r-ptw: update dependencies

var/spack/repos/builtin/packages/r-a4/package.py

@@ -13,6 +13,9 @@ class RA4(RPackage):
 
     bioc = "a4"
 
+    version("1.54.0", commit="56cb1bc42bc4994e42071af04dcb75ebc0b24437")
+    version("1.52.0", commit="1270e4dd069313355c941c0470cf79352dc55b7f")
+    version("1.50.1", commit="3dba5687e0d029febfadbafcdcca5e54a4341a5b")
     version("1.48.0", commit="89ef9f4afdde5270acecc7c65be3752b71237eba")
     version("1.46.0", commit="1b8f1300025fb0940e7f24cff7ffec9fca02d0e4")
     version("1.44.0", commit="5b0fc5a9971d8f3688ad1f88a4f5ee1498e91633")

var/spack/repos/builtin/packages/r-a4base/package.py

@@ -13,6 +13,9 @@ class RA4base(RPackage):
 
     bioc = "a4Base"
 
+    version("1.54.0", commit="e45169b98e872087736bddbbc213fcd1951ed8ce")
+    version("1.52.0", commit="7312ef9ce99a61742a8c684739ae3e96b4733c02")
+    version("1.50.0", commit="26439bbad1e79464154cc5eb6adbcc69b3a231a0")
     version("1.48.0", commit="26d5793de3163091125feeed1de82e5406777b60")
     version("1.46.0", commit="be70ae723bb6031cdf9540d62dc6113761074e88")
     version("1.44.0", commit="9ae69e03118c7b14df0e6c9e3b25362b09f25bbe")

var/spack/repos/builtin/packages/r-a4classif/package.py

@@ -14,6 +14,9 @@ class RA4classif(RPackage):
 
     bioc = "a4Classif"
 
+    version("1.54.0", commit="9540e623465e1b67f1f2dc1cb566f47b76952a16")
+    version("1.52.0", commit="0366c84be3eddd933ed36acc07bd57b1fea4ae4a")
+    version("1.50.0", commit="1a416537c532a37a46a2719aa591e244cca6e779")
     version("1.48.0", commit="1e2ff90d5af6332beac630395a7494c8fd30aff4")
     version("1.46.0", commit="96794183a76ab7da7a1863ccd421640254447af5")
     version("1.44.0", commit="df0fce781f9bc480a1159d958c9a63c314a9ed01")

var/spack/repos/builtin/packages/r-a4core/package.py

@@ -13,6 +13,9 @@ class RA4core(RPackage):
 
     bioc = "a4Core"
 
+    version("1.54.0", commit="247927f7b6fdec427fac10291eeb4ebe8d5cb279")
+    version("1.52.0", commit="13a748dc52233ee90f6ff8f957ecba0b2b0d94d2")
+    version("1.50.0", commit="efe662190be692270d9bbb2c5e00baf46b23a442")
     version("1.48.0", commit="3dd09f0a662745fcfd3fee7048301f3524e8ac5c")
     version("1.46.0", commit="8999fe146be6d04ae36c725d2b6324a6ce8ceb83")
     version("1.44.0", commit="61a7f3a51a41af615bfd4c22984e4c4a82874e8c")

var/spack/repos/builtin/packages/r-a4preproc/package.py

@@ -13,6 +13,9 @@ class RA4preproc(RPackage):
 
     bioc = "a4Preproc"
 
+    version("1.54.0", commit="8b1a156f988e90f2cc8e4c6a17d4ac6452a46ce3")
+    version("1.52.0", commit="cfc6b6f66815c8d812144266298cab96a3c6c9b2")
+    version("1.50.0", commit="7f02ff9d1b65409c110ca2b695dceba6231c06cf")
     version("1.48.0", commit="d3bf8b82d7cabd2ef77253bb9a741dcde3ca3a41")
     version("1.46.0", commit="8463958692c73fd655a6dfec39ea99c915513719")
     version("1.44.0", commit="252381265b96b83803a93e0c2014dd6b0574e57f")

var/spack/repos/builtin/packages/r-a4reporting/package.py

@@ -13,6 +13,9 @@ class RA4reporting(RPackage):
 
     bioc = "a4Reporting"
 
+    version("1.54.0", commit="87a5a7498541f9fec60983c78d0ade920266e4d9")
+    version("1.52.0", commit="ce1eea6021b3e829ced7dcef8bf42440344ea8cf")
+    version("1.50.0", commit="5facc73ff067e1c1fa0e07d20e4151bcefad9b36")
     version("1.48.0", commit="de8c4b76f6b7ef502d77d55289df0d64fe70447c")
     version("1.46.0", commit="00b82d25bef4d518ae92f615d3a6f7931c0618dc")
     version("1.44.0", commit="bfe83507daf53e2e327474ea3012f0dc920efac1")

var/spack/repos/builtin/packages/r-absseq/package.py

@@ -16,6 +16,9 @@ class RAbsseq(RPackage):
 
     bioc = "ABSSeq"
 
+    version("1.60.0", commit="39efc102aaf3f65155be949ea0e2b4fae112d969")
+    version("1.58.0", commit="05f507feb439ca16983c24de32fcbd784476be40")
+    version("1.56.0", commit="60fbebd28c1be53f1d991b46eed5925a27c30f72")
     version("1.54.0", commit="5e7de8c2a6532073012660f22243c9f7a5568ef6")
     version("1.52.0", commit="07038c047775e17d5d29909927d2143efb63e9cb")
     version("1.50.0", commit="4f384d04ebaae6ea0b56e5cff9a9dcdcb6c8afb0")

var/spack/repos/builtin/packages/r-acde/package.py

@@ -21,6 +21,9 @@ class RAcde(RPackage):
 
     bioc = "acde"
 
