca7da798971e2c3a595d8dc8d0d86f14dc53") version("2.64.1", commit="ffe263e958463bd1edb5d5d9316cfd89905be53c") version("2.64.0", commit="c7ad3c7af607bc8fe4a5e1c37f09e6c9bf70b4f6") version("2.62.0", commit="53ed287e03d16fa523789af3131c60375ccf587f") @@ -41,10 +42,12 @@ class RBiostrings(RPackage): depends_on("r-iranges@2.13.24:", type=("build", "run"), when="@2.48.0:") depends_on("r-iranges@2.23.9:", type=("build", "run"), when="@2.58.0:") depends_on("r-iranges@2.30.1:", type=("build", "run"), when="@2.64.1:") + depends_on("r-iranges@2.31.2:", type=("build", "run"), when="@2.66.0:") depends_on("r-xvector@0.11.6:", type=("build", "run")) depends_on("r-xvector@0.19.8:", type=("build", "run"), when="@2.48.0:") depends_on("r-xvector@0.21.4:", type=("build", "run"), when="@2.50.2:") depends_on("r-xvector@0.23.2:", type=("build", "run"), when="@2.52.0:") depends_on("r-xvector@0.29.2:", type=("build", "run"), when="@2.58.0:") + depends_on("r-xvector@0.37.1:", type=("build", "run"), when="@2.66.0:") depends_on("r-genomeinfodb", type=("build", "run"), when="@2.62.0:") depends_on("r-crayon", type=("build", "run"), when="@2.58.0:") diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py index 4bd20f3965..9ddb8c3bc7 100644 --- a/var/spack/repos/builtin/packages/r-biovizbase/package.py +++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py @@ -16,6 +16,7 @@ class RBiovizbase(RPackage): bioc = "biovizBase" + version("1.46.0", commit="a47060cfb68e3f3b4876114af932823aed5d2d57") version("1.44.0", commit="a8f05c56c27b278524033cb896a6c97f3ee0081c") version("1.42.0", commit="f1627b2b567471837daca6e763acfc3e13937461") version("1.38.0", commit="d0f3362e0ad0e90b4b1d3e47b13ed57907d03403") diff --git a/var/spack/repos/builtin/packages/r-bluster/package.py b/var/spack/repos/builtin/packages/r-bluster/package.py index 7b31b4e185..990f70a480 100644 --- a/var/spack/repos/builtin/packages/r-bluster/package.py +++ b/var/spack/repos/builtin/packages/r-bluster/package.py @@ -16,6 +16,7 @@ class RBluster(RPackage): bioc = "bluster" + version("1.8.0", commit="156115c8960c0b66b2c588d9fd8bbdfe56e5f0be") version("1.6.0", commit="ff86c7d8d36233e838d4f00e6a4e173e7bf16816") depends_on("r-cluster", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py index e5ef5bf9f8..fbabec3e85 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py @@ -19,13 +19,13 @@ class RBsgenomeHsapiensUcscHg19(RPackage): version( "1.4.3", - sha256="5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a", url="https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz", + sha256="5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a", ) version( "1.4.0", - sha256="88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8", url="https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz", + sha256="88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8", ) depends_on("r-bsgenome@1.33.5:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py index 8780cdcdb3..5d4dba97e0 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py @@ -14,6 +14,7 @@ class RBsgenome(RPackage): bioc = "BSgenome" + version("1.66.1", commit="d1efdfa8e7242bc0f54cc1c3a9583ea555c924f6") version("1.64.0", commit="59cdebde613e9702985c003f699f4aea2b0f0e7b") version("1.62.0", commit="9b1859e11ffa082833f035a45274af6e4e83e863") version("1.58.0", commit="3a4926e03a7a1d7140a10c1b2bf6090808470145") diff --git a/var/spack/repos/builtin/packages/r-bsseq/package.py b/var/spack/repos/builtin/packages/r-bsseq/package.py index b67d75090c..76d5474d5c 100644 --- a/var/spack/repos/builtin/packages/r-bsseq/package.py +++ b/var/spack/repos/builtin/packages/r-bsseq/package.py @@ -14,6 +14,7 @@ class RBsseq(RPackage): bioc = "bsseq" + version("1.34.0", commit="98239c07d74e1362c7ba2a3bf4f6119830fc95dc") version("1.32.0", commit="a0c1eacbc479c57bd836e885e162c28bbe08e115") version("1.30.0", commit="7eb5223e9ee02fd08a52be56eaa9316a67c0d66b") version("1.26.0", commit="fae32292687625012a2938a48c93df55ad4257b5") diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py index a6b8e6b07c..5df9e1cff7 100644 --- a/var/spack/repos/builtin/packages/r-bumphunter/package.py +++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py @@ -13,6 +13,7 @@ class RBumphunter(RPackage): bioc = "bumphunter" + version("1.40.0", commit="3de207a3659859737d4c748fc8023694943da43b") version("1.38.0", commit="06e2fa87b342d48793d0d2f1f7d94a95a6613995") version("1.36.0", commit="db50fcf7798c2eddfe48fd510d081dda82f2ee4e") version("1.32.0", commit="b7d39c2a6385ca217dceefc918b3ccd5c31bbaa0") diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py index cdcc8555f8..0b6c60d41c 100644 --- a/var/spack/repos/builtin/packages/r-category/package.py +++ b/var/spack/repos/builtin/packages/r-category/package.py @@ -14,6 +14,7 @@ class RCategory(RPackage): bioc = "Category" + version("2.64.0", commit="b512cbeb22fc50a2f6d767a2eef356fb143a974e") version("2.62.0", commit="0fe801c0c443aebd5d4cefa8c30e4e7d0931b673") version("2.60.0", commit="55210d8c539474954d18cf913a219dce883eac2e") version("2.56.0", commit="ad478caa9d693dbc2770608e79dd852375b9a223") diff --git a/var/spack/repos/builtin/packages/r-champ/package.py b/var/spack/repos/builtin/packages/r-champ/package.py index 0950bc4718..4968a82559 100644 --- a/var/spack/repos/builtin/packages/r-champ/package.py +++ b/var/spack/repos/builtin/packages/r-champ/package.py @@ -16,6 +16,7 @@ class RChamp(RPackage): bioc = "ChAMP" + version("2.28.0", commit="3d27ac67a738afea8cc9ece6ea1301120e4b48f7") version("2.26.0", commit="1548910bf53e1e5f7a8d80c83b742a94297d8a34") version("2.24.0", commit="7ba19da74b61e1c40ced162ba753f0f9b9c7647a") version("2.20.1", commit="99ea0463bce59f5b06bcc91f479dcd4065074896") diff --git a/var/spack/repos/builtin/packages/r-champdata/package.py b/var/spack/repos/builtin/packages/r-champdata/package.py index d99fe71baa..00dcdc1724 100644 --- a/var/spack/repos/builtin/packages/r-champdata/package.py +++ b/var/spack/repos/builtin/packages/r-champdata/package.py @@ -14,6 +14,7 @@ class RChampdata(RPackage): bioc = "ChAMPdata" + version("2.30.0", commit="6e05b8f7b004b1a5185ec4b387c32725e8bd95cb") version("2.28.0", commit="601555bf599828b6cfa125beffa51aebccdc8503") version("2.26.0", commit="ea7882707921af33eefab5133a1ccd4a409f045d") version("2.22.0", commit="eeedd4c477fac79f00743da8ff7da064221c5f3d") diff --git a/var/spack/repos/builtin/packages/r-chipseq/package.py b/var/spack/repos/builtin/packages/r-chipseq/package.py index d1d302dd58..bbaaff8afd 100644 --- a/var/spack/repos/builtin/packages/r-chipseq/package.py +++ b/var/spack/repos/builtin/packages/r-chipseq/package.py @@ -15,6 +15,7 @@ class RChipseq(RPackage): maintainers = ["dorton21"] + version("1.48.0", commit="9c78296001b6dd4102318879c8504dac70015822") version("1.46.0", commit="76b00397cd117d5432158f50fc1032d50485bd24") version("1.44.0", commit="b64d0d28e9fcf0fdab9a7f9c521baf729426a594") version("1.40.0", commit="84bcbc0b7ad732730b5989a308f1624a6a358df1") diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py index 3f3d83bb60..1c0ec2592d 100644 --- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py +++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py @@ -15,6 +15,7 @@ class RClusterprofiler(RPackage): bioc = "clusterProfiler" + version("4.6.0", commit="2644118c36a3aa14408bc0c97ac20a545e40344d") version("4.4.4", commit="9fca9a45ca1793884d8dcfd0f077353dbf75df29") version("4.4.1", commit="daad11fb80be2dd9b825e0b484815a0a2b1592a4") version("4.2.2", commit="4ebb9de8e03eedc971f54a57cf5bf1b250ed43d5") @@ -34,12 +35,14 @@ class RClusterprofiler(RPackage): depends_on("r-dose@3.3.2:", type=("build", "run"), when="@3.6.0:") depends_on("r-dose@3.5.1:", type=("build", "run"), when="@3.8.1:") depends_on("r-dose@3.13.1:", type=("build", "run"), when="@3.18.0:") + depends_on("r-dose@3.23.2:", type=("build", "run"), when="@4.6.0:") depends_on("r-dplyr", type=("build", "run"), when="@3.18.0:") depends_on("r-enrichplot@0.99.7:", type=("build", "run"), when="@3.8.1:") depends_on("r-enrichplot@1.9.3:", type=("build", "run"), when="@3.18.0:") depends_on("r-go-db", type=("build", "run")) depends_on("r-gosemsim", type=("build", "run")) depends_on("r-gosemsim@2.0.0:", type=("build", "run"), when="@3.4.4:3.6.0") + depends_on("r-gson@0.0.7:", type=("build", "run"), when="@4.6.0:") depends_on("r-magrittr", type=("build", "run")) depends_on("r-plyr", type=("build", "run")) depends_on("r-qvalue", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py index 194127a0af..32d8a30e52 100644 --- a/var/spack/repos/builtin/packages/r-cner/package.py +++ b/var/spack/repos/builtin/packages/r-cner/package.py @@ -14,6 +14,7 @@ class RCner(RPackage): bioc = "CNEr" + version("1.34.0", commit="878de98d18f6f959ad5e014ecd8165d3105d8b48") version("1.32.0", commit="1c92f3d7f3dccf76ab7d54f286117b09bc470b8f") version("1.30.0", commit="e682f2a7c8ebb561c872cf51a58ba36eed341187") version("1.26.0", commit="e5e582da6feeae0618c4460f16ece724215e3b20") diff --git a/var/spack/repos/builtin/packages/r-codex/package.py b/var/spack/repos/builtin/packages/r-codex/package.py index 9a1232625e..19cd0d800b 100644 --- a/var/spack/repos/builtin/packages/r-codex/package.py +++ b/var/spack/repos/builtin/packages/r-codex/package.py @@ -22,6 +22,7 @@ class RCodex(RPackage): bioc = "CODEX" + version("1.30.0", commit="0694f11be9e0b02ab15047d01db2afce943f92d8") version("1.28.0", commit="c707497bd93aa4a0516fcf3671a64997c28c9f67") version("1.26.0", commit="729fd10bd42d12edcedd65b5a8fb1579e5949718") version("1.22.0", commit="aa0ee4278111a46e0c790312b0526ba07aab22eb") diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py index 6cf4964280..637742cc97 100644 --- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py +++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py @@ -16,6 +16,7 @@ class RComplexheatmap(RPackage): bioc = "ComplexHeatmap" + version("2.14.0", commit="57fcaa040b08917c97fb66b963eb240d5fd5a8c7") version("2.12.1", commit="2c5fe70724219008174d4e6f83189cddbd895ec6") version("2.12.0", commit="8a5f060b06646f9d6a5032832ea72e3f183ca5d7") version("2.10.0", commit="170df82a1568e879e4019e0ff6feb0047851684f") diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py index 9cf4fe2cd3..e60256ebac 100644 --- a/var/spack/repos/builtin/packages/r-ctc/package.py +++ b/var/spack/repos/builtin/packages/r-ctc/package.py @@ -14,6 +14,7 @@ class RCtc(RPackage): bioc = "ctc" + version("1.72.0", commit="0a4b464e1768e6407c1c2ce64ec4ae5a4577be65") version("1.70.0", commit="05dc046ecfddbc1eeadf77e8f3ec0ce054794437") version("1.68.0", commit="c2733534ef9d948e07ea654d1998a67ed8f7a98a") version("1.64.0", commit="35dbe620a21056b8f69890e6f9a7c320528d8621") diff --git a/var/spack/repos/builtin/packages/r-decipher/package.py b/var/spack/repos/builtin/packages/r-decipher/package.py index b4cac08fe1..4c7981fcbb 100644 --- a/var/spack/repos/builtin/packages/r-decipher/package.py +++ b/var/spack/repos/builtin/packages/r-decipher/package.py @@ -13,6 +13,7 @@ class RDecipher(RPackage): bioc = "DECIPHER" + version("2.26.0", commit="7de99ec5e79f1f645f29dfbe24d2a106c2b0e69a") version("2.24.0", commit="437e60005ab281bd836f47756a367795bc16755d") version("2.22.0", commit="45da5cab5869d83af797aa82b08ebcd24f5bdab3") version("2.18.1", commit="6a708421550e6705d05e2fb50a0f5ab4f9041cb0") diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py index 0d756bb18d..3242fe5b14 100644 --- a/var/spack/repos/builtin/packages/r-delayedarray/package.py +++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py @@ -20,6 +20,7 @@ class RDelayedarray(RPackage): bioc = "DelayedArray" + version("0.24.0", commit="68ee3d0626c234ee1e9248a6cb95b901e4b3ad90") version("0.22.0", commit="4a5afd117b189b40bd409c7aff60e09d41797472") version("0.20.0", commit="829b52916ec54bb4f1a3c6f06c9955f3e28b3592") version("0.16.1", commit="c95eba771ad3fee1b49ec38c51cd8fd1486feadc") @@ -37,6 +38,7 @@ class RDelayedarray(RPackage): depends_on("r-biocgenerics@0.27.1:", type=("build", "run"), when="@0.8.0:") depends_on("r-biocgenerics@0.31.5:", type=("build", "run"), when="@0.16.1:") depends_on("r-biocgenerics@0.37.0:", type=("build", "run"), when="@0.20.1:") + depends_on("r-biocgenerics@0.43.4:", type=("build", "run"), when="@0.24.0:") depends_on("r-matrixgenerics@1.1.3:", type=("build", "run"), when="@0.16.1:") depends_on("r-s4vectors@0.14.3:", type=("build", "run")) depends_on("r-s4vectors@0.15.3:", type=("build", "run"), when="@0.4.1:") diff --git a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py index df0e57aa98..10513efd62 100644 --- a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py @@ -18,6 +18,7 @@ class RDelayedmatrixstats(RPackage): bioc = "DelayedMatrixStats" + version("1.20.0", commit="1ed14250e8731e60bccb44946cafad4c2b3ac5b0") version("1.18.1", commit="9c4658d11fc20b7d88e05b9c52140c2ca8a65768") version("1.18.0", commit="50c9aab259b6e8f68abf44b78122662a41c8bf47") version("1.16.0", commit="d44a3d765769cb022193428a77af25bf19916be7") @@ -41,7 +42,7 @@ class RDelayedmatrixstats(RPackage): depends_on("r-matrixstats@0.60.0:", type=("build", "run"), when="@1.16.0:") depends_on("r-sparsematrixstats", type=("build", "run"), when="@1.12.2:") depends_on("r-matrix", type=("build", "run")) - depends_on("r-matrix@1.5.0:", type=("build", "run"), when="@1.18.1:") + depends_on("r-matrix@1.5-0:", type=("build", "run"), when="@1.18.1:") depends_on("r-s4vectors", type=("build", "run")) depends_on("r-s4vectors@0.17.5:", type=("build", "run"), when="@1.2.0:") depends_on("r-iranges", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py index 073f0f09e9..e8bb9939f3 100644 --- a/var/spack/repos/builtin/packages/r-deseq2/package.py +++ b/var/spack/repos/builtin/packages/r-deseq2/package.py @@ -17,6 +17,7 @@ class RDeseq2(RPackage): homepage = "https://bioconductor.org/packages/DESeq2" git = "https://git.bioconductor.org/packages/DESeq2.git" + version("1.38.0", commit="0e059f425d4ce6a5203685a4ad434f15bbd6e211") version("1.36.0", commit="2800b78ae52c0600f7e603c54af59beed3a2ed17") version("1.34.0", commit="25d4f74be59548122ccfbe8687d30c0bae5cf49a") version("1.30.0", commit="f4b47b208ee26ab23fe65c345f907fcfe70b3f77") diff --git a/var/spack/repos/builtin/packages/r-dexseq/package.py b/var/spack/repos/builtin/packages/r-dexseq/package.py index 2bbfeeb0da..5350a6b0d1 100644 --- a/var/spack/repos/builtin/packages/r-dexseq/package.py +++ b/var/spack/repos/builtin/packages/r-dexseq/package.py @@ -21,6 +21,7 @@ class RDexseq(RPackage): maintainers = ["dorton21"] + version("1.44.0", commit="9660d7372d5ced1a7e324ed9a61b935023b7d135") version("1.42.0", commit="d91de62a27d0cab2ef12ef1a5f23dc2f7a0cfadd") version("1.40.0", commit="7d2d639b3a157e443058fc557132cd2629bb36f3") version("1.36.0", commit="f0a361af6954fcc2abb2db801c26e303570669b2") diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py index 5d31fa160b..6a1c2d6642 100644 --- a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py +++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py @@ -18,6 +18,7 @@ class RDirichletmultinomial(RPackage): bioc = "DirichletMultinomial" + version("1.40.0", commit="200176f8c72ff127788c500629b71872bc6b1f83") version("1.38.0", commit="b4de83d354e974fdb7cb3526d029487f24aab670") version("1.36.0", commit="926baff6c75cb498945c5895f25cc143c907a357") version("1.32.0", commit="6949abab2462b2c09f7a0ca5b5cbf0c95a40ad16") diff --git a/var/spack/repos/builtin/packages/r-dmrcate/package.py b/var/spack/repos/builtin/packages/r-dmrcate/package.py index ff453de01a..5e810413ff 100644 --- a/var/spack/repos/builtin/packages/r-dmrcate/package.py +++ b/var/spack/repos/builtin/packages/r-dmrcate/package.py @@ -17,6 +17,7 @@ class RDmrcate(RPackage): bioc = "DMRcate" + version("2.12.0", commit="560dd5067b05715631739d0fb58ef9cebdbf7078") version("2.10.0", commit="81e83701da5c55ac83d0e0b5e640a9d431f09551") version("2.8.5", commit="c65dc79a33a047c10932a98b3383709a6bcb8903") version("2.4.1", commit="bc6242a0291a9b997872f575a4417d38550c9550") diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py index 79f7f39efc..6dcd859e24 100644 --- a/var/spack/repos/builtin/packages/r-dnacopy/package.py +++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py @@ -15,6 +15,7 @@ class RDnacopy(RPackage): bioc = "DNAcopy" + version("1.72.0", commit="1a1ae854c3425aee68b060e3e7ab788db5bed08c") version("1.70.0", commit="9595d0ad7c78af4ed568cbd210b894d3350eae0a") version("1.68.0", commit="08f039f58bc2f5ed2cc3117ae817dbac333002a6") version("1.64.0", commit="01650266ea7a4e5c600de545fe70a1103e79b2d8") diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py index 99c36609ab..1fc1357242 100644 --- a/var/spack/repos/builtin/packages/r-dose/package.py +++ b/var/spack/repos/builtin/packages/r-dose/package.py @@ -18,6 +18,7 @@ class RDose(RPackage): bioc = "DOSE" + version("3.24.1", commit="a78995d3b12bd4baabb69c497102687814cd4c68") version("3.22.1", commit="6b711a0f076a9fefcb00ddef66e8f198039e6dfa") version("3.22.0", commit="242ac1b746c44fbbf281fbe6e5e4424a8dc74375") version("3.20.1", commit="bf434f24d035217822cb1b0ab08a486b9a53edb4") @@ -32,11 +33,12 @@ class RDose(RPackage): depends_on("r@3.4.0:", type=("build", "run"), when="@3.6.1:") depends_on("r@3.5.0:", type=("build", "run"), when="@3.16.0:") depends_on("r-annotationdbi", type=("build", "run")) + depends_on("r-hdo-db", type=("build", "run"), when="@3.24.1:") depends_on("r-biocparallel", type=("build", "run")) - depends_on("r-do-db", type=("build", "run")) depends_on("r-fgsea", type=("build", "run")) depends_on("r-ggplot2", type=("build", "run")) depends_on("r-gosemsim@2.0.0:", type=("build", "run")) + depends_on("r-gosemsim@2.23.1:", type=("build", "run"), when="@3.24.1:") depends_on("r-qvalue", type=("build", "run")) depends_on("r-reshape2", type=("build", "run")) @@ -44,3 +46,5 @@ class RDose(RPackage): depends_on("r-scales", type=("build", "run"), when="@3.2.0:3.4.0") depends_on("r-rvcheck", type=("build", "run"), when="@3.4.0") depends_on("r-igraph", type=("build", "run"), when="@3.2.0:3.4.0") + depends_on("r-do-db", type=("build", "run")) + depends_on("r-do-db", when="@:3.22.1") diff --git a/var/spack/repos/builtin/packages/r-dss/package.py b/var/spack/repos/builtin/packages/r-dss/package.py index 227cac4fd5..0ee45ba6e2 100644 --- a/var/spack/repos/builtin/packages/r-dss/package.py +++ b/var/spack/repos/builtin/packages/r-dss/package.py @@ -18,6 +18,7 @@ class RDss(RPackage): bioc = "DSS" + version("2.46.0", commit="debfbac4bc741961ba57915d4f2d98534f02cc21") version("2.44.0", commit="b9f44106f139c93564dfb4afab50555d24a657ba") version("2.42.0", commit="33e87450fbb64bb3e321688ff613e83cd40efe48") version("2.38.0", commit="82e65b92e6e227f1f99620362db8b03059e07e98") @@ -30,6 +31,7 @@ class RDss(RPackage): depends_on("r-biobase", type=("build", "run")) depends_on("r-biocparallel", type=("build", "run"), when="@2.36.0:") depends_on("r-bsseq", type=("build", "run")) - depends_on("r-matrixstats", type=("build", "run"), when="@2.44.0:") depends_on("r-delayedarray", type=("build", "run"), when="@2.36.0:2.42.0") + depends_on("r-matrixstats", type=("build", "run"), when="@2.44.0:") + depends_on("r-matrixstats", when="@:2.44.0") diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py index 2dc5026083..0142e6d928 100644 --- a/var/spack/repos/builtin/packages/r-edger/package.py +++ b/var/spack/repos/builtin/packages/r-edger/package.py @@ -19,6 +19,7 @@ class REdger(RPackage): bioc = "edgeR" + version("3.40.0", commit="0b25adcc6b3cb0a8c641964d1274536ee07ee162") version("3.38.4", commit="f5a3bb568a23b34146ac66329a95ee4785093536") version("3.38.1", commit="e58bf52f34ec451096f593126922ad7e5d517f7e") version("3.36.0", commit="c7db03addfc42138a1901834409c02da9d873026") diff --git a/var/spack/repos/builtin/packages/r-enrichplot/package.py b/var/spack/repos/builtin/packages/r-enrichplot/package.py index 24f204a5ea..b7c9c34079 100644 --- a/var/spack/repos/builtin/packages/r-enrichplot/package.py +++ b/var/spack/repos/builtin/packages/r-enrichplot/package.py @@ -16,6 +16,7 @@ class REnrichplot(RPackage): bioc = "enrichplot" + version("1.18.0", commit="61ea941784a1ed6cc604af1c1cc4532b8b5fcea7") version("1.16.2", commit="eeb21345288d96c116ac308649fa772d03760259") version("1.16.1", commit="cff77b622b2312be546714ec437aa4bc585bac87") version("1.14.1", commit="ccf3a6d9b7cd9cffd8de6d6263efdffe59d2ec36") @@ -27,9 +28,11 @@ class REnrichplot(RPackage): depends_on("r@3.4.0:", type=("build", "run")) depends_on("r@3.5.0:", type=("build", "run"), when="@1.10.2:") depends_on("r-aplot", type=("build", "run"), when="@1.14.1:") + depends_on("r-aplot@0.1.4:", type=("build", "run"), when="@1.18.0:") depends_on("r-dose@3.5.1:", type=("build", "run")) depends_on("r-dose@3.13.1:", type=("build", "run"), when="@1.8.1:") depends_on("r-dose@3.16.0:", type=("build", "run"), when="@1.12.3:") + depends_on("r-ggnewscale", type=("build", "run"), when="@1.18.0:") depends_on("r-ggplot2", type=("build", "run")) depends_on("r-ggraph", type=("build", "run")) depends_on("r-igraph", type=("build", "run")) @@ -37,6 +40,7 @@ class REnrichplot(RPackage): depends_on("r-purrr", type=("build", "run"), when="@1.2.0:") depends_on("r-rcolorbrewer", type=("build", "run"), when="@1.2.0:") depends_on("r-reshape2", type=("build", "run")) + depends_on("r-rlang", type=("build", "run"), when="@1.18.0:") depends_on("r-scatterpie", type=("build", "run"), when="@1.10.2:") depends_on("r-shadowtext", type=("build", "run"), when="@1.10.2:") depends_on("r-gosemsim", type=("build", "run")) @@ -52,3 +56,4 @@ class REnrichplot(RPackage): depends_on("r-gridextra", type=("build", "run"), when="@1.2.0:1.4.0") depends_on("r-cowplot", type=("build", "run")) depends_on("r-cowplot", when="@:1.16.1") + depends_on("r-cowplot", when="@:1.16.2") diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py index da2dc2dfe2..8977dfabfa 100644 --- a/var/spack/repos/builtin/packages/r-ensembldb/package.py +++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py @@ -24,6 +24,7 @@ class REnsembldb(RPackage): bioc = "ensembldb" + version("2.22.0", commit="4dda178a14e080c643bbd8c4dd6378bfe4e6ee9f") version("2.20.2", commit="ac1fb8389efd88099600af298d6bb3384206f9ed") version("2.20.1", commit="e547d184730cfe5e65f59e4f3512395fb1cdba1a") version("2.18.3", commit="e2fcfc0c7700110df070a171d2d542b37ec098f3") @@ -40,6 +41,7 @@ class REnsembldb(RPackage): depends_on("r-genomicranges@1.31.18:", type=("build", "run"), when="@2.4.1:") depends_on("r-genomicfeatures@1.23.18:", type=("build", "run")) depends_on("r-genomicfeatures@1.29.10:", type=("build", "run"), when="@2.2.2:") + depends_on("r-genomicfeatures@1.49.6:", type=("build", "run"), when="@2.22.0:") depends_on("r-annotationfilter@0.99.7:", type=("build", "run")) depends_on("r-annotationfilter@1.1.9:", type=("build", "run"), when="@2.2.2:") depends_on("r-annotationfilter@1.5.2:", type=("build", "run"), when="@2.6.8:") diff --git a/var/spack/repos/builtin/packages/r-exomecopy/package.py b/var/spack/repos/builtin/packages/r-exomecopy/package.py index faf211f5c7..db7757dbb4 100644 --- a/var/spack/repos/builtin/packages/r-exomecopy/package.py +++ b/var/spack/repos/builtin/packages/r-exomecopy/package.py @@ -17,6 +17,7 @@ class RExomecopy(RPackage): bioc = "exomeCopy" + version("1.44.0", commit="2dd6598d5fb14d49f7a42e597284c7a929c0cd62") version("1.42.0", commit="ba0979cf5fbdefed841022f2dc0604941315c1b8") version("1.40.0", commit="ebde39be67baace2c326359421fd17f4a02fd4fe") version("1.36.0", commit="cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26") diff --git a/var/spack/repos/builtin/packages/r-experimenthub/package.py b/var/spack/repos/builtin/packages/r-experimenthub/package.py index 389c047d2a..5b79822a03 100644 --- a/var/spack/repos/builtin/packages/r-experimenthub/package.py +++ b/var/spack/repos/builtin/packages/r-experimenthub/package.py @@ -18,6 +18,7 @@ class RExperimenthub(RPackage): bioc = "ExperimentHub" + version("2.6.0", commit="557ba29720bce85902a85445dd0435b7356cdd7f") version("2.4.0", commit="bdce35d3a89e8633cc395f28991e6b5d1eccbe8e") version("2.2.1", commit="4e10686fa72baefef5d2990f41a7c44c527a7a7d") version("1.16.1", commit="61d51b7ca968d6cc1befe299e0784d9a19ca51f6") diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py index 8eadef9819..9e6ed953a0 100644 --- a/var/spack/repos/builtin/packages/r-fgsea/package.py +++ b/var/spack/repos/builtin/packages/r-fgsea/package.py @@ -16,6 +16,7 @@ class RFgsea(RPackage): bioc = "fgsea" + version("1.24.0", commit="ac74ccd935c15623b8584caa791835aec514144b") version("1.22.0", commit="e4e203aa64faa984e0406fed5d87a422d9df92f2") version("1.20.0", commit="b704f81687dc16afdaafc6d30108c62a067856b2") version("1.16.0", commit="9d9df596c7e160afa18e067b7637cfc465494318") @@ -30,7 +31,9 @@ class RFgsea(RPackage): depends_on("r-data-table", type=("build", "run")) depends_on("r-biocparallel", type=("build", "run")) depends_on("r-ggplot2@2.2.0:", type=("build", "run")) - depends_on("r-gridextra", type=("build", "run")) + depends_on("r-cowplot", type=("build", "run"), when="@1.24.0:") depends_on("r-fastmatch", type=("build", "run")) depends_on("r-matrix", type=("build", "run"), when="@1.6.0:") depends_on("r-bh", type=("build", "run"), when="@1.10.1:") + depends_on("r-gridextra", type=("build", "run")) + depends_on("r-gridextra", when="@:1.22.0") diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py index a169685f1e..9f447948dd 100644 --- a/var/spack/repos/builtin/packages/r-gcrma/package.py +++ b/var/spack/repos/builtin/packages/r-gcrma/package.py @@ -13,6 +13,7 @@ class RGcrma(RPackage): bioc = "gcrma" + version("2.70.0", commit="095f38914525d8812524a3cb38db8075382f8121") version("2.68.0", commit="c14063ff5490fac8d60530826613d728e68b3d66") version("2.66.0", commit="ba134b392def89d36b5639a187e0c25a4353457b") version("2.62.0", commit="b91bdf5bf4e875defedb4d4e3e1e75867773287a") diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py index d4dbdf4917..4cb8b167e6 100644 --- a/var/spack/repos/builtin/packages/r-gdsfmt/package.py +++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py @@ -24,6 +24,7 @@ class RGdsfmt(RPackage): bioc = "gdsfmt" + version("1.34.0", commit="ab912c393d8eb6dc26f844a13422a29b9ce7265b") version("1.32.0", commit="06f2097cc10b1888739f86e635383a0f2ee7e208") version("1.30.0", commit="d27dde6a70bb2295f5bbc8961152b45ccee7a652") version("1.26.1", commit="bd180b21b1ace120035f0da255cbf6f13088f069") diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py index 65f63068ad..269b872f20 100644 --- a/var/spack/repos/builtin/packages/r-genefilter/package.py +++ b/var/spack/repos/builtin/packages/r-genefilter/package.py @@ -13,6 +13,7 @@ class RGenefilter(RPackage): bioc = "genefilter" + version("1.80.0", commit="14fbc2d776916e572583e3c268ea9ba60ed60a9a") version("1.78.0", commit="2f574388971641d3a71858f5c34606c04fcd2ba2") version("1.76.0", commit="8d630fd25f0d2a4101e05e123c3959591203a7ea") version("1.72.1", commit="b01b00a766982ef7d80b90a252085c8c4f085e1b") diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py index 85287fea85..ee1d491f97 100644 --- a/var/spack/repos/builtin/packages/r-genelendatabase/package.py +++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py @@ -14,6 +14,7 @@ class RGenelendatabase(RPackage): bioc = "geneLenDataBase" + version("1.34.0", commit="e26cf8e3fc20b5d183cbd39b7b28a8cc866f6ead") version("1.32.0", commit="eaa193a2c6d502c6d59113fd42f66761b8730594") version("1.30.0", commit="b3cc755f1ffcbb2eacd9ea45e11f39f1639782b1") version("1.26.0", commit="2724715ae23a6647d1c0c6e934720aad9377d65e") diff --git a/var/spack/repos/builtin/packages/r-genemeta/package.py b/var/spack/repos/builtin/packages/r-genemeta/package.py index 0e036ae6df..4da5f962f9 100644 --- a/var/spack/repos/builtin/packages/r-genemeta/package.py +++ b/var/spack/repos/builtin/packages/r-genemeta/package.py @@ -14,6 +14,7 @@ class RGenemeta(RPackage): bioc = "GeneMeta" + version("1.70.0", commit="e5db82e04efc4572358abce7e0c09273f94c9d72") version("1.68.0", commit="4213c0205d477660195300a0aa9751972f86bf91") version("1.66.0", commit="c16eb09492f08f6cc0f253fafa3fa5dce35dcdba") version("1.62.0", commit="eb4273ff5867e39592f50b97b454fa5e32b4a9bf") diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py index 580092dd4c..61020b3bc4 100644 --- a/var/spack/repos/builtin/packages/r-geneplotter/package.py +++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py @@ -13,6 +13,7 @@ class RGeneplotter(RPackage): bioc = "geneplotter" + version("1.76.0", commit="4eb6a787d0c66110ec9a7d34fc76b64030fbde5d") version("1.74.0", commit="ca819565829eac7a9a98e3cafafd6c06a466fddf") version("1.72.0", commit="57a1d830ba7844fda5236af0153d5b5587634f96") version("1.68.0", commit="f1fea7e468fb24fdfa93ef4493600a4d8d183f69") diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py index 7c89db642d..7754af09f0 100644 --- a/var/spack/repos/builtin/packages/r-genie3/package.py +++ b/var/spack/repos/builtin/packages/r-genie3/package.py @@ -14,6 +14,7 @@ class RGenie3(RPackage): bioc = "GENIE3" + version("1.20.0", commit="aea2e686a262f30b16c068241938d04f21251a0d") version("1.18.0", commit="f16b25ef50978a4a497eb2f911e21f2e839fa33c") version("1.16.0", commit="5543b1b883d3a1c92e955de6668444278edc2bdf") version("1.12.0", commit="14289cee9bed113ab35ba03bcaac4a30e5784497") diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py index e9218f10e0..1fe9e10dfe 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py @@ -17,6 +17,7 @@ class RGenomeinfodb(RPackage): bioc = "GenomeInfoDb" + version("1.34.3", commit="ea6f131f1d1ee61535d6733ce76fabf3c62185fc") version("1.32.4", commit="69df6a5a10027fecf6a6d1c8298f3f686b990d8f") version("1.32.2", commit="2e40af38f00ee86d2c83d140e234c1349baa27de") version("1.30.1", commit="bf8b385a2ffcecf9b41e581794056f267895863d") diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py index 7226c97b66..69063558c7 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py @@ -14,6 +14,11 @@ class RGenomeinfodbdata(RPackage): url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz" version( + "1.2.9", + url="https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz", + sha256="e63a719a8eceefeda39fc95de83e7aa41caad39705efc712a44ab4021adc45fa", + ) + version( "1.2.8", url="https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz", sha256="576750330a011c1eccb47c7154ca1b40ae4cd473fd7973f6c2955237a0729eb4", diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py index 20f659508c..87347b796e 100644 --- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py +++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py @@ -16,6 +16,7 @@ class RGenomicalignments(RPackage): bioc = "GenomicAlignments" + version("1.34.0", commit="c6eb78079c8aa21d47c95b3d16a606e8c2c5d799") version("1.32.1", commit="2553580d0b8a8a5fd7835c1446616b39f707b8a9") version("1.32.0", commit="7a660a914a04e2eb0758082b6f64c4124a887ef3") version("1.30.0", commit="2d2c5fce3529c2962fdcefd736d8b7f7c0ec2d54") diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py index 2da0705694..34cfcb4b87 100644 --- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py +++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py @@ -20,6 +20,7 @@ class RGenomicfeatures(RPackage): bioc = "GenomicFeatures" + version("1.50.2", commit="4fc9120ceed9ff59f390c8bbdbd79b212ee35b84") version("1.48.4", commit="06e37dc1847d49d91391264caec877ed33abf359") version("1.48.3", commit="b0ddea0e101e3861928f3ad353348df047d90382") version("1.46.4", commit="d3ab6fd069624904ce7fcdf75dad884473f97975") @@ -41,6 +42,7 @@ class RGenomicfeatures(RPackage): depends_on("r-genomeinfodb@1.13.1:", type=("build", "run"), when="@1.30.3:") depends_on("r-genomeinfodb@1.15.4:", type=("build", "run"), when="@1.32.3:") depends_on("r-genomeinfodb@1.25.7:", type=("build", "run"), when="@1.42.1:") + depends_on("r-genomeinfodb@1.34.1:", type=("build", "run"), when="@1.50.2:") depends_on("r-genomicranges@1.27.6:", type=("build", "run")) depends_on("r-genomicranges@1.29.14:", type=("build", "run"), when="@1.30.3:") depends_on("r-genomicranges@1.31.17:", type=("build", "run"), when="@1.32.3:") diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py index e553fab641..1b2e01cb30 100644 --- a/var/spack/repos/builtin/packages/r-genomicranges/package.py +++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py @@ -22,6 +22,7 @@ class RGenomicranges(RPackage): bioc = "GenomicRanges" + version("1.50.1", commit="6b3fb388ec038fb43f3cd26684ce778ee0e80e81") version("1.48.0", commit="2bce60814db7c20949892587740fb484aa435978") version("1.46.1", commit="e422642f64815cdfee8fc340681ad87a7eafc3bb") version("1.42.0", commit="32baca734b599d60fa13bdbe31c5712e648f538d") @@ -46,6 +47,7 @@ class RGenomicranges(RPackage): depends_on("r-iranges@2.15.12:", type=("build", "run"), when="@1.34.0:") depends_on("r-iranges@2.17.1:", type=("build", "run"), when="@1.36.1:") depends_on("r-iranges@2.23.9:", type=("build", "run"), when="@1.42.0:") + depends_on("r-iranges@2.31.2:", type=("build", "run"), when="@1.50.1:") depends_on("r-genomeinfodb@1.11.5:", type=("build", "run")) depends_on("r-genomeinfodb@1.13.1:", type=("build", "run"), when="@1.30.3:") depends_on("r-genomeinfodb@1.15.2:", type=("build", "run"), when="@1.32.7:") diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py index aacfc2c0f5..cd748cb55d 100644 --- a/var/spack/repos/builtin/packages/r-geoquery/package.py +++ b/var/spack/repos/builtin/packages/r-geoquery/package.py @@ -16,6 +16,7 @@ class RGeoquery(RPackage): bioc = "GEOquery" + version("2.66.0", commit="00a954e9f8223607b43cf112943ab575d03a0eb6") version("2.64.2", commit="e9b7f075a4a6a952660443ca93ed392d7a4fd6d7") version("2.62.2", commit="1966c108fe8a58ac39ef53c3c452fd160efa526e") version("2.58.0", commit="6332ca3791ddcfb233b9ad75b5904b3d60f49b93") diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py index 1ea9655c07..06266f5c1a 100644 --- a/var/spack/repos/builtin/packages/r-ggbio/package.py +++ b/var/spack/repos/builtin/packages/r-ggbio/package.py @@ -21,6 +21,7 @@ class RGgbio(RPackage): bioc = "ggbio" + version("1.46.0", commit="d9c6cb495c7268bcaaab141231a9038aec8498bc") version("1.44.1", commit="0301d9464e304a8113ea4479185cd358855ca365") version("1.44.0", commit="cb21284a9803917fa76e116adfc456525c95f660") version("1.42.0", commit="3540047ef018957d59fba8af7d3c58e4659f8e26") diff --git a/var/spack/repos/builtin/packages/r-ggnewscale/package.py b/var/spack/repos/builtin/packages/r-ggnewscale/package.py new file mode 100644 index 0000000000..1ab182ba98 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggnewscale/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RGgnewscale(RPackage): + """Multiple Fill and Colour Scales in 'ggplot2'. + + Use multiple fill and colour scales in 'ggplot2'.""" + + cran = "ggnewscale" + + version("0.4.8", sha256="c7fefa6941ecbc789507e59be13fa96327fe2549681a938c43beb06ca22a9700") + + depends_on("r-ggplot2@3.0.0:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-ggrastr/package.py b/var/spack/repos/builtin/packages/r-ggrastr/package.py new file mode 100644 index 0000000000..7f78a50dea --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggrastr/package.py @@ -0,0 +1,26 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RGgrastr(RPackage): + """Rasterize Layers for 'ggplot2'. + + Rasterize only specific layers of a 'ggplot2' plot while simultaneously + keeping all labels and text in vector format. This allows users to keep + plots within the reasonable size limit without loosing vector properties of + the scale-sensitive information.""" + + cran = "ggrastr" + + version("1.0.1", sha256="82d6e90fa38dec85e829f71018532ed5b709a50a585455fc07cb3bae282f5d1f") + + depends_on("r@3.2.2:", type=("build", "run")) + depends_on("r-ggplot2@2.1.0:", type=("build", "run")) + depends_on("r-cairo@1.5.9:", type=("build", "run")) + depends_on("r-ggbeeswarm", type=("build", "run")) + depends_on("r-png", type=("build", "run")) + depends_on("r-ragg", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-ggtree/package.py b/var/spack/repos/builtin/packages/r-ggtree/package.py index 9128cffcf8..8d015a3729 100644 --- a/var/spack/repos/builtin/packages/r-ggtree/package.py +++ b/var/spack/repos/builtin/packages/r-ggtree/package.py @@ -16,6 +16,7 @@ class RGgtree(RPackage): bioc = "ggtree" + version("3.6.2", commit="431ec37bc0f0159b08a7990ce1d9374e160b9f44") version("3.4.4", commit="8e48d3e2ea445b6c2213f0471462108a7a72b333") version("3.4.0", commit="23f08a3da1829d1bbb6827ed1c4cf878daa4b539") version("3.2.1", commit="d3747e636fe1a6a9e09b56a3a3899208ebd05547") @@ -26,6 +27,7 @@ class RGgtree(RPackage): depends_on("r-aplot", type=("build", "run"), when="@3.4.0:") depends_on("r-dplyr", type=("build", "run")) depends_on("r-ggplot2@3.0.0:", type=("build", "run")) + depends_on("r-ggplot2@3.4.0:", type=("build", "run"), when="@3.6.2:") depends_on("r-magrittr", type=("build", "run")) depends_on("r-purrr", type=("build", "run")) depends_on("r-rlang", type=("build", "run")) @@ -37,3 +39,4 @@ class RGgtree(RPackage): depends_on("r-tidytree@0.3.9:", type=("build", "run"), when="@3.4.0:") depends_on("r-treeio@1.8.0:", type=("build", "run")) depends_on("r-scales", type=("build", "run")) + depends_on("r-cli", type=("build", "run"), when="@3.6.2:") diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py index 0ec9a49c57..441673be76 100644 --- a/var/spack/repos/builtin/packages/r-glimma/package.py +++ b/var/spack/repos/builtin/packages/r-glimma/package.py @@ -17,6 +17,7 @@ class RGlimma(RPackage): bioc = "Glimma" + version("2.8.0", commit="09cec82e9af9c6775192570f8c28f050c0df08ac") version("2.6.0", commit="23220d9b90476059aab035b5de11b7ce04b331c8") version("2.4.0", commit="caa270e44ec6994035d2e915c0f68a14ccbb58db") version("2.0.0", commit="40bebaa79e8c87c5686cff7285def4461c11bca9") diff --git a/var/spack/repos/builtin/packages/r-glmgampoi/package.py b/var/spack/repos/builtin/packages/r-glmgampoi/package.py index 13e5a507a2..18acd22ce2 100644 --- a/var/spack/repos/builtin/packages/r-glmgampoi/package.py +++ b/var/spack/repos/builtin/packages/r-glmgampoi/package.py @@ -16,14 +16,18 @@ class RGlmgampoi(RPackage): bioc = "glmGamPoi" + version("1.10.0", commit="048e17384209fc07031e09875ec6eea35e90ef46") version("1.8.0", commit="b723d61e05c1ad50a3cf6a6393ec3d97adc7edb4") depends_on("r-rcpp", type=("build", "run")) depends_on("r-delayedmatrixstats", type=("build", "run")) depends_on("r-matrixstats", type=("build", "run")) + depends_on("r-matrixgenerics", type=("build", "run"), when="@1.10.0:") depends_on("r-delayedarray", type=("build", "run")) depends_on("r-hdf5array", type=("build", "run")) depends_on("r-summarizedexperiment", type=("build", "run")) + depends_on("r-singlecellexperiment", type=("build", "run"), when="@1.10.0:") depends_on("r-biocgenerics", type=("build", "run")) + depends_on("r-rlang", type=("build", "run"), when="@1.10.0:") depends_on("r-rcpparmadillo", type=("build", "run")) depends_on("r-beachmat", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-globaltest/package.py b/var/spack/repos/builtin/packages/r-globaltest/package.py index 6adce26b49..c4ec01ee10 100644 --- a/var/spack/repos/builtin/packages/r-globaltest/package.py +++ b/var/spack/repos/builtin/packages/r-globaltest/package.py @@ -18,6 +18,7 @@ class RGlobaltest(RPackage): bioc = "globaltest" + version("5.52.0", commit="a1fc3ad206454d1151bcc940644fd8a5c4164d63") version("5.50.0", commit="08612a06eb1cc7381f9bf70f6fe198bb401a21df") version("5.48.0", commit="86c2c8f35734dcbc8c8ca791d8a190dc525beac9") version("5.44.0", commit="571933d5c779a241740be913ff49ecdd59bcbc45") diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py index 04f934edd5..3947e40dfe 100644 --- a/var/spack/repos/builtin/packages/r-go-db/package.py +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -16,24 +16,29 @@ class RGoDb(RPackage): url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" version( + "3.16.0", + url="https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GO.db_3.16.0.tar.gz", + sha256="4652812d8ba380aeeb9b136efbc9365156397eec99c5ca36cfb8294139493b8e", + ) + version( "3.15.0", - sha256="bac91d73c57f206fa5bc4a501a2aaf61b365cf411181ce44353370cdbc132d99", url="https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GO.db_3.15.0.tar.gz", + sha256="bac91d73c57f206fa5bc4a501a2aaf61b365cf411181ce44353370cdbc132d99", ) version( "3.14.0", - sha256="45d0a681a662667d45b2472d160b72f7058ad0a28dd0ca24742e11ddfd87d8e7", url="https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GO.db_3.14.0.tar.gz", + sha256="45d0a681a662667d45b2472d160b72f7058ad0a28dd0ca24742e11ddfd87d8e7", ) version( "3.12.1", - sha256="e0316959d3d32096f9432c897413dff74fce53e15ead7917a7724467d971dab9", url="https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GO.db_3.12.1.tar.gz", + sha256="e0316959d3d32096f9432c897413dff74fce53e15ead7917a7724467d971dab9", ) version( "3.4.1", - sha256="2fc2048e9d26edb98e35e4adc4d18c6df54f44836b5cc4a482d36ed99e058cc1", url="https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz", + sha256="2fc2048e9d26edb98e35e4adc4d18c6df54f44836b5cc4a482d36ed99e058cc1", ) depends_on("r@2.7.0:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-gofuncr/package.py b/var/spack/repos/builtin/packages/r-gofuncr/package.py index e87b20fd2a..b279565b12 100644 --- a/var/spack/repos/builtin/packages/r-gofuncr/package.py +++ b/var/spack/repos/builtin/packages/r-gofuncr/package.py @@ -28,6 +28,7 @@ class RGofuncr(RPackage): bioc = "GOfuncR" + version("1.18.0", commit="49182411e40a5d72abf99a5cca9287f34f870b19") version("1.16.0", commit="603fc79e13b58ec4612b6092f37d2450078dbfe1") version("1.14.0", commit="b3d445acf95851241d1fdb673d108ee115bdc17b") version("1.10.0", commit="51b01a2b9afa03fde2e1628036096cbeafaa2ef4") diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py index 410c63f9f4..2bbee0c8c4 100644 --- a/var/spack/repos/builtin/packages/r-gosemsim/package.py +++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py @@ -19,6 +19,7 @@ class RGosemsim(RPackage): bioc = "GOSemSim" + version("2.24.0", commit="ed7334f3cf3ac7ce5be76003934c29b598089f4d") version("2.22.0", commit="fd74aeba2371ebf9db0595cf18674441bdac9618") version("2.20.0", commit="fa82442aaa4ad1a8dacc05ee2c54f5e5e770a794") version("2.16.1", commit="92f1d567f3584fe488f434abce87c2e1950081c0") diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py index 74afd94f10..61f3212bec 100644 --- a/var/spack/repos/builtin/packages/r-goseq/package.py +++ b/var/spack/repos/builtin/packages/r-goseq/package.py @@ -14,6 +14,7 @@ class RGoseq(RPackage): bioc = "goseq" + version("1.50.0", commit="f9fad238e2d08a87b14c3c8c228ad332efa60f14") version("1.48.0", commit="d077fda56986cc7218a88f7db37a42412b227025") version("1.46.0", commit="1fb5626cc80f595499af511a830322ed12bbe144") version("1.42.0", commit="8164b90e7505bbc1035105fdc15219c764ef8b8d") diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py index 988b236cb1..5901349f1d 100644 --- a/var/spack/repos/builtin/packages/r-gostats/package.py +++ b/var/spack/repos/builtin/packages/r-gostats/package.py @@ -15,6 +15,7 @@ class RGostats(RPackage): bioc = "GOstats" + version("2.64.0", commit="62813253249dc02d2ddaafa7f0249e69d6f2c6b0") version("2.62.0", commit="217db032272010ebb8fe3af4647153428f42cd47") version("2.60.0", commit="a20055cc1c04a91b0291a918dadd9ea912c187ce") version("2.56.0", commit="8f988c3b4b1ce7e05626aae8956004c7bbdd6f3a") diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py index af38c84d8e..2867bdf9c2 100644 --- a/var/spack/repos/builtin/packages/r-graph/package.py +++ b/var/spack/repos/builtin/packages/r-graph/package.py @@ -13,6 +13,7 @@ class RGraph(RPackage): bioc = "graph" + version("1.76.0", commit="e3efc108716e98bd3363621d17a6f9c3ef975d19") version("1.74.0", commit="4af608a5d9e1de33fda6ae28fb73bff9272ee296") version("1.72.0", commit="7afbd26ecd76e55e6bbd74915a561d7a9b15f907") version("1.68.0", commit="03ad9ed088095605e317510b8234501318994e94") diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py index fbe4621655..ddaf248877 100644 --- a/var/spack/repos/builtin/packages/r-gseabase/package.py +++ b/var/spack/repos/builtin/packages/r-gseabase/package.py @@ -14,6 +14,7 @@ class RGseabase(RPackage): bioc = "GSEABase" + version("1.60.0", commit="aae4e52b50b076550967601f98031e952fb97765") version("1.58.0", commit="7de04442fb1ab63ffde29f4e3daf13ad32e90bdb") version("1.56.0", commit="ee7c3ca4ad0f1f3e9b9162db1515413802860ecc") version("1.52.1", commit="257dfccbc5b507d82099fac6b06bb03825e995e8") diff --git a/var/spack/repos/builtin/packages/r-gson/package.py b/var/spack/repos/builtin/packages/r-gson/package.py new file mode 100644 index 0000000000..2e3b6ba1b2 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gson/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RGson(RPackage): + """Base Class and Methods for 'gson' Format. + + Proposes a new file format ('gson') for storing gene set and related + information, and provides read, write and other utilities to process this + file format.""" + + cran = "gson" + + version("0.0.9", sha256="f694765cd2872efb73dd7be66ef8e31395915f9b277f59e0891cff138777b118") + + depends_on("r-jsonlite", type=("build", "run")) + depends_on("r-rlang", type=("build", "run")) + depends_on("r-tidyr", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py index 829463f4e9..ef38b461a9 100644 --- a/var/spack/repos/builtin/packages/r-gtrellis/package.py +++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py @@ -18,6 +18,7 @@ class RGtrellis(RPackage): bioc = "gtrellis" + version("1.30.0", commit="da93b30ef812e231c47aa83da5c521f1801b3d14") version("1.28.0", commit="d770a7b3441e4003869c88cfd8e21fd6508b86c4") version("1.26.0", commit="f2c3121b31ad1b422e2cf503435d0590e903ff3f") version("1.22.0", commit="c071c5631f3dedda212aed87d9c02954b5ed6611") diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py index a4b61d0f30..ebe7880d88 100644 --- a/var/spack/repos/builtin/packages/r-gviz/package.py +++ b/var/spack/repos/builtin/packages/r-gviz/package.py @@ -18,6 +18,7 @@ class RGviz(RPackage): bioc = "Gviz" + version("1.42.0", commit="4eddb688bca3fdeb65fd536d653d7ba7f7976121") version("1.40.1", commit="d21843710cd05135353de5cd4ce4d35cdd333b7c") version("1.38.3", commit="c4b352a16455a5744533c511e59354977814cb9e") version("1.34.0", commit="445fadff2aedd8734580fa908aa47ff1216a8182") diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py index ca60baa1e1..878fbd7665 100644 --- a/var/spack/repos/builtin/packages/r-hdf5array/package.py +++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py @@ -20,6 +20,7 @@ class RHdf5array(RPackage): bioc = "HDF5Array" + version("1.26.0", commit="38b7bd603f7281245605048d8d57237e00b74d79") version("1.24.2", commit="fb213ba36631b04dfe754705f701f3a015c4fc82") version("1.24.1", commit="d002fe70c84baaadb62058ce467d6c1ea032d8f5") version("1.22.1", commit="b3f091fbc159609e8e0792d2bf9fbef52c6ceede") diff --git a/var/spack/repos/builtin/packages/r-hdo-db/package.py b/var/spack/repos/builtin/packages/r-hdo-db/package.py new file mode 100644 index 0000000000..abbd5c70f7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-hdo-db/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class RHdoDb(RPackage): + """A set of annotation maps describing the entire Human Disease Ontology. + + A set of annotation maps describing the entire Human Disease Ontology + assembled using data from DO. Its annotation data comes from + https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.""" + + url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/HDO.db_0.99.1.tar.gz" + bioc = "HDO.db" + + version("0.99.1", sha256="c17cf28d06621d91148a64d47fdeaa906d8621aba7a688715fb9571a55f7cf92") + + depends_on("r@4.2.0:", type=("build", "run")) + depends_on("r-annotationdbi", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py index 79a69b1322..4a47bcdbd6 100644 --- a/var/spack/repos/builtin/packages/r-hypergraph/package.py +++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py @@ -14,6 +14,7 @@ class RHypergraph(RPackage): bioc = "hypergraph" + version("1.70.0", commit="a5ffeafa8b999b5e7e77f93f4e6284abafc81621") version("1.68.0", commit="7d53b5050f4ebe0a7007c02b76e93498195da3a4") version("1.66.0", commit="e9c47336df6409006622818f541f258103163a39") version("1.62.0", commit="a286bbb70289e9f3cdf41407d52e5976bd6ed11e") diff --git a/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py b/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py index d084516808..5046952167 100644 --- a/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py +++ b/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py @@ -15,6 +15,7 @@ class RIllumina450probevariantsDb(RPackage): bioc = "Illumina450ProbeVariants.db" + version("1.34.0", commit="6c0f0b4d2bcf13da852b2f132a8ce1229fa5269e") version("1.32.0", commit="a15602253e675a104303627957653a08876d8d7c") version("1.30.0", commit="ba1296b4aafc287dea61f5f37c6c99fd553e52a2") version("1.26.0", commit="fffe6033cc8d87354078c14de1e29976eaedd611") diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py index 2548c31d31..c9643a5f5e 100644 --- a/var/spack/repos/builtin/packages/r-illuminaio/package.py +++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py @@ -13,6 +13,7 @@ class RIlluminaio(RPackage): bioc = "illuminaio" + version("0.40.0", commit="1d7045697eaf09e5c61447a6f61e2eeaaf7a5095") version("0.38.0", commit="b16231b7417b4d6e9cff1e2724ed3529871dff92") version("0.36.0", commit="c5b6e9164b73c650c0a9f055f4fd0580ac64fae7") version("0.32.0", commit="e1322c781dd475a5e8ff6c0422bebb3deb47fa80") diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py index fb37ef92e6..69d4ceaa8c 100644 --- a/var/spack/repos/builtin/packages/r-impute/package.py +++ b/var/spack/repos/builtin/packages/r-impute/package.py @@ -13,6 +13,7 @@ class RImpute(RPackage): bioc = "impute" + version("1.72.0", commit="638ac916464f5a392b947ef5bb426b8445d27325") version("1.70.0", commit="970b2c28d908e26369b01dddf36dab2f8916d4af") version("1.68.0", commit="fa4e4d883e609633c49d865a44acd6a79954eaac") version("1.64.0", commit="31a5636f4dfbb1fd61386738786a0de048a620c2") diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py index 671ff6d93a..c73c93b4cd 100644 --- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py +++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py @@ -16,6 +16,7 @@ class RInteractivedisplaybase(RPackage): bioc = "interactiveDisplayBase" + version("1.36.0", commit="79a0552bd467367866ceda2efc2b60a04a81f5fb") version("1.34.0", commit="fafbb13a42bb7549f17aa08cdb0e51728c5e825e") version("1.32.0", commit="0f88b2ac3689d51abb6ac0045b3207ca77963a5a") version("1.28.0", commit="a74c02c971c4f9c7086e14abd23f1a4190da4599") diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py index 4cf880670a..ea775bd009 100644 --- a/var/spack/repos/builtin/packages/r-iranges/package.py +++ b/var/spack/repos/builtin/packages/r-iranges/package.py @@ -18,6 +18,7 @@ class RIranges(RPackage): bioc = "IRanges" + version("2.32.0", commit="2b5c9fc706c8cdc96f0c46508087863df1502f81") version("2.30.1", commit="ead506a14d6cc89ac2f14b55a4b04496755e4e50") version("2.30.0", commit="9b5f3ca12812fb76c23b1550aa3a794384384d9b") version("2.28.0", commit="d85ee908a379e12d1e32599e999c71ab37c25e57") diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py index 8b0f69a5a6..cbb213692e 100644 --- a/var/spack/repos/builtin/packages/r-kegg-db/package.py +++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py @@ -18,14 +18,14 @@ class RKeggDb(RPackage): version( "3.2.4", - sha256="2e60d1b664cbd1491cc00ed13a22904706c5a4651150f70daca04bf3ba9ead88", url="https://bioconductor.org/packages/3.12/data/annotation/src/contrib/KEGG.db_3.2.4.tar.gz", + sha256="2e60d1b664cbd1491cc00ed13a22904706c5a4651150f70daca04bf3ba9ead88", deprecated=True, ) version( "3.2.3", - sha256="02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963", url="https://bioconductor.org/packages/3.10/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz", + sha256="02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963", deprecated=True, ) diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py index a6842397d8..3041d08644 100644 --- a/var/spack/repos/builtin/packages/r-kegggraph/package.py +++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py @@ -18,6 +18,7 @@ class RKegggraph(RPackage): bioc = "KEGGgraph" + version("1.58.0", commit="7c3f148b57903b8df517f94824f07f38bbd3b591") version("1.56.0", commit="e95cbf9f8a095d59b78a053463191b89c00d5ded") version("1.54.0", commit="135ee3dad30ca208e21acd0a2d81120b74b64079") version("1.50.0", commit="3335e85cdba264c04e6e36378578cf6c83a30eb8") diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py index 20bf8b0e31..4b1b633531 100644 --- a/var/spack/repos/builtin/packages/r-keggrest/package.py +++ b/var/spack/repos/builtin/packages/r-keggrest/package.py @@ -15,6 +15,7 @@ class RKeggrest(RPackage): bioc = "KEGGREST" + version("1.38.0", commit="4dfbff9f6662227bd49d64d18a342f469dd88ad3") version("1.36.3", commit="1827cde76863aa80c83264a0dd95514654358df3") version("1.36.0", commit="591818bbc9195bfd0657cf4f5c7c771ea7f86830") version("1.34.0", commit="2056750dc202fa04a34b84c6c712e884c7cad2bd") diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py index 8d92ec5505..1b428a8d37 100644 --- a/var/spack/repos/builtin/packages/r-limma/package.py +++ b/var/spack/repos/builtin/packages/r-limma/package.py @@ -14,6 +14,7 @@ class RLimma(RPackage): bioc = "limma" + version("3.54.0", commit="1d1fa843d4fe2f8c94fd843bb1e80b8384d8306e") version("3.52.4", commit="3226c29ad8c18aa7e6722f4a2c95ff8ac900437e") version("3.52.1", commit="c81c539a217ac1cf46e850f8a20266cecfafed50") version("3.50.0", commit="657b19bbc33c5c941af79aeb68967bf42ea40e23") diff --git a/var/spack/repos/builtin/packages/r-lumi/package.py b/var/spack/repos/builtin/packages/r-lumi/package.py index 4c3f362ddf..995d6befbb 100644 --- a/var/spack/repos/builtin/packages/r-lumi/package.py +++ b/var/spack/repos/builtin/packages/r-lumi/package.py @@ -19,6 +19,7 @@ class RLumi(RPackage): bioc = "lumi" + version("2.50.0", commit="8711b77a1b5b0a58770d25d3d079ad02208704f5") version("2.48.0", commit="1f988ffe04d2c0707b2202d2074d02b679a3204b") version("2.46.0", commit="a68932c17a61c99e58ebbd8008d078bec6adb4e7") version("2.42.0", commit="a643b3ba46fee951b8566ddd8216af7e6c92f6f6") diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py index 92646ec040..4bae309055 100644 --- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py +++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py @@ -16,6 +16,7 @@ class RMakecdfenv(RPackage): bioc = "makecdfenv" + version("1.74.0", commit="412affc333ba51cad0ff3c7919e2eadaaf426359") version("1.72.0", commit="85c89688e6b6e8bff46b92cbeba49e38c510492e") version("1.70.0", commit="82ecd0fa8ac401e4ac8f1e9139556d2be4a3c4f3") version("1.66.0", commit="02aa975d543089f5495cb3b4e8edbcf0ff05148a") diff --git a/var/spack/repos/builtin/packages/r-marray/package.py b/var/spack/repos/builtin/packages/r-marray/package.py index 2e4859e3ca..914f433d74 100644 --- a/var/spack/repos/builtin/packages/r-marray/package.py +++ b/var/spack/repos/builtin/packages/r-marray/package.py @@ -14,6 +14,7 @@ class RMarray(RPackage): bioc = "marray" + version("1.76.0", commit="88cb0fd21cc60ac65410ca4314eca2e351933ec5") version("1.74.0", commit="9130a936fffb7d2d445ff21d04520e78b62625ac") version("1.72.0", commit="da35e8b8d2c9ef17e779013a5d252f38a1c66633") version("1.68.0", commit="67b3080486abdba7dd19fccd7fb731b0e8b5b3f9") diff --git a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py index 289f23d36a..c12475dc45 100644 --- a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py @@ -19,6 +19,7 @@ class RMatrixgenerics(RPackage): bioc = "MatrixGenerics" + version("1.10.0", commit="6d9d907e8c4d1fc96a32160fb9f3ab805d6eb356") version("1.8.1", commit="a4a21089e9f78275dd4a6f0df0c4b6b45c4650c7") version("1.8.0", commit="e4cc34d53bcfb9a5914afd79fda31ecd5037a47a") version("1.6.0", commit="4588a60e5cc691424c17faa281bdd7d99d83ec34") diff --git a/var/spack/repos/builtin/packages/r-metapod/package.py b/var/spack/repos/builtin/packages/r-metapod/package.py index b3759f931b..a0f58a38bc 100644 --- a/var/spack/repos/builtin/packages/r-metapod/package.py +++ b/var/spack/repos/builtin/packages/r-metapod/package.py @@ -19,6 +19,7 @@ class RMetapod(RPackage): bioc = "metapod" + version("1.6.0", commit="cfeaa959f5c6b2119df270f40af9c3ea718c4b00") version("1.4.0", commit="e71c2072e5b39f74599e279b28f4da7923b515fb") depends_on("r-rcpp", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-methylumi/package.py b/var/spack/repos/builtin/packages/r-methylumi/package.py index 699023f6c5..edd96956d5 100644 --- a/var/spack/repos/builtin/packages/r-methylumi/package.py +++ b/var/spack/repos/builtin/packages/r-methylumi/package.py @@ -20,6 +20,7 @@ class RMethylumi(RPackage): bioc = "methylumi" + version("2.44.0", commit="8f1f1f944993800da2776cb3240b4482c09429ad") version("2.42.0", commit="73e9c7fe1252c4ca20dc7b4e58decf04bf22d5e0") version("2.40.1", commit="211039225ca6fca9af75b8266f656161912ce10f") version("2.36.0", commit="5fb0b609f9c9181ac99f902745958774e5489606") diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py index 5caaad94ba..1613435f1f 100644 --- a/var/spack/repos/builtin/packages/r-minfi/package.py +++ b/var/spack/repos/builtin/packages/r-minfi/package.py @@ -13,6 +13,7 @@ class RMinfi(RPackage): bioc = "minfi" + version("1.44.0", commit="7c89fefc2e174d43ed9891b3f30b51ee19e916a6") version("1.42.0", commit="30fc7059460a9ec0be734fc26e608426ca9f5614") version("1.40.0", commit="17fa2b5d6cdbef6cbfb690242bd3f660731431f1") version("1.36.0", commit="94301da343226be7cd878c2a6c1bb529564785d6") diff --git a/var/spack/repos/builtin/packages/r-missmethyl/package.py b/var/spack/repos/builtin/packages/r-missmethyl/package.py index 59f285e0fa..2b92180696 100644 --- a/var/spack/repos/builtin/packages/r-missmethyl/package.py +++ b/var/spack/repos/builtin/packages/r-missmethyl/package.py @@ -23,6 +23,7 @@ class RMissmethyl(RPackage): bioc = "missMethyl" + version("1.32.0", commit="969b892e400b9821398099bcea46f2d0431daedf") version("1.30.0", commit="734846653f332f10e557b87aca4cb5d100b62469") version("1.28.0", commit="6a36aee28837736291ac630c1da3909f0e9c8d6a") version("1.24.0", commit="f6c86048911dc0e302fb593b7d0623f6e77ac332") diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py index c253097489..f866be23d3 100644 --- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py +++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py @@ -15,6 +15,7 @@ class RMlinterfaces(RPackage): bioc = "MLInterfaces" + version("1.78.0", commit="0988b95d282a6bffe56b7df4da2e23485e96d12c") version("1.76.0", commit="935323d8ce1e4bbf41844a1f9b6c946c5a30c673") version("1.74.0", commit="5ee73b6491b1d68d7b49ddce6483df98ad880946") version("1.70.0", commit="7b076c3e85314dd5fd5bd8a98e8123d08d9acd3b") @@ -46,5 +47,6 @@ class RMlinterfaces(RPackage): depends_on("r-threejs@0.2.2:", type=("build", "run")) depends_on("r-mlbench", type=("build", "run")) depends_on("r-magrittr", type=("build", "run"), when="@1.74.0:") + depends_on("r-summarizedexperiment", type=("build", "run"), when="@1.78.0:") depends_on("r-rda", type=("build", "run"), when="@:1.64.1") diff --git a/var/spack/repos/builtin/packages/r-mscoreutils/package.py b/var/spack/repos/builtin/packages/r-mscoreutils/package.py index 552f57c8cf..9abfe140f5 100644 --- a/var/spack/repos/builtin/packages/r-mscoreutils/package.py +++ b/var/spack/repos/builtin/packages/r-mscoreutils/package.py @@ -19,6 +19,7 @@ class RMscoreutils(RPackage): bioc = "MsCoreUtils" + version("1.10.0", commit="742c0c7143b1c32f75cc96b555e9f8cd265096c9") version("1.8.0", commit="8b7e2c31009276aad0b418ba5cdfc94d03e1973e") version("1.6.0", commit="9ed95b2d20dacaa83567fadd04349c81db9127ef") diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py index 44e0debcf6..54d5c60d96 100644 --- a/var/spack/repos/builtin/packages/r-msnbase/package.py +++ b/var/spack/repos/builtin/packages/r-msnbase/package.py @@ -15,6 +15,7 @@ class RMsnbase(RPackage): bioc = "MSnbase" + version("2.24.0", commit="b96e0142c663c2cb01e92479816a503c46caa1a8") version("2.22.0", commit="4f6e5767eee91b2105781b494fcabcfed16eba2d") version("2.20.4", commit="c86ac8b341832f2b577f2153258c1abf064e6448") version("2.16.1", commit="4d88b4edd1af59474462b1b06ad0ec5831f3a878") @@ -40,6 +41,7 @@ class RMsnbase(RPackage): depends_on("r-protgenerics@1.19.3:", type=("build", "run"), when="@2.16.1:") depends_on("r-protgenerics@1.25.1:", type=("build", "run"), when="@2.20.4:") depends_on("r-protgenerics@1.27.2:", type=("build", "run"), when="@2.22.0:") + depends_on("r-protgenerics@1.29.1:", type=("build", "run"), when="@2.24.0:") depends_on("r-mscoreutils", type=("build", "run"), when="@2.20.4:") depends_on("r-biocparallel", type=("build", "run")) depends_on("r-iranges", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py index 977db5ea2e..0150b55c73 100644 --- a/var/spack/repos/builtin/packages/r-multtest/package.py +++ b/var/spack/repos/builtin/packages/r-multtest/package.py @@ -29,6 +29,7 @@ class RMulttest(RPackage): bioc = "multtest" + version("2.54.0", commit="4e2c9e939dfd9984d8ff4bab0a95e1bd0457ec72") version("2.52.0", commit="00cfc9beb6d063c2b04fc83495a76824f8a33a64") version("2.50.0", commit="1de96649a942b115d3d554394514745e86eb3fd3") version("2.46.0", commit="c4dd27b333c80313a88668b59d0299988c6478a2") diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py