+    version("1.36.0", commit="d779819cf0900a11ce15bd6a80ff794c4b6430a1")
+    version("1.34.0", commit="e99a19bb1d0c95a574b37376e3471f7dca12b1a3")
+    version("1.32.0", commit="1f7d0ce5c9c8666a73934bc4c0ec4a3e0db30ec6")
     version("1.30.0", commit="4c16b9fd6c91a433bf1345252e022571c4983cb5")
     version("1.28.0", commit="0edccca7be2475fa2ae3b3c36d0d64924c37b3c0")
     version("1.26.0", commit="dfef9a435062e948efd5eda22942a0d500baa992")

var/spack/repos/builtin/packages/r-acgh/package.py

@@ -15,6 +15,9 @@ class RAcgh(RPackage):
 
     bioc = "aCGH"
 
+    version("1.84.0", commit="e992a615337d0d2b4c4d369fa9b33f5f3a32ed1c")
+    version("1.82.0", commit="617c195db8de204f147370dcf1624df2ea48dff4")
+    version("1.80.0", commit="5ec9dd3644069574dd2ffd81c9ca0ac5d86e3d21")
     version("1.78.0", commit="75df3a4839af66ce177d1bbc3cec4ac03c21dc8e")
     version("1.76.0", commit="c6068522854ed0b1c3feb006619ef25590f70ad6")
     version("1.74.0", commit="e7ba380af0da138788eb6c86f5dbe453269c0810")

var/spack/repos/builtin/packages/r-acme/package.py

@@ -20,6 +20,9 @@ class RAcme(RPackage):
 
     bioc = "ACME"
 
+    version("2.62.0", commit="f631445a51969d2f11ed1698e8ad7fc4cee1fbf6")
+    version("2.60.0", commit="7a1f0e4c6e89d68a3887fba157374892f9dd2c8d")
+    version("2.58.0", commit="1b192d9040fd42346790d900bf02f6b4c7313696")
     version("2.56.0", commit="083af1249e67db11fd471babe67b146eb9c1700c")
     version("2.54.0", commit="8d39d9d6623adf427f5eba308790e1de01213870")
     version("2.52.0", commit="14a97c722d0201654af9e583e7e462b458c28a77")

var/spack/repos/builtin/packages/r-adsplit/package.py

@@ -15,6 +15,9 @@ class RAdsplit(RPackage):
 
     bioc = "adSplit"
 
+    version("1.76.0", commit="3bfef6d1d8a4e11632aeeadf25a00801564d5949")
+    version("1.74.0", commit="3df3361641cc343e106525e33bfcea675ec05e3a")
+    version("1.72.0", commit="194ddb23b683bc8633c9522456acc49c85b369b5")
     version("1.70.0", commit="a08a994215a459b856eae051c778e2b9144f52d9")
     version("1.68.0", commit="705977b5e1cb7dd69793cc673fa215baaba42af5")
     version("1.66.0", commit="64580a6f7a9bc6b16334267c90df48fbb839cc16")

var/spack/repos/builtin/packages/r-affxparser/package.py

@@ -19,6 +19,9 @@ class RAffxparser(RPackage):
 
     bioc = "affxparser"
 
+    version("1.78.0", commit="fab9ee2c921c61e84245601eb19d2b7c5c3acc3e")
+    version("1.76.0", commit="4f86ff876074195c1de2f4b36d74d98409b7055a")
+    version("1.74.0", commit="cada520ac224840d0de93d05c8924ad2006d77c3")
     version("1.72.0", commit="6e976af32f77835143f6b4e0c01c6016dc1b331c")
     version("1.70.0", commit="28f94cd3477e9500942be89cbcb5cad1bbb369fe")
     version("1.68.1", commit="821a01a2df18115a3b7864b3f45418255b7123eb")

var/spack/repos/builtin/packages/r-affy/package.py

@@ -14,6 +14,9 @@ class RAffy(RPackage):
 
     bioc = "affy"
 
+    version("1.84.0", commit="1174adf7e83ee46603189397cd557044802cda01")
+    version("1.82.0", commit="fb130de33532f6d15fe99ba02ff35cce07922308")
+    version("1.80.0", commit="a0d64dfdadfff1a1d7a4c39ba73e843e5e3fc6da")
     version("1.78.0", commit="cc7eac358b6e10ee86a7a93d2e436758f6fbd9b5")
     version("1.76.0", commit="3bb309388d5d6402c356d4a5270ee83c5b88942f")
     version("1.74.0", commit="2266c4a46eda7e5b64f7f3e17e8b61e7b85579ff")
@@ -27,6 +30,7 @@ class RAffy(RPackage):
 
     depends_on("c", type="build")  # generated
 
+    depends_on("r@2.8.0:", type=("build", "run"))
     depends_on("r@2.8.0:4.0", type=("build", "run"), when="@:1.68.0")
     depends_on("r-biocgenerics@0.1.12:", type=("build", "run"))
     depends_on("r-biobase@2.5.5:", type=("build", "run"))

var/spack/repos/builtin/packages/r-affycomp/package.py

@@ -13,6 +13,9 @@ class RAffycomp(RPackage):
 
     bioc = "affycomp"
 
+    version("1.82.0", commit="646461c2af419067de1d95691ca27e2ace50a436")
+    version("1.80.0", commit="2b69f9c6ec9f7c90287e254ba5bb9d658ce5820f")
+    version("1.78.0", commit="65cc8f00be57876705853adf0670b05a4ed6bf12")
     version("1.76.0", commit="8bfc628de26a739c5e0cb47aa22bfda7c8d0a922")
     version("1.74.0", commit="1160d6395f23085456938ba2bd38fb45597fc92f")
     version("1.72.0", commit="c52baea98b80abd4a99380ac9d4b68ef91869d40")

var/spack/repos/builtin/packages/r-affycontam/package.py

@@ -13,6 +13,9 @@ class RAffycontam(RPackage):
 
     bioc = "affyContam"
 
+    version("1.64.0", commit="c7cf836b166f981f9d87bf38cb2d8e2a6ab1bf6b")
+    version("1.62.0", commit="b0ced2ce1dff00e6eab4f0e091cebd6994298588")
+    version("1.60.0", commit="f2e21b7d4d700e135ae3bd0fa3531e001a7aa950")
     version("1.58.0", commit="5e91d79d7653a4f484b62eae7fd7e908de8cb9b6")
     version("1.56.0", commit="e2b8a4fba1648255eadce954a848f2dd8e22bcb3")
     version("1.54.0", commit="c5208b48b8881983ff53a4713244327e8ad13b78")

var/spack/repos/builtin/packages/r-affycoretools/package.py

@@ -14,6 +14,9 @@ class RAffycoretools(RPackage):
 
     bioc = "affycoretools"
 
+    version("1.78.0", commit="2eb1cc5d748832ecd4f8e610397b43c88099ccd4")
+    version("1.76.0", commit="4733a16c9629a62c5dc6fb3fef3a6e6def049a02")
+    version("1.74.0", commit="c04ad6fe6a8809b769bdff4cefb6d47a23e7a891")
     version("1.72.0", commit="229ae09efc1a66e64ea395019c32d16387bf81ac")
     version("1.70.0", commit="f09a788aa83e1e052a7c5f148a451a99fe9c9c96")
     version("1.68.1", commit="69546b1fe5edd71eca130d53d33f0fb0fcf62c97")

var/spack/repos/builtin/packages/r-affydata/package.py

@@ -14,6 +14,9 @@ class RAffydata(RPackage):
 
     bioc = "affydata"
 
+    version("1.54.0", commit="b3765c212d7721c189cd7326c18c4141b5227da0")
+    version("1.52.0", commit="54b35381b1b13161e0d0ef10627efc26ed8dc0c5")
+    version("1.50.0", commit="203e040f737bdeb65d8cd2123dc76036f23e4e3a")
     version("1.48.0", commit="037b86c86c114761ff1bcca64ab4e0bcd68063d3")
     version("1.46.0", commit="870745b886df9f1fbbd6130d266c0ef96f3afa66")
     version("1.44.0", commit="f18304a356cee8cd7297bab362b13c40e50439df")

var/spack/repos/builtin/packages/r-affyexpress/package.py

@@ -14,6 +14,7 @@ class RAffyexpress(RPackage):
 
     bioc = "AffyExpress"
 
+    version("1.58.0", commit="3b0f72dc19d923a87cc462673d933e58760a9cc9")
     version("1.56.0", commit="e07085833de2bbf81537410cad526d39f8a82478")
     version("1.50.0", commit="8b98703b63396df9692afb0e15b594658125cc96")
     version("1.48.0", commit="dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92")

var/spack/repos/builtin/packages/r-affyilm/package.py

@@ -15,6 +15,9 @@ class RAffyilm(RPackage):
 
     bioc = "affyILM"
 
+    version("1.58.0", commit="0ceee74b89a9e2dcd8793371cb37e60a9c9a79da")
+    version("1.56.0", commit="ee6044051fce374b0c7ec858e5d300bba28cfafa")
+    version("1.54.0", commit="4586915a1be400f54e37506ebc1ddffb91480e89")
     version("1.52.0", commit="08ed8c60921ba1b9e04fa90e156eef1a3c899d15")
     version("1.50.0", commit="185cd8e4712a3378ce7a156d4940224bbb2c4122")
     version("1.48.0", commit="4603a4c4d6c2330a8a56a7bb657dc56c51a9393a")

var/spack/repos/builtin/packages/r-affyio/package.py

@@ -14,6 +14,9 @@ class RAffyio(RPackage):
 
     bioc = "affyio"
 
+    version("1.76.0", commit="ed8b074ada05f3b3eeba3032b1214179e3034a42")
+    version("1.74.0", commit="1d0948e7a76a00da985b9fdd38d36fa0ca85c2af")
+    version("1.72.0", commit="2f97a7e3710e44886b0b732d1c0dbb3165e9b84c")
     version("1.70.0", commit="95560567e27088863c64e868a8e5069fc725b8d7")
     version("1.68.0", commit="33080c5eeb14c0ca40f0d231706af4e0c2c1ef8b")
     version("1.66.0", commit="3a0b90704fc46cddd99a72b985a6bdb348f69b50")
@@ -28,5 +31,6 @@ class RAffyio(RPackage):
     depends_on("c", type="build")  # generated
 
     depends_on("r@2.6.0:", type=("build", "run"))
-    depends_on("r-zlibbioc", type=("build", "run"))
     depends_on("zlib-api")
+
+    depends_on("r-zlibbioc", type=("build", "run"), when="@:1.77.0")

var/spack/repos/builtin/packages/r-affypdnn/package.py

@@ -13,6 +13,8 @@ class RAffypdnn(RPackage):
 
     bioc = "affypdnn"
 
+    version("1.62.0", commit="22a6e97303bd60c8b365b51c38e4312d5b7ee995")
+    version("1.60.0", commit="9f8998fa4405fbbaea6f7a7eb6d3c1b29c3f5e09")
     version("1.58.0", commit="83d8b6b0d9606845bd77dbf7164dd5b160f32ccf")
     version("1.56.0", commit="5fd9c5265fb895a1f646cf72e8d5169669d979f2")
     version("1.54.0", commit="ea971b1b9cc443695a6614bef92e8e116ee87d55")

var/spack/repos/builtin/packages/r-affyplm/package.py

@@ -16,6 +16,9 @@ class RAffyplm(RPackage):
 
     bioc = "affyPLM"
 
+    version("1.82.0", commit="16d738761d115c14f72a083266e501edb72ce548")
+    version("1.80.0", commit="b0584edcaba058d5cfb06d64e22a4859c7d15b60")
+    version("1.78.0", commit="1fa54e253098269e93b3e8f88bc592041b855334")
     version("1.76.0", commit="45557df5a32f56aa5240439737c5718738fb4c27")
     version("1.74.0", commit="5f76ef92e69deabc19c5395eaec4adb85c66b63d")
     version("1.72.0", commit="394c0a8e213f188d0b1d01e20516df8bf1bc5c09")

var/spack/repos/builtin/packages/r-affyqcreport/package.py

@@ -14,6 +14,7 @@ class RAffyqcreport(RPackage):
 
     bioc = "affyQCReport"
 