index 63d58b8a8e..54c137d8d4 100644 --- a/var/spack/repos/builtin/packages/r-mzid/package.py +++ b/var/spack/repos/builtin/packages/r-mzid/package.py @@ -17,6 +17,7 @@ class RMzid(RPackage): bioc = "mzID" + version("1.36.0", commit="d6525edce3389fd4a05ff5fd42e9d611f00a545d") version("1.34.0", commit="bef64db159a0a4d241ba2ba271f70266c1522b2b") version("1.32.0", commit="d4146385b54f4d8361e23fc2c2aef79e952f4730") version("1.28.0", commit="cd006631c8222ce5b4af0577a7401b39cc58fd9c") diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py index 3db1724496..e784ba3968 100644 --- a/var/spack/repos/builtin/packages/r-mzr/package.py +++ b/var/spack/repos/builtin/packages/r-mzr/package.py @@ -19,6 +19,7 @@ class RMzr(RPackage): bioc = "mzR" + version("2.32.0", commit="ef57d59205398558898a748ba9c8de66b0bddb81") version("2.30.0", commit="563ae755cfc7de1ac8862247779182b7b3aebdcc") version("2.28.0", commit="bee7d6fb5f99e1fab5444ae1ad27b0bc6e83be9e") version("2.24.1", commit="e1d4de8761e6729fd45320d842691c8fe9116b7b") diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py index 610fe3f533..6ca569d131 100644 --- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py +++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py @@ -15,6 +15,7 @@ class ROligoclasses(RPackage): bioc = "oligoClasses" + version("1.60.0", commit="cf9d76c2551ad061d8b882ff1dc0a5cadc64a8a7") version("1.58.0", commit="5544e937913bb0df54c66d738d279c38efeb30cd") version("1.56.0", commit="6e6c7b4ba54095d1d3c44c081839f57af9261cbf") version("1.52.0", commit="7995efbd2d26b8fa950830d62db92bdaf5cbeeea") diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py index 2892bc3480..cf8df40e66 100644 --- a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py +++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py @@ -13,32 +13,37 @@ class ROrgHsEgDb(RPackage): Gene identifiers.""" bioc = "org.Hs.eg.db" - url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz" + url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz" version( + "3.16.0", + url="https://www.bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz", + sha256="2d2e6fdefa0dbb61c86d4736e5a0d430745ae733e310f240b97b2cb3703a2c0a", + ) + version( "3.15.0", - sha256="1dc9bb6019e0f0a222b9ec84a1c5870cdbca480f45d9ad08e35f77278baa3c5f", url="https://www.bioconductor.org/packages/3.15/data/annotation/src/contrib/org.Hs.eg.db_3.15.0.tar.gz", + sha256="1dc9bb6019e0f0a222b9ec84a1c5870cdbca480f45d9ad08e35f77278baa3c5f", ) version( "3.14.0", - sha256="0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00", url="https://www.bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Hs.eg.db_3.14.0.tar.gz", + sha256="0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00", ) version( "3.12.0", - sha256="48a1ab5347ec7a8602c555d9aba233102b61ffa2765826e5c8890ff0003249bb", url="https://www.bioconductor.org/packages/3.12/data/annotation/src/contrib/org.Hs.eg.db_3.12.0.tar.gz", + sha256="48a1ab5347ec7a8602c555d9aba233102b61ffa2765826e5c8890ff0003249bb", ) version( "3.8.2", - sha256="a0a16b7428f9e3d6ba54ebf4e05cd97a7bd298510ec4cf46ed2bed3e8f80db02", url="https://www.bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Hs.eg.db_3.8.2.tar.gz", + sha256="a0a16b7428f9e3d6ba54ebf4e05cd97a7bd298510ec4cf46ed2bed3e8f80db02", ) version( "3.4.1", - sha256="0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00", url="https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz", + sha256="0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00", ) depends_on("r@2.7.0:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py index 5ae90de629..75d2e41e48 100644 --- a/var/spack/repos/builtin/packages/r-organismdbi/package.py +++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py @@ -16,6 +16,7 @@ class ROrganismdbi(RPackage): bioc = "OrganismDbi" + version("1.40.0", commit="fac971dabef3b6d2473d2061bc1723e3de59c9d7") version("1.38.1", commit="fa8da4dd42ab15e1d21fd9f8286440596d50b1ec") version("1.38.0", commit="2ca01830a6ffcd0c0018d2bdbd3de8b4df716771") version("1.36.0", commit="3e7a90d248ff09f05ccd381ff921e12373a4b330") diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py index 92b017f158..2728ae5a16 100644 --- a/var/spack/repos/builtin/packages/r-pathview/package.py +++ b/var/spack/repos/builtin/packages/r-pathview/package.py @@ -20,6 +20,7 @@ class RPathview(RPackage): bioc = "pathview" + version("1.38.0", commit="8229376ffd45278b74a6e4ccfb3abea8992667f7") version("1.36.1", commit="f2e86b106c1cd91aac703337f968b7593a61c68d") version("1.36.0", commit="4f6be090a4089b5259d8e796d62f9830e2d63943") version("1.34.0", commit="a8788902a3bb047f8ee785966e57f84596076bbd") diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py index 0c68eedd77..5a199f032a 100644 --- a/var/spack/repos/builtin/packages/r-pcamethods/package.py +++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py @@ -21,6 +21,7 @@ class RPcamethods(RPackage): bioc = "pcaMethods" + version("1.90.0", commit="52474bc6d125122e89834328a1a780988349756f") version("1.88.0", commit="02fb58d6fe35579b86fb2ebd2eaf92e6b53444d2") version("1.86.0", commit="9419cfa18c18dfbd1e1194127fd120ab456c3657") version("1.82.0", commit="d500b3363308f1f8ca70625c5cd10cce59b27641") diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py index b5eff1358c..56394edbfa 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -16,29 +16,34 @@ class RPfamDb(RPackage): url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" version( + "3.16.0", + url="https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PFAM.db_3.16.0.tar.gz", + sha256="8082aaa94eb962b2cf42cfaead8ff9e1bdbd12fdeae82a49d0f3b37bd50eb30c", + ) + version( "3.15.0", - sha256="e7036a5f76779ab6e8a32eb659c54f52426c4824dee02903cffd85bed372720f", url="https://bioconductor.org/packages/3.15/data/annotation/src/contrib/PFAM.db_3.15.0.tar.gz", + sha256="e7036a5f76779ab6e8a32eb659c54f52426c4824dee02903cffd85bed372720f", ) version( "3.14.0", - sha256="25c1915079e8f93d04e2cc1ab791f7f47813aaab5ac394feaf57520bb292d616", url="https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PFAM.db_3.14.0.tar.gz", + sha256="25c1915079e8f93d04e2cc1ab791f7f47813aaab5ac394feaf57520bb292d616", ) version( "3.12.0", - sha256="ec42d067522baf2d7d3ca78d4f8cc0dac08a4b98f1d890f52424e5d5b16f2fe9", url="https://bioconductor.org/packages/3.12/data/annotation/src/contrib/PFAM.db_3.12.0.tar.gz", + sha256="ec42d067522baf2d7d3ca78d4f8cc0dac08a4b98f1d890f52424e5d5b16f2fe9", ) version( "3.10.0", - sha256="038888f95ce69230ac0e0b08aa3bcb09965682415520d437a7fb0a031eefe158", url="https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PFAM.db_3.10.0.tar.gz", + sha256="038888f95ce69230ac0e0b08aa3bcb09965682415520d437a7fb0a031eefe158", ) version( "3.4.1", - sha256="fc45a0d53139daf85873f67bd3f1b68f2d883617f4447caddbd2d7dcc58a393f", url="https://bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz", + sha256="fc45a0d53139daf85873f67bd3f1b68f2d883617f4447caddbd2d7dcc58a393f", ) depends_on("r@2.7.0:", when="@3.4.1:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py index 4d84a4c9d4..e001d1dd67 100644 --- a/var/spack/repos/builtin/packages/r-phyloseq/package.py +++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py @@ -14,6 +14,7 @@ class RPhyloseq(RPackage): bioc = "phyloseq" + version("1.42.0", commit="de6be71fe9902bdfe7791163acb7b67d238424dc") version("1.40.0", commit="20bb27d5e6e0d4368978a15671b829990b1f4568") version("1.38.0", commit="1e2409a6ed3c23e308275098c2dc9fdba9d5e5f6") version("1.34.0", commit="cbed93ead5528fe9024d646c597dab9fc95952d3") @@ -25,7 +26,7 @@ class RPhyloseq(RPackage): depends_on("r@3.3.0:", type=("build", "run")) depends_on("r@3.4.0:", type=("build", "run"), when="@1.22.3") - depends_on("r-ade4@1.7.4:", type=("build", "run")) + depends_on("r-ade4@1.7-4:", type=("build", "run")) depends_on("r-ape@3.4:", type=("build", "run")) depends_on("r-ape@5.0:", type=("build", "run"), when="@1.22.3:") depends_on("r-biobase", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py index 7f779764f7..2ac07e759e 100644 --- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py +++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py @@ -13,6 +13,7 @@ class RPreprocesscore(RPackage): bioc = "preprocessCore" + version("1.60.0", commit="7f62a7d54776a21ab6c2d3df4668382d531d1ee8") version("1.58.0", commit="2995e3e1a8f428a80aee200db42ee44743d893f6") version("1.56.0", commit="8f3272219507aa85e0c876fb434dc3b926c22c5d") version("1.52.1", commit="91de4ab67315dc2af68554ae3c48823f4b1ea8ac") diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py index edc8461666..a6920ae838 100644 --- a/var/spack/repos/builtin/packages/r-protgenerics/package.py +++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py @@ -13,6 +13,7 @@ class RProtgenerics(RPackage): bioc = "ProtGenerics" + version("1.30.0", commit="fcd566bf04034cf52db3338b5d6de7447443cf77") version("1.28.0", commit="cfcd0a9ebd642515764ba70c5c4e9c2a0f2f07ac") version("1.26.0", commit="2033289ab928034b86c321e56c37e502e557c7a1") version("1.22.0", commit="2bb3011fb0d79536e1c50251084a7057004449c6") diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py index 0752d2675c..264c7e3c03 100644 --- a/var/spack/repos/builtin/packages/r-quantro/package.py +++ b/var/spack/repos/builtin/packages/r-quantro/package.py @@ -18,6 +18,7 @@ class RQuantro(RPackage): bioc = "quantro" + version("1.32.0", commit="0c70b787866d915abb720f2ab326a83eb1e775b7") version("1.30.0", commit="e756c439cdc5a6fb4d7879aff56a8368475513b5") version("1.28.0", commit="109e7452a349f273e10d2ffb79d5624260b67dd5") version("1.24.0", commit="c7c0180292156a01722d91b353da44324e72d68f") diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py index 08e2ad826e..e83ae67597 100644 --- a/var/spack/repos/builtin/packages/r-qvalue/package.py +++ b/var/spack/repos/builtin/packages/r-qvalue/package.py @@ -23,6 +23,7 @@ class RQvalue(RPackage): bioc = "qvalue" + version("2.30.0", commit="e8a4c22d035f860ee730aa7c5a4dbc7460afcedc") version("2.28.0", commit="aaa62d5ab5a960e0a626928abaf5b3a5c5f73374") version("2.26.0", commit="6d7410d4b8673bcf9065e054670c1fbcb917a27e") version("2.22.0", commit="b4bde8198252737b287fd7f9a4ed697f57fad92c") diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py index 0dc6b70b20..7a641a9dc0 100644 --- a/var/spack/repos/builtin/packages/r-rbgl/package.py +++ b/var/spack/repos/builtin/packages/r-rbgl/package.py @@ -14,6 +14,7 @@ class RRbgl(RPackage): bioc = "RBGL" + version("1.74.0", commit="e698db897b719992a8c0747138735c0e7d9dfb21") version("1.72.0", commit="a86f3102f2795e1ffb530bb061247e3a42ca22f7") version("1.70.0", commit="9cfd5fdad4f1f438ff748317f32e822aede8921b") version("1.66.0", commit="bf0c111dbc231de6d3423c28e115b54fb010e1ea") diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py index 3a8462d49d..6647e7c391 100644 --- a/var/spack/repos/builtin/packages/r-reportingtools/package.py +++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py @@ -23,6 +23,7 @@ class RReportingtools(RPackage): bioc = "ReportingTools" + version("2.38.0", commit="5c4971eebbaf3577ef20b74bf36c2db4e91561cc") version("2.36.0", commit="34122d4bde5ce43415f63f2e39e3a088c55282cc") version("2.34.0", commit="fb5aef0b6e1c6166d0f025d9e6ca60e54c68dbaf") version("2.30.0", commit="fb9aee416f38cfd308d6d7264ccbcda0467642a7") diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py index d842308c57..00fb2e0dd1 100644 --- a/var/spack/repos/builtin/packages/r-rgraphviz/package.py +++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py @@ -14,6 +14,7 @@ class RRgraphviz(RPackage): bioc = "Rgraphviz" + version("2.42.0", commit="f6877441ab256876ef6a62c2e6faf980c2190b20") version("2.40.0", commit="d864c9741c9177bc627cca1198673be2b1bfbc3e") version("2.38.0", commit="004de09a5b171211aff6cbaa1969ab8e3a5d6c61") version("2.34.0", commit="9746623211be794226258631992dfcccccfd7487") diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py index 734258a57a..8f35f14454 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py @@ -19,6 +19,7 @@ class RRhdf5(RPackage): bioc = "rhdf5" + version("2.42.0", commit="fa26027d57b5b6d1c297446d9bbed74d5710c5d2") version("2.40.0", commit="fb6c15a3199f3ffd746fb9a381d574d17fef45a2") version("2.38.0", commit="f6fdfa807f5cd5a4d11d4aa6ebfaa81c118b4c3f") version("2.34.0", commit="ec861b81fc6962e844bf56b7549ba565a7e4c69c") diff --git a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py index 9f9a785bdc..96a635e40a 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py @@ -13,6 +13,7 @@ class RRhdf5filters(RPackage): bioc = "rhdf5filters" + version("1.10.0", commit="6131538e2c5896dca0af33882bc2da961d79e49a") version("1.8.0", commit="b0b588b71a5595b30f4e698a50b84310dc19745d") version("1.6.0", commit="5f7f3a5b7dabd6e7d0c50cda70290e2472ff4f53") version("1.2.0", commit="25af0180f926b4b3ea11b30ec9277d26ad3d56b3") diff --git a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py index 9ac3e4c706..1f05e633c2 100644 --- a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py +++ b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py @@ -13,6 +13,7 @@ class RRhdf5lib(RPackage): bioc = "Rhdf5lib" + version("1.20.0", commit="760679995f17996a9de328cf7a8bcaa6c87286d4") version("1.18.2", commit="d104bbfdb91ac5ec7db3c453f23e4d1d6feb671f") version("1.16.0", commit="534c49705dbdb27ae0c564acff2c72df2b27b3f1") version("1.12.1", commit="cf464f40fd95274d0d351cf28b586c49307c4f0b") diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py index f2bc370896..94bee68036 100644 --- a/var/spack/repos/builtin/packages/r-rhtslib/package.py +++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py @@ -27,6 +27,7 @@ class RRhtslib(RPackage): # branches. # Aborting # version("1.28.0", commit='214fde2218bdbca89f1e12a30d2e081e76915aef') + version("2.0.0", commit="1757333eb88625158505e5fa47840081110cf8a4") version("1.28.0", branch="RELEASE_3_15") version("1.26.0", commit="f5b20e97b283942877529f750b28398782552655") version("1.22.0", commit="899b79faa54d42c7c9b9a2bc49972109637d367f") @@ -48,9 +49,9 @@ class RRhtslib(RPackage): # available depends_on("patchelf", type="build", when="@1.12:1.14") - patch("use_spack_Makeconf.patch", when="@1.12:") + patch("use_spack_Makeconf.patch", when="@1.12:1.28.0") patch("find_deps-1.12.patch", when="@1.12:1.14") - patch("find_deps-1.16.patch", when="@1.16:") + patch("find_deps-1.16.patch", when="@1.16:1.28.0") @when("@1.12:") def setup_build_environment(self, env): diff --git a/var/spack/repos/builtin/packages/r-roc/package.py b/var/spack/repos/builtin/packages/r-roc/package.py index 5016b505cd..9fe3611826 100644 --- a/var/spack/repos/builtin/packages/r-roc/package.py +++ b/var/spack/repos/builtin/packages/r-roc/package.py @@ -13,6 +13,7 @@ class RRoc(RPackage): bioc = "ROC" + version("1.74.0", commit="982ad4d3606b19b8460e8a8af7cfe7c30b83f9b9") version("1.72.0", commit="c5d083b01314280dd43eb4cddd8a7fde8b5dce18") version("1.70.0", commit="44fd639958b9b1be4f8f731dc2be9dd91b2fa632") version("1.66.0", commit="62701ee41f48f99d15344127384fa032db69486f") diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py index 49f3fb1311..f4aa29bdf4 100644 --- a/var/spack/repos/builtin/packages/r-rots/package.py +++ b/var/spack/repos/builtin/packages/r-rots/package.py @@ -14,6 +14,7 @@ class RRots(RPackage): bioc = "ROTS" + version("1.26.0", commit="8bb45fe78779583ae4d30cf0dc3af0d8de405fdf") version("1.24.0", commit="372e4623b39f585d4196d21164436c1ba013173f") version("1.22.0", commit="a53ec77c40ed3b3c84e91d794c1602dd509cad83") version("1.18.0", commit="1d4e206a8ce68d5a1417ff51c26174ed9d0ba7d2") diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py index e9e6f4de8f..0f80a3faf3 100644 --- a/var/spack/repos/builtin/packages/r-rsamtools/package.py +++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py @@ -17,6 +17,7 @@ class RRsamtools(RPackage): bioc = "Rsamtools" + version("2.14.0", commit="8302eb7fa1c40384f1af5855222d94f2efbdcad1") version("2.12.0", commit="d6a65dd57c5a17e4c441a27492e92072f69b175e") version("2.10.0", commit="b19738e85a467f9032fc7903be3ba10e655e7061") version("2.6.0", commit="f2aea061517c5a55e314c039251ece9831c7fad2") @@ -46,6 +47,7 @@ class RRsamtools(RPackage): depends_on("r-biocparallel", type=("build", "run")) depends_on("r-rhtslib@1.16.3", type=("build", "run"), when="@2.0.3") depends_on("r-rhtslib@1.17.7:", type=("build", "run"), when="@2.2.1:") + depends_on("r-rhtslib@1.99.3:", type=("build", "run"), when="@2.14.0:") depends_on("gmake", type="build") # this is not a listed dependency but is needed diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py index a52013b329..5a8bf6b0fb 100644 --- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py +++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py @@ -18,6 +18,7 @@ class RRtracklayer(RPackage): bioc = "rtracklayer" + version("1.58.0", commit="54a74972c08775fdf1e83e6e22cd0b8fad677fc1") version("1.56.1", commit="4c6d2201fcb102d471bd88f4f51cc34317669955") version("1.56.0", commit="1d70f7dc464ad87a1fde61588cd9ae0cb86b6e86") version("1.54.0", commit="04cdd75521a8364e67a49d7352500dd4a3e83c55") diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py index cdd2485c5c..dffb0e2652 100644 --- a/var/spack/repos/builtin/packages/r-s4vectors/package.py +++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py @@ -20,6 +20,7 @@ class RS4vectors(RPackage): bioc = "S4Vectors" + version("0.36.0", commit="af58701957ffdd9209031dd6a8dee3acdc58e999") version("0.34.0", commit="f590de3ec4d896a63351d0c1925d3856c0bd5292") version("0.32.3", commit="ad90e78fd3a4059cfcf2846498fb0748b4394e1a") version("0.28.1", commit="994cb7ef830e76f8b43169cc72b553869fafb2ed") diff --git a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py index b49f1235d5..e4c8e970a3 100644 --- a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py +++ b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py @@ -16,6 +16,7 @@ class RScaledmatrix(RPackage): bioc = "ScaledMatrix" + version("1.6.0", commit="45a29d3662e2766f973b281ed86ce2654be84b70") version("1.4.1", commit="15e2efcb6b11e26c31ef2d44968355f71cc1f4fc") version("1.4.0", commit="32e6e918bc7bb64bbf75613d353ca268c7d04292") version("1.2.0", commit="d0573e14ca537b40ade7dd1c9cf0cadae60d4349") diff --git a/var/spack/repos/builtin/packages/r-scater/package.py b/var/spack/repos/builtin/packages/r-scater/package.py index 4bd42177ef..0366c51bbf 100644 --- a/var/spack/repos/builtin/packages/r-scater/package.py +++ b/var/spack/repos/builtin/packages/r-scater/package.py @@ -15,6 +15,7 @@ class RScater(RPackage): bioc = "scater" + version("1.26.0", commit="a548ddc8424e185bfb06f48bfc174071e69fc687") version("1.24.0", commit="013f0935a1a225139986ca5a3f0e9d08a1558153") version("1.22.0", commit="ea2c95c53adb8c6fab558c1cb869e2eab36aa9f8") version("1.18.3", commit="a94e7f413bf0f5f527b41b0b34e7a8e5c947ae37") @@ -48,6 +49,9 @@ class RScater(RPackage): depends_on("r-rtsne", type=("build", "run"), when="@1.22.0:") depends_on("r-rcolorbrewer", type=("build", "run"), when="@1.22.0:") depends_on("r-rcppml", type=("build", "run"), when="@1.24.0:") + depends_on("r-ggrastr", type=("build", "run"), when="@1.26.0:") + depends_on("r-pheatmap", type=("build", "run"), when="@1.26.0:") + depends_on("r-uwot", type=("build", "run"), when="@1.26.0:") depends_on("r-ggrepel", type=("build", "run"), when="@1.22.0:") depends_on("r-biobase", type=("build", "run"), when="@1.4.0:1.8.4") diff --git a/var/spack/repos/builtin/packages/r-scdblfinder/package.py b/var/spack/repos/builtin/packages/r-scdblfinder/package.py index 2dcd41c257..8a3446d041 100644 --- a/var/spack/repos/builtin/packages/r-scdblfinder/package.py +++ b/var/spack/repos/builtin/packages/r-scdblfinder/package.py @@ -16,6 +16,7 @@ class RScdblfinder(RPackage): bioc = "scDblFinder" + version("1.12.0", commit="65a88be3a4ca98ccad0a1829a19652df1a3c94fd") version("1.10.0", commit="03512cad0cdfe3cddbef66ec5e330b53661eccfc") depends_on("r@4.0:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/r-scran/package.py b/var/spack/repos/builtin/packages/r-scran/package.py index cac48a6e17..0a4704351c 100644 --- a/var/spack/repos/builtin/packages/r-scran/package.py +++ b/var/spack/repos/builtin/packages/r-scran/package.py @@ -17,6 +17,7 @@ class RScran(RPackage): bioc = "scran" + version("1.26.0", commit="df66576d6958a088c38bd45e1cad9c16cbb52991") version("1.24.1", commit="1a83eb7c948b1dc49253080c23b26cefb3a0f3b9") version("1.24.0", commit="c3f9e169c4538ce827d4f14a4141571c2366cd31") diff --git a/var/spack/repos/builtin/packages/r-scuttle/package.py b/var/spack/repos/builtin/packages/r-scuttle/package.py index 2ed9145d15..5c201471a4 100644 --- a/var/spack/repos/builtin/packages/r-scuttle/package.py +++ b/var/spack/repos/builtin/packages/r-scuttle/package.py @@ -16,6 +16,7 @@ class RScuttle(RPackage): bioc = "scuttle" + version("1.8.0", commit="dabf6b95e478d599557ebbed03edd44031fd6b78") version("1.6.3", commit="df23680da9fa4d685df77e4561467f491c850b50") version("1.6.2", commit="afdfc555151d84cc332757b4ec0b97cb7f39d2d5") version("1.4.0", commit="b335263dd56bb859b5dd3ea27ee00dffa0215313") diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py index 64df020002..5d8500fecc 100644 --- a/var/spack/repos/builtin/packages/r-seqlogo/package.py +++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py @@ -15,6 +15,7 @@ class RSeqlogo(RPackage): bioc = "seqLogo" + version("1.64.0", commit="75ff6c0689fce541f054d33750acb6224d14ed4e") version("1.62.0", commit="f2d0b53b1411ea98299201a8125a85f4cbf7c9cd") version("1.60.0", commit="4115c8e1d01accb8c8cc1cf96f23359466827e16") version("1.56.0", commit="169260c43fc58dc75becb3b7842cac3d0038a8d5") diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py index 2ac41c3f15..685689516a 100644 --- a/var/spack/repos/builtin/packages/r-shortread/package.py +++ b/var/spack/repos/builtin/packages/r-shortread/package.py @@ -18,6 +18,7 @@ class RShortread(RPackage): bioc = "ShortRead" + version("1.56.0", commit="df25d0872d52aac3610998abda0d7bfd37298726") version("1.54.0", commit="a1082a335120860d019aa0065a975d41890351f7") version("1.52.0", commit="4d7304d7b5a0ca5c904c0b919d6c95599db72a39") version("1.48.0", commit="ba44cd2517bc0e6f46d2cfcfce393f86eec814d0") diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py index 4aa7b29ddf..0f04add8e9 100644 --- a/var/spack/repos/builtin/packages/r-siggenes/package.py +++ b/var/spack/repos/builtin/packages/r-siggenes/package.py @@ -16,6 +16,7 @@ class RSiggenes(RPackage): bioc = "siggenes" + version("1.72.0", commit="4f93d1a28087c941b275e6c6bae9e42d721cf422") version("1.70.0", commit="c263daa14cf87c61b41e3a9e88573ba339c66179") version("1.68.0", commit="a29bf02b19cc9003c8401608831232b7c2af26e7") version("1.64.0", commit="3b528d37c16fc41bbc5c98165f606394313aa050") diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py index 47719faeb7..faf18c04d7 100644 --- a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py @@ -16,6 +16,7 @@ class RSinglecellexperiment(RPackage): bioc = "SingleCellExperiment" + version("1.20.0", commit="467f02c0346e3ca5ec8825a6faa80a90d20fcd29") version("1.18.1", commit="db7768a7cb5eca724bcf7e4cea3234992ac714a1") version("1.18.0", commit="3a72dcd97e628055b2d02294eaecca9a41aba604") version("1.16.0", commit="bb27609ba08052607fc08529ffbbbcf1eab265cb") diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py index 13fbb24aa3..b4a63e35fa 100644 --- a/var/spack/repos/builtin/packages/r-snprelate/package.py +++ b/var/spack/repos/builtin/packages/r-snprelate/package.py @@ -29,6 +29,7 @@ class RSnprelate(RPackage): bioc = "SNPRelate" + version("1.32.0", commit="2e8cc807baa74fca5137148b672f3945c36689b2") version("1.30.1", commit="baef8a71d3908287a2307768348c02db0720d125") version("1.28.0", commit="8fcd837f4627a3bb77cb8d992b2baedd0589d123") version("1.24.0", commit="419b13b761ea39a8b1b9bc73097fb0359c59f1c2") diff --git a/var/spack/repos/builtin/packages/r-snpstats/package.py b/var/spack/repos/builtin/packages/r-snpstats/package.py index 56ad1b8933..56e7c7eee6 100644 --- a/var/spack/repos/builtin/packages/r-snpstats/package.py +++ b/var/spack/repos/builtin/packages/r-snpstats/package.py @@ -15,6 +15,7 @@ class RSnpstats(RPackage): bioc = "snpStats" + version("1.48.0", commit="7d4cec7275b9360d98cb59d15c4140bed3e6a74c") version("1.46.0", commit="1e70784b113eaca231bc5f91fc8ae5aadb151ddb") version("1.44.0", commit="72392dab4e75de2da459b1e95f1d48947811597b") version("1.40.0", commit="5fcac6f3b4bb6f45c19dff8f3089b693b74a56ce") diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py