+    version("1.70.0", commit="9e49c8c376d8b1d79981628920e5adc238bddeca")
     version("1.68.0", commit="34b42a16f87a90a595146f4a1802ed04f6bfccca")
     version("1.62.0", commit="92d4124b688b90a6a9b8a21ab9d13d92b368cee4")
     version("1.60.0", commit="d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa")

var/spack/repos/builtin/packages/r-affyrnadegradation/package.py

@@ -17,6 +17,9 @@ class RAffyrnadegradation(RPackage):
 
     bioc = "AffyRNADegradation"
 
+    version("1.52.0", commit="14b087a0fbe2796398ceaebe6232553bce90a2f1")
+    version("1.50.0", commit="2be3cbcdb710b069e82610c123c73a4cc4651a30")
+    version("1.48.0", commit="dfc274be6d53250bc516c9772022c771706c7545")
     version("1.46.0", commit="431ae61c9b3809829697ef71672c57171d93311e")
     version("1.44.0", commit="63881f41fc67cc7322b189446dcffb4e1060e303")
     version("1.42.0", commit="5775f41f538b3c8ee4d07d38cec1b49c548cebe6")

var/spack/repos/builtin/packages/r-agdex/package.py

@@ -13,6 +13,9 @@ class RAgdex(RPackage):
 
     bioc = "AGDEX"
 
+    version("1.54.0", commit="0dc73a6f55bf53ddea0689df48dc72d4983faf87")
+    version("1.52.0", commit="69fe01a6ce7045afe612daea363365b6deaeaed7")
+    version("1.50.0", commit="5b2ecdae7bbafee5c48de5b7181a55bda95143ba")
     version("1.48.0", commit="917920b397493b0ea40093044ebe36fff7c389ad")
     version("1.46.0", commit="d7c38e8bdcaa7b0261117c605e7f61e2b07e8316")
     version("1.44.0", commit="9d3eb90eaf7bf093c7fa73facb3df89506a85185")

var/spack/repos/builtin/packages/r-agilp/package.py

@@ -12,6 +12,9 @@ class RAgilp(RPackage):
 
     bioc = "agilp"
 
+    version("3.38.0", commit="5ed3359c61678afed7709bd3795702b9e94f46f3")
+    version("3.36.0", commit="204ae1003390b0b4efa5aa7d43f96c256e59fc9e")
+    version("3.34.0", commit="12c94ca5c5c1b6bc909571c1bee897a6268d9e39")
     version("3.32.0", commit="8291f7b7c1b6167952568f51593116afc6d0fc27")
     version("3.30.0", commit="a2c898dc901ccdda4b8582caff079ab20b1bfc28")
     version("3.28.0", commit="2c6dfccc76473b5bef13b75fa59adf46b3381f55")

var/spack/repos/builtin/packages/r-agimicrorna/package.py

@@ -13,6 +13,9 @@ class RAgimicrorna(RPackage):
 
     bioc = "AgiMicroRna"
 
+    version("2.56.0", commit="5e277127c2557b8cff752d3fca9f3a41b373d497")
+    version("2.54.0", commit="2c8850f9b62308a3932d74548689b24741347bab")
+    version("2.52.0", commit="73e65fb29170d1bee3b849f82a25ae7da3c6cd3b")
     version("2.50.0", commit="a812b0f4f215b093ca685889b65de60c6701b695")
     version("2.48.0", commit="4c163b1b730150a3a60a3815bd8c08fa04d71fc1")
     version("2.46.0", commit="8c6d73e1c3f1f9cc019bdb219b19e6179bb1efe4")

var/spack/repos/builtin/packages/r-aims/package.py

@@ -16,6 +16,9 @@ class RAims(RPackage):
 
     bioc = "AIMS"
 
+    version("1.38.0", commit="b7d238e6573f1921a4f255f9c7cd673a31482c1c")
+    version("1.36.0", commit="8c8f6120501a37595034c1c1759ccfb751e995e1")
+    version("1.34.0", commit="61910444b05ce6e438467177202a93046c700e32")
     version("1.32.0", commit="019415a6362e805465d43c157606e1774aed9e51")
     version("1.30.0", commit="2ab61159c5aa0902cc33fc1502f7853b66912cce")
     version("1.28.0", commit="84608df638b5694c08158ed77ad2c8a64c4e594b")

var/spack/repos/builtin/packages/r-aldex2/package.py

@@ -24,6 +24,9 @@ class RAldex2(RPackage):
 
     license("GPL-3.0-only")
 
+    version("1.38.0", commit="701515c185aa747e53c863afbb3730a9a331e242")
+    version("1.36.0", commit="c7a4c4bfc66baba750ef58163193f6b53830cf9b")
+    version("1.34.0", commit="eda12f9208ed90e9e2c2d6a47415a5c73c107e4b")
     version("1.32.0", commit="ba32b9a9b6a8f42906ea094318f00116f15e42eb")
     version("1.30.0", commit="cb6670515a8722f9cfedac12a8c2747a5298ee46")
     version("1.28.1", commit="f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6")

var/spack/repos/builtin/packages/r-allelicimbalance/package.py

@@ -13,6 +13,9 @@ class RAllelicimbalance(RPackage):
 
     bioc = "AllelicImbalance"
 
+    version("1.44.0", commit="c46bcc17963050a7fd01a23615de796fd3e8bd4b")
+    version("1.42.0", commit="4dc686c08a02d051ba1d8e82c909c2c751dc5613")
+    version("1.40.0", commit="e3fc91108af4816a237b588b23cc40133f6eee30")
     version("1.38.0", commit="75a3b0fefe635a0892eae338d0fdd4a9e091f957")
     version("1.36.0", commit="cb4910c1fd58cc4272c21251a8f120990e1aa431")
     version("1.34.0", commit="290708ccc4ceae1fbb9e9257cb254916449d389b")

var/spack/repos/builtin/packages/r-alsace/package.py

@@ -18,6 +18,7 @@ class RAlsace(RPackage):
     bioc = "alsace"
 
     version("1.30.0", commit="d0e09b283da2b4869d5d6e6801399676246bc5bc")
+    version("1.28.0", commit="03344a1f12a5c86e61a8d69b68d9d16c3ed07561")
     version("1.26.0", commit="40a76404acb1466723a78a55d87c67eec3e6f306")
     version("1.20.0", commit="47f1cf8daafc864e5e3418009f349ce85d6b0389")
     version("1.18.0", commit="c9fc43c7b441de43b14ef1be69926c4c4a566191")

var/spack/repos/builtin/packages/r-altcdfenvs/package.py

@@ -12,6 +12,9 @@ class RAltcdfenvs(RPackage):
 
     bioc = "altcdfenvs"
 
+    version("2.68.0", commit="53038c86c7c743272e00a71b5fcb4252b068cf13")
+    version("2.66.0", commit="34a3f5bc0b36543e20de6dd2035db3776677e8e2")
+    version("2.64.0", commit="86cec42b52c7b2450ae6dbc7b0ab73a98c32fc3b")
     version("2.62.0", commit="aedf0e9f98639d60b327e50957e504cf24b64bbb")
     version("2.60.0", commit="0bc0b4493b8e9fe2eb47fb8e9377123ce8f472bb")
     version("2.58.0", commit="08255a777ffa1e1414d3dd3062d95bfdd3dfd47c")

var/spack/repos/builtin/packages/r-analysispageserver/package.py

@@ -14,6 +14,8 @@ class RAnalysispageserver(RPackage):
 
     bioc = "AnalysisPageServer"
 
+    version("1.22.0", commit="2a18bb215ccaef5da08ea4d0e37cfb591b9dc783")
+    version("1.20.0", commit="aafd0364f9f5d9778a36bda9f2c399360af4d8ad")
     version("1.18.1", commit="08bd85e872d3f2b0c1fa148cf30bcd2d1a29b630")
     version("1.16.0", commit="67b063523f80e2af1d26262367ff50f34e195174")
     version("1.14.0", commit="620c0ea1e129ddd1a0866e2c9d7c3fcf06a8baf4")

var/spack/repos/builtin/packages/r-anaquin/package.py

@@ -16,6 +16,9 @@ class RAnaquin(RPackage):
 
     bioc = "Anaquin"
 
+    version("2.30.0", commit="281f04476cf037429251e74e461e0d8827975560")
+    version("2.28.0", commit="b547d11c1108c18f8e28a805cdf5ffa43c27783d")
+    version("2.26.0", commit="ca9494432f5e2acbd32a74fff6ad271c05f9e4d9")
     version("2.24.0", commit="0eefabdc4036b98505032c460d08375839b1fc3e")
     version("2.22.0", commit="d848a9bd7bf9d1d62202cc477300bf1a65b3e36c")
     version("2.20.0", commit="61598dd3430b09b57f31d7d550ea95126a2d73c8")

var/spack/repos/builtin/packages/r-aneufinder/package.py

@@ -14,6 +14,9 @@ class RAneufinder(RPackage):
 
     bioc = "AneuFinder"
 
+    version("1.34.0", commit="b69e323eefb2a3485fcd46491b2229042eb57335")
+    version("1.32.0", commit="c7a1f1812e203a0e52db7f8228cf361abc954486")
+    version("1.30.0", commit="f0c9ccfd4bb3761460efdf8fcd5c4d0faf8467ff")
     version("1.28.0", commit="e17d810171bdab1c6a26a3ab7b7931db4e073e7e")
     version("1.26.0", commit="7cd59a1e24c6512f2e4fcbe2c53a0d3cd2d06217")
     version("1.24.0", commit="4c6906eee514eba3e8ac159654a6953e37a99bba")

var/spack/repos/builtin/packages/r-aneufinderdata/package.py

@@ -13,6 +13,9 @@ class RAneufinderdata(RPackage):
 
     bioc = "AneuFinderData"
 
+    version("1.34.0", commit="4c07ed4ce577a25fc8f1e20da0962a2f3f978620")
+    version("1.32.0", commit="79c9b4efa2db70e46af1b52d3dc7fb992beef35d")
+    version("1.30.0", commit="573710c04570ea62746a161cb8083c6690be95d6")
     version("1.28.0", commit="d04255e60173ce478d31b1e1e5c73e6ed9e3b20c")
     version("1.26.0", commit="4b810599b62a3fb39239bfd98ed960c93989e86b")
     version("1.24.0", commit="cf6f3852702aab28e3170fc56b695d00b7389666")

var/spack/repos/builtin/packages/r-annaffy/package.py

@@ -17,6 +17,9 @@ class RAnnaffy(RPackage):
 
     license("LGPL-2.1-or-later")
 
+    version("1.78.0", commit="095b5607fc77e49ba5dbad76ff3857f3a1ad9e5b")
+    version("1.76.0", commit="9a349617a9ebce7ebc81d64fd733497bf27b968f")
+    version("1.74.0", commit="15d4c6a754cb51daaca554255fc41f39dc303006")
     version("1.72.0", commit="7cb439706a7e93fb5b44ead374010077a44ea78b")
     version("1.70.0", commit="c99e81259adb39b5d8e954fd7afe7f93675229bc")
     version("1.68.0", commit="fa930c0bbdca9828a130ab06d86c65d451380830")

var/spack/repos/builtin/packages/r-annotate/package.py

@@ -12,6 +12,9 @@ class RAnnotate(RPackage):
 
     bioc = "annotate"
 