index 2bb6b00eb9..7c639b6d1c 100644 --- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py +++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py @@ -16,6 +16,7 @@ class RSomaticsignatures(RPackage): bioc = "SomaticSignatures" + version("2.34.0", commit="249b1ef7cef3c94cfb96cc8aa2a16e00c2bd5d1f") version("2.32.0", commit="444d37661d147618f6830fd5de01a83ddf2a694d") version("2.30.0", commit="03f7ad707f6530fa7f62093f808884b6e83b0526") version("2.26.0", commit="9d4bed6e118ac76755ffb7abd058b09bac58a9d7") diff --git a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py index f1e5cd4dbc..bc043acc49 100644 --- a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py @@ -17,6 +17,7 @@ class RSparsematrixstats(RPackage): bioc = "sparseMatrixStats" + version("1.10.0", commit="75d85ba2c9c4c36887fef1a007883167aa85bd94") version("1.8.0", commit="4f1e2213e5b0d6b3d817c2c9129b7566288916f6") version("1.6.0", commit="78627a842790af42b6634893087b2bb1f4ac0392") version("1.2.1", commit="9726f3d5e0f03b50c332d85d5e4c339c18b0494c") diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py index 72835d96a9..1f32be4b15 100644 --- a/var/spack/repos/builtin/packages/r-spem/package.py +++ b/var/spack/repos/builtin/packages/r-spem/package.py @@ -14,6 +14,7 @@ class RSpem(RPackage): bioc = "SPEM" + version("1.38.0", commit="43ff6b0a84e7aef947d1a793583d2e9a0119c99d") version("1.36.0", commit="75832966ba3e2bae6b56aa138764f7a98c7ba9b1") version("1.34.0", commit="53fd404638a04ec8e2e826e55c3f2d91d8b28e3d") version("1.30.0", commit="6b2eb64bfe6287846b1408297dd46dc772431031") diff --git a/var/spack/repos/builtin/packages/r-sseq/package.py b/var/spack/repos/builtin/packages/r-sseq/package.py index 2fa6962015..a72ba78db3 100644 --- a/var/spack/repos/builtin/packages/r-sseq/package.py +++ b/var/spack/repos/builtin/packages/r-sseq/package.py @@ -23,6 +23,7 @@ class RSseq(RPackage): bioc = "sSeq" + version("1.36.0", commit="0345ac579c4bdcc9c42c24831ad86fc6225c5cb9") version("1.34.0", commit="882bea1664f55d85550a7185cbd4a0108c35df36") version("1.32.0", commit="c0d3c305755d888f64d334a4ab5fa54c623054cf") version("1.28.0", commit="401f6805628bdf6579cc0e643b7ed54319f024be") diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py index dc635ff538..80575fbee3 100644 --- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py +++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py @@ -16,6 +16,7 @@ class RSummarizedexperiment(RPackage): bioc = "SummarizedExperiment" + version("1.28.0", commit="ba55dac12224f0aafe8f52f1397611b5efb41626") version("1.26.1", commit="c8cbd3b4f0fa1d686c4d7ce5b8614a24c74b2074") version("1.24.0", commit="d37f19383d03c107a8a41c0df2326e28efe46b28") version("1.20.0", commit="874aa87a481e4076a0ec3369f55c9c0a1ab8025e") diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py index 8d162f2b2a..94fc3dbf0e 100644 --- a/var/spack/repos/builtin/packages/r-sva/package.py +++ b/var/spack/repos/builtin/packages/r-sva/package.py @@ -30,6 +30,7 @@ class RSva(RPackage): bioc = "sva" + version("3.46.0", commit="4aac49cf806f05bb98e08a6be539adebbecbfdb2") version("3.44.0", commit="45ab2c1d6643bcda4de2d95a81b9b28d33a1a8a1") version("3.42.0", commit="54c843cc46437be233ecb43b6aa868e968d71138") version("3.38.0", commit="5ded8ba649200ec4829051f86a59e1a2548a7ab8") diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py index e4a9f9c3f8..81ae6752be 100644 --- a/var/spack/repos/builtin/packages/r-tfbstools/package.py +++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py @@ -18,6 +18,7 @@ class RTfbstools(RPackage): bioc = "TFBSTools" + version("1.36.0", commit="3358c89227a4d2e237ee5f8c532f468460a16ee2") version("1.34.0", commit="7f8d0cb58a527a5d7ba94a773279f13aedca6ec7") version("1.32.0", commit="235505626b910de29156a07e1f990daa3b5d57d9") version("1.28.0", commit="15e7cf76f39ee3280a27284d58f7adef1c33f193") diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py index c66dc11902..5f52b60946 100644 --- a/var/spack/repos/builtin/packages/r-tmixclust/package.py +++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py @@ -18,6 +18,7 @@ class RTmixclust(RPackage): bioc = "TMixClust" + version("1.20.0", commit="df27f53d088b02cf596504b44909f2762900ab49") version("1.18.0", commit="71f80a7ace481f46471f36c91223effb85e17186") version("1.16.0", commit="e525cfd9c729a73a1964c243e5c34c37343f7bfa") version("1.12.0", commit="982b31bd7e22a3dc638bbda0336546220444f0c2") diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py index b7832224a2..b6e4e3061f 100644 --- a/var/spack/repos/builtin/packages/r-topgo/package.py +++ b/var/spack/repos/builtin/packages/r-topgo/package.py @@ -16,6 +16,7 @@ class RTopgo(RPackage): bioc = "topGO" + version("2.50.0", commit="befbff4e67c1b01e23f111d147274641a8b7b0f5") version("2.48.0", commit="a47f0079319c7d74db4aeda6399e06f12a34b585") version("2.46.0", commit="2bfa9dff41fff261aa6188f8368aebd6e8250b18") version("2.42.0", commit="3a33cf53883de45bda506953303e1809ab982adc") diff --git a/var/spack/repos/builtin/packages/r-treeio/package.py b/var/spack/repos/builtin/packages/r-treeio/package.py index 17cf92167d..9b02d298a0 100644 --- a/var/spack/repos/builtin/packages/r-treeio/package.py +++ b/var/spack/repos/builtin/packages/r-treeio/package.py @@ -18,6 +18,7 @@ class RTreeio(RPackage): bioc = "treeio" + version("1.22.0", commit="eb24a854806a671e7b37ef36dafc60b4eb9ddaa1") version("1.20.2", commit="ed457d6fd85a50e0993c8c9acbd9b701be01a348") version("1.20.0", commit="5f7c3704fc8202c52451d092148fdcfe683f026a") version("1.18.1", commit="a06b6b3d2a64f1b22c6c8c5f97c08f5863349c83") diff --git a/var/spack/repos/builtin/packages/r-tximport/package.py b/var/spack/repos/builtin/packages/r-tximport/package.py index 0b86335fdd..0d9c9f7f58 100644 --- a/var/spack/repos/builtin/packages/r-tximport/package.py +++ b/var/spack/repos/builtin/packages/r-tximport/package.py @@ -19,6 +19,7 @@ class RTximport(RPackage): bioc = "tximport" + version("1.26.0", commit="5ae7139edf9d3445210ea014026813fd030212a8") version("1.24.0", commit="58524f39bdd55299cfe80a726f99b714b724be20") version("1.22.0", commit="335213baee3492fbf6baaa8b4e067ac0ef384684") version("1.18.0", commit="58b20cbc566648586b6990b30ebc70bef308cb05") diff --git a/var/spack/repos/builtin/packages/r-tximportdata/package.py b/var/spack/repos/builtin/packages/r-tximportdata/package.py index 3538a4b8ac..19bb5aaa6f 100644 --- a/var/spack/repos/builtin/packages/r-tximportdata/package.py +++ b/var/spack/repos/builtin/packages/r-tximportdata/package.py @@ -18,6 +18,7 @@ class RTximportdata(RPackage): bioc = "tximportData" + version("1.26.0", commit="8f6ef3e3ae54e6eb99fe915364f5174c4f50a986") version("1.24.0", commit="646f366fb25be359c95dc97c9369961c8d5ed942") version("1.22.0", commit="c576b18e43985baf8beab327cbc54afe8324659c") version("1.18.0", commit="24945f8dd1e4e441ad5145fb7a37a1630912f929") diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py index 7e5e5ae6cf..276c6189b8 100644 --- a/var/spack/repos/builtin/packages/r-variantannotation/package.py +++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py @@ -14,6 +14,7 @@ class RVariantannotation(RPackage): bioc = "VariantAnnotation" + version("1.44.0", commit="2e7e0a3b7c1918c0d64170dc7c173a636d3764f4") version("1.42.1", commit="d1121696c76c189d6b4df9914806bf585a495845") version("1.40.0", commit="50ead7cb60cedf3c053853fab92d9f104f9f85bd") version("1.36.0", commit="9918bd19a2e6f89e5edc5fe03c8812f500bb3e19") @@ -62,6 +63,7 @@ class RVariantannotation(RPackage): depends_on("r-genomicfeatures@1.27.4:", type=("build", "run")) depends_on("r-genomicfeatures@1.31.3:", type=("build", "run"), when="@1.26.1:") depends_on("r-rhtslib", type=("build", "run"), when="@1.30.1:") + depends_on("r-rhtslib@1.99.3:", type=("build", "run"), when="@1.44.0:") depends_on("gmake", type="build") # Not listed but needed diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py index b3ad289aee..41556028d8 100644 --- a/var/spack/repos/builtin/packages/r-vsn/package.py +++ b/var/spack/repos/builtin/packages/r-vsn/package.py @@ -24,6 +24,7 @@ class RVsn(RPackage): bioc = "vsn" + version("3.66.0", commit="ddccd6c74ebea426056794c2bfad2dfd02631092") version("3.64.0", commit="1f09f20ee7f81100fb0bf66288c4caf0049b5508") version("3.62.0", commit="6ae7f4e07ec1a5a9482cab892d98175983bfcd50") version("3.58.0", commit="a451e6ae989623750feacf26d99683a7955adf85") diff --git a/var/spack/repos/builtin/packages/r-watermelon/package.py b/var/spack/repos/builtin/packages/r-watermelon/package.py index 2b6c8f4606..48d40ad70c 100644 --- a/var/spack/repos/builtin/packages/r-watermelon/package.py +++ b/var/spack/repos/builtin/packages/r-watermelon/package.py @@ -14,6 +14,7 @@ class RWatermelon(RPackage): bioc = "wateRmelon" + version("2.4.0", commit="31c15255511940b8b83d039c42ec89e43ceb0885") version("2.2.0", commit="6ec49efe98aef31d0789b31ab048eb46edec762c") version("2.0.0", commit="f6a331bdf50e0e5c94009fb67be873d996348ade") version("1.34.0", commit="3fa2745535c22068a438747b41b9d793196098d4") diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py index b871a0ec1f..ab363bb062 100644 --- a/var/spack/repos/builtin/packages/r-xde/package.py +++ b/var/spack/repos/builtin/packages/r-xde/package.py @@ -15,6 +15,7 @@ class RXde(RPackage): bioc = "XDE" + version("2.44.0", commit="a6ddedb91afe381f223e52ae49c6704f8f046916") version("2.42.0", commit="298e83eff7fc5f72a2bb76b559c5115c6cd3ee84") version("2.40.0", commit="bfc3c54787aec97b70bef7b99a6adc75d2cf5ed2") version("2.36.0", commit="0277f9dffbd7d1880be77cb8581fc614501b3293") diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py index edec8cbf69..c5950abe14 100644 --- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py +++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py @@ -14,6 +14,7 @@ class RXmapbridge(RPackage): bioc = "xmapbridge" + version("1.56.0", commit="fdf2cafca8ad348813d3381fee57623fab53f0ab") version("1.54.0", commit="a316e2399894191646c229378fa138b7461c75ab") version("1.52.0", commit="fe32fcd2a83432c721eb948cb3af73dd187065f6") version("1.48.0", commit="1cefe6b56c6dcb1f18028b3b7d6a67d490bc9730") diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py index 45e5a84bbb..c687a0f800 100644 --- a/var/spack/repos/builtin/packages/r-xvector/package.py +++ b/var/spack/repos/builtin/packages/r-xvector/package.py @@ -15,6 +15,7 @@ class RXvector(RPackage): bioc = "XVector" + version("0.38.0", commit="8cad08446091dcc7cd759e880c0f3e47228278dd") version("0.36.0", commit="ff6f818ff4357eb9bf00654de9e0f508a5285408") version("0.34.0", commit="06adb25ac51c707b90fb8e0637fa06df237a863c") version("0.30.0", commit="985e963e0b1c3ff004dd0b07ad7c9ff7ed853ec0") diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py index 49d0df645c..ade9f0b36a 100644 --- a/var/spack/repos/builtin/packages/r-yapsa/package.py +++ b/var/spack/repos/builtin/packages/r-yapsa/package.py @@ -18,6 +18,7 @@ class RYapsa(RPackage): bioc = "YAPSA" + version("1.24.0", commit="68d1c9c71af3ade4a44237ec2d3003688378f898") version("1.22.0", commit="55c2886874f154c737264ce6843089bf3565fa57") version("1.20.1", commit="6c3f437911859df6f6e4a9af5571c3a5aafbffb2") version("1.16.0", commit="f344cdb81bb886c633f9325f811912fb59d58eb1") diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py index c1ba22aa5c..6c519947b5 100644 --- a/var/spack/repos/builtin/packages/r-yarn/package.py +++ b/var/spack/repos/builtin/packages/r-yarn/package.py @@ -18,6 +18,7 @@ class RYarn(RPackage): bioc = "yarn" + version("1.24.0", commit="d3a9c5cc1f97bff111dc9332f32ded676e3709d3") version("1.22.0", commit="0d94152eee4224bf1ca467fad7f2b35c2e1df6b2") version("1.20.0", commit="b41e4ef14f980518af2fc59f202ad8ec148e8b47") version("1.16.0", commit="ff5a18cb946ffec3cb773fe32af401c8a72d674a") diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py index 5e8aaf8ca7..4bcd29ffb2 100644 --- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py +++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py @@ -16,6 +16,7 @@ class RZlibbioc(RPackage): bioc = "zlibbioc" + version("1.44.0", commit="d39f0b02fa108ab907b4042c00a114569430a333") version("1.42.0", commit="aa074d72515df745ad65133ca21d3cad778ccc0e") version("1.40.0", commit="3f116b39d104c1ea8288f6b8f0ef94bb95f41f69") version("1.36.0", commit="62e888cd7fb482d512c6c31961b657e0b924e357") |