+    version("1.84.0", commit="6188ffbe46daf9b0fbf49de8ac81068df775c136")
+    version("1.82.0", commit="9710d81c5d0316382c076fbfa0648c4945f72d6c")
+    version("1.80.0", commit="45a42c3691e7707f96286c7c3234332a8ea39870")
     version("1.78.0", commit="ca6415a463ec682f340ba5d1dc6246a92e836143")
     version("1.76.0", commit="0181d5c41d594e36be06adb6a02302db0ad2c507")
     version("1.74.0", commit="200c71743417792880f8171d59b2ac0ddd3902a8")

var/spack/repos/builtin/packages/r-annotationdbi/package.py

@@ -13,6 +13,9 @@ class RAnnotationdbi(RPackage):
 
     bioc = "AnnotationDbi"
 
+    version("1.68.0", commit="6a2aa3361bb114fbfe7a25b51bcaed36450a57e0")
+    version("1.66.0", commit="989c1dcf56db17646e79bd7caa70484e4cda73d1")
+    version("1.64.1", commit="e5b997eac9f538d6ad5418fbe90716848d8c5f2e")
     version("1.62.0", commit="7ca03a0332d0a284ea27d16edb7b386c86cf99ea")
     version("1.60.0", commit="cd61bd1b1538e2f1f411fd7087820749ecf39da8")
     version("1.58.0", commit="05fcf7a28a6b15b195da23474d7ba89bd0cfd891")

var/spack/repos/builtin/packages/r-annotationfilter/package.py

@@ -14,6 +14,9 @@ class RAnnotationfilter(RPackage):
 
     bioc = "AnnotationFilter"
 
+    version("1.30.0", commit="1204cb5c19fde6628e99279ffca8e1b0b2a1219b")
+    version("1.28.0", commit="61709ad226a834e6c80b02199c170d7784f23196")
+    version("1.26.0", commit="be933b32635c36571f43c1aa6ec3b1efab0dd1da")
     version("1.24.0", commit="172d9c149d9025154f7b26982d07f571499b03e8")
     version("1.22.0", commit="c9fea4a829ce9419b6e0af987915b2d469358597")
     version("1.20.0", commit="2818aff6502fd6fe819521cd8d97695ef6f9198e")

var/spack/repos/builtin/packages/r-annotationforge/package.py

@@ -13,6 +13,9 @@ class RAnnotationforge(RPackage):
 
     bioc = "AnnotationForge"
 
+    version("1.48.0", commit="a22ccaf712a0737cf10fd5981a1a48f9c4e1395d")
+    version("1.46.0", commit="50d67131ed398f517b87263a6d5adfc189835ee5")
+    version("1.44.0", commit="1a9bb5fb6d66be5002b00b5abf5023ce81755b33")
     version("1.42.0", commit="2eac005012b11317c33c8b0062b968b2ac378308")
     version("1.40.0", commit="f77d3a942eb6b18c18888b7af3f0e652596cf19f")
     version("1.38.1", commit="2dcedf353bc57bf80818e6adb1f7129c21886f6b")

var/spack/repos/builtin/packages/r-annotationhub/package.py

@@ -19,6 +19,9 @@ class RAnnotationhub(RPackage):
 
     bioc = "AnnotationHub"
 
+    version("3.14.0", commit="f93a396134b69cb408946569c721dbe7ea7e1978")
+    version("3.12.0", commit="7c17d78eb590e7e3b6abeb678d8a4a38657a9765")
+    version("3.10.1", commit="290bd8e0792ec6f8f90d600eecbfae2c93fea227")
     version("3.8.0", commit="975022dd33706824bd02f67cc9c3a42f3567f4a5")
     version("3.6.0", commit="3315a73b7803a92412ed18209dd37b378195b86f")
     version("3.4.0", commit="e74e54ca44f50c2c15c60f8620e3d1721f8f5b6d")

var/spack/repos/builtin/packages/r-aroma-light/package.py

@@ -15,6 +15,9 @@ class RAromaLight(RPackage):
 
     bioc = "aroma.light"
 
+    version("3.36.0", commit="d421a4eb2af87b0b58c10aad160385d8fc034a43")
+    version("3.34.0", commit="8ae145cc50f51ae6b0321f085169cbd276987e63")
+    version("3.32.0", commit="21984e1f4fbeb51744bb462844748041c1a3b7e6")
     version("3.30.0", commit="a1882c2126622cb389a7ef1ef5b5c565e603a282")
     version("3.28.0", commit="7749dd7033e9885ec2546a5cac0562bac2fea04d")
     version("3.26.0", commit="7ead7517a77bc8b4b4b42aace69957a17e8fe016")

var/spack/repos/builtin/packages/r-assorthead/package.py

@@ -0,0 +1,14 @@
+# Copyright 2013-2024 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 RAssorthead(RPackage):
+    """Assorted header-only C++ libraries for Bioconductor."""
+
+    bioc = "assorthead"
+
+    version("1.0.1", commit="4aa44624adb6981c75db9f5e200114784f343e32")

var/spack/repos/builtin/packages/r-bamsignals/package.py

@@ -15,6 +15,9 @@ class RBamsignals(RPackage):
 
     bioc = "bamsignals"
 
+    version("1.38.0", commit="579649b2878b7d70ad42926273863d21ef4b8ee4")
+    version("1.36.0", commit="5b8df63f3f42a02c6df75030d590a55919ff82c0")
+    version("1.34.0", commit="58fa17f3b093788c8799c23718fba8b0f0126476")
     version("1.32.0", commit="34bfc4e8b58e47c3b94347fd2976aeae07fc28c2")
     version("1.30.0", commit="aac37dffd6f6876b4626866e3d40bb7af75620fe")
     version("1.28.0", commit="27b70be6f73747d9d32054da043f4a37ea55b917")

var/spack/repos/builtin/packages/r-basilisk-utils/package.py

@@ -20,6 +20,9 @@ class RBasiliskUtils(RPackage):
 
     license("GPL-3.0-only")
 
+    version("1.18.0", commit="9a5711487c31502fca734fca35360bc8372462ac")
+    version("1.16.0", commit="04f649cb529456dbce44cc8896471ea7ad24b01f")
+    version("1.14.1", commit="62f0819320510ad291642ea7d19af39a61c95d82")
     version("1.12.0", commit="8314f9a72ecc0f20b180431aec93647320de8c2c")
 
     depends_on("r-dir-expiry", type=("build", "run"))

var/spack/repos/builtin/packages/r-basilisk/package.py

@@ -18,8 +18,12 @@ class RBasilisk(RPackage):
 
     license("GPL-3.0-or-later")
 
+    version("1.18.0", commit="31887d4d482a1d604fbcad15020fc30d441a66b4")
+    version("1.16.0", commit="0a27ae63be9d7fa486f55992332f84b4259c97af")
+    version("1.14.3", commit="6412875836db012cd9c490539a82b9887afd6389")
     version("1.12.0", commit="26c1c354526eb8d806268427a7c40b31bb89f489")
 
     depends_on("r-reticulate", type=("build", "run"))
     depends_on("r-dir-expiry", type=("build", "run"))
     depends_on("r-basilisk-utils", type=("build", "run"))
+    depends_on("r-basilisk-utils@1.15.1:", type=("build", "run"), when="@1.15.1:")

var/spack/repos/builtin/packages/r-beachmat/package.py

@@ -16,6 +16,9 @@ class RBeachmat(RPackage):
 
     bioc = "beachmat"
 
+    version("2.22.0", commit="a1438568f8f83d73a4f5f3ec5b6cd7d4b6955e74")
+    version("2.20.0", commit="fe0b11965d2192ae5ffab503e69f31ae0bc450b0")
+    version("2.18.1", commit="39ef12f2aa1bbc2d057aa90c1964e67e8c5c5715")
     version("2.16.0", commit="4cc8e50dcae767a2ef84ffc7a581ea182f05f300")
     version("2.14.0", commit="5a4b85f4a22f3447f12d03157ab95de73f6137c6")
     version("2.12.0", commit="3e6af145bdcdf0a0b722d8256ba1a38b8a36b2f5")
@@ -34,10 +37,13 @@ class RBeachmat(RPackage):
     depends_on("r-delayedarray@0.5.30:", type=("build", "run"), when="@1.2.1")
     depends_on("r-delayedarray@0.7.38:", type=("build", "run"), when="@1.4.0")
     depends_on("r-delayedarray@0.15.14:", type=("build", "run"), when="@2.6.4")
+    depends_on("r-delayedarray@0.27.2:", type=("build", "run"), when="@2.17.1:")
+    depends_on("r-sparsearray", type=("build", "run"), when="@2.17.8:")
     depends_on("r-biocgenerics", type=("build", "run"), when="@1.4.0:")
     depends_on("r-matrix", type=("build", "run"), when="@2.6.4:")
     depends_on("r-rcpp@0.12.14:", type=("build", "run"), when="@1.0.2:")
     depends_on("r-rcpp", type=("build", "run"), when="@2.10.0:")
+    depends_on("r-assorthead", type=("build", "run"), when="@2.21.6:")
 
     depends_on("r-rhdf5lib", type=("build", "run"), when="@1.0.2:1.4.0")
     depends_on("r-rhdf5lib@1.1.4:", type=("build", "run"), when="@1.2.1")

var/spack/repos/builtin/packages/r-biobase/package.py

@@ -13,6 +13,9 @@ class RBiobase(RPackage):
 
     bioc = "Biobase"
 
+    version("2.66.0", commit="2cd604ff9935fa312b4cd3ffce6033e398714ed5")
+    version("2.64.0", commit="a3b75b7e1cb89e621af1d91b02fe527e7bb223f3")
+    version("2.62.0", commit="8201fbbe5eba57315ff8202507fa025def83879e")
     version("2.60.0", commit="8dc10d2d26dc0847740ff2b4f16cc1ae2e936464")
     version("2.58.0", commit="767f2f33f158f233616178e12ce08cdb03d2a5a2")
     version("2.56.0", commit="3b2dd91b333677c2f27257c7624014a55e73c52b")

var/spack/repos/builtin/packages/r-biocfilecache/package.py

@@ -15,6 +15,9 @@ class RBiocfilecache(RPackage):
 
     bioc = "BiocFileCache"
 
+    version("2.14.0", commit="66862c5799d375340e335b3b0dfced400d4654b4")
+    version("2.12.0", commit="a655653e56119435b76830d78c2a7a80501ed083")
+    version("2.10.2", commit="c95edcc03bdf09e28d86af2284a6580264595de7")
     version("2.8.0", commit="d088b3224bcee4661d954c77fe38ba8c45ecc51a")
     version("2.6.0", commit="f5b8368c1402b15e8db8eab59217f1176e902e6f")
     version("2.4.0", commit="2c00eee40d95fddad223f115f959b09e1a14f75d")

var/spack/repos/builtin/packages/r-biocgenerics/package.py

@@ -12,6 +12,9 @@ class RBiocgenerics(RPackage):
 
     bioc = "BiocGenerics"
 
+    version("0.52.0", commit="14221156721c9e73f746314cf50f775d15882f31")
+    version("0.50.0", commit="d23d8dde2e8cfe377b55a036eb397aa5e6275880")
+    version("0.48.1", commit="5fd6dfe93786292484dc53023ec681391f4559e0")
     version("0.46.0", commit="a90f0c5976a24417e47e009ba602fc98515ac9ab")
     version("0.44.0", commit="d7cd9c19958bd8d4573d980494188fa15ab16e45")
     version("0.42.0", commit="3582d47b836387afc08157f3d6a5013fd64334ed")
@@ -26,3 +29,5 @@ class RBiocgenerics(RPackage):
 
     depends_on("r@3.6.0:", type=("build", "run"), when="@0.30.0:")
     depends_on("r@4.0.0:", type=("build", "run"), when="@0.36.0:")
+
+    depends_on("r-generics", type=("build", "run"), when="@0.53.1:")

var/spack/repos/builtin/packages/r-biocio/package.py

@@ -21,6 +21,9 @@ class RBiocio(RPackage):
 
     bioc = "BiocIO"
 
+    version("1.16.0", commit="8e80624cf870839295bedc34ca68d1625b43c9d4")
+    version("1.14.0", commit="ecae62ea60c474556d1080387630f81f72116501")
+    version("1.12.0", commit="893a6ebe50e781dbb1077ad7b4fefa660be542f1")
     version("1.10.0", commit="1368ff1a7ddbb62515a87a88d7ec39981de557d5")
     version("1.8.0", commit="4a719fa41e014b7b948f7b245e581ede6a04eda1")
     version("1.6.0", commit="60c8aa1a961e43bf0ee5d563a6d9fcec84f7f8f8")

var/spack/repos/builtin/packages/r-biocneighbors/package.py

@@ -20,6 +20,9 @@ class RBiocneighbors(RPackage):
 
     bioc = "BiocNeighbors"
 
+    version("2.0.1", commit="4b02c76afa357e429f7a61c8c10d9e0f8c0fdf4b")
+    version("1.22.0", commit="c9f4480ff8ca96d60f3191c3c9cbc500ba7f5762")
+    version("1.20.2", commit="f792beec27e6fa75064b6a39a541f5d15dada54d")
     version("1.18.0", commit="4b19ef2a76baa0b001c426bad540ab9295bec78e")
     version("1.16.0", commit="3b227beead424314aab5ef847222f8f4243c684f")
     version("1.14.0", commit="670a1bd4d82636d28fbff50cea2157e16bb1a858")
@@ -32,10 +35,11 @@ class RBiocneighbors(RPackage):
 
     depends_on("r@3.5:", type=("build", "run"), when="@1.0.0")
     depends_on("r-rcpp", type=("build", "run"))
-    depends_on("r-s4vectors", type=("build", "run"))
-    depends_on("r-biocparallel", type=("build", "run"))
-    depends_on("r-matrix", type=("build", "run"), when="@1.8.2:")
-    depends_on("r-rcpphnsw", type=("build", "run"), when="@1.2.0:")
+    depends_on("r-assorthead", type=("build", "run"), when="@1.99.0:")
 
+    depends_on("r-s4vectors", type=("build", "run"), when="@:1.21")
+    depends_on("r-biocparallel", type=("build", "run"), when="@:1.21")
+    depends_on("r-matrix", type=("build", "run"), when="@1.8.2:1.21")
+    depends_on("r-rcpphnsw", type=("build", "run"), when="@1.2.0:1.21")
     depends_on("r-rcppannoy", type=("build", "run"), when="@:1.2.0")
     depends_on("r-biocgenerics", type=("build", "run"), when="@1.2.0")

var/spack/repos/builtin/packages/r-biocparallel/package.py

@@ -14,6 +14,9 @@ class RBiocparallel(RPackage):
 
     bioc = "BiocParallel"
 
+    version("1.40.0", commit="a57b78842ae2847cb83710da0564e1a71001687e")
+    version("1.38.0", commit="d180bc0969a0f719e01ba127af45173c5bd8e27f")
+    version("1.36.0", commit="ba4ec2934579d5d1a1e2d0e69d44342221e49013")
     version("1.34.0", commit="f3bbc0a2d38da034c50ca1e4704fc4ee99a2dc9e")
     version("1.32.1", commit="6c85dbad596a74a6d3022173a4a11c6b81a4a2c2")
     version("1.30.4", commit="1229ebe9f6d8305f9f61e562464f83f9ba86e699")

var/spack/repos/builtin/packages/r-biocsingular/package.py

@@ -16,6 +16,9 @@ class RBiocsingular(RPackage):
 
     bioc = "BiocSingular"
 
+    version("1.22.0", commit="aa0f642bd9e85704f8cc023585a73cc403f54a15")
+    version("1.20.0", commit="c5dafa54d65a84dab6275e06355b6921ccd07aac")
+    version("1.18.0", commit="53deff4eb0126e7e6db0c5f0a2385fd4d946af3e")
     version("1.16.0", commit="0db9a691d4eb21551c532d8bde8f64dcc19b6c66")
     version("1.14.0", commit="6dc42b30110e498f6694f18037f991c1006c71b7")
     version("1.12.0", commit="7d1b8f4954e9e6f2c30a5111cdab9aabc8bcc3a6")

var/spack/repos/builtin/packages/r-biocstyle/package.py

@@ -13,6 +13,9 @@ class RBiocstyle(RPackage):
 
     bioc = "BiocStyle"
 
+    version("2.34.0", commit="0a042423c1f4e8bc6dece3c31fcc5e9750a2f9ab")
+    version("2.32.1", commit="bd5e8295d5a1891189553c1f5b0177ea90001366")
+    version("2.30.0", commit="48deba5c4d84ea9d236256a673a58ab3f1d6c2cf")
     version("2.28.0", commit="b358aa5d3f9c68629e9abf50ffceccbf77226ea8")
     version("2.26.0", commit="add035498bdce76d71a0afa22a063c2d8e5588bc")
     version("2.24.0", commit="53095b534b7e6c80a33a67b5f2db0db8f00db902")

var/spack/repos/builtin/packages/r-biocversion/package.py

@@ -13,7 +13,8 @@ class RBiocversion(RPackage):
 
     bioc = "BiocVersion"
 
-    version("3.17.1", commit="a2d0c4c489be1cafdb51bf8d205161429b09ac7f")
+    version("3.20.0", commit="43c716aa5d110bc2ac42053033edde0fce3fe9cf")
+    version("3.18.1", commit="70680b8e1f121361244f4755e5c3ec384b5a6a3a")
     version("3.16.0", commit="c681e06fe30ea6815f958c1a3c74c090863680ba")
     version("3.15.2", commit="818ab03b6a3551993b712e3702126040f9fb7600")
     version("3.14.0", commit="aa56d93d0ea5dcdbf301f120502981740fd91e1e")
@@ -23,3 +24,4 @@ class RBiocversion(RPackage):
     depends_on("r@4.1.0:", type=("build", "run"), when="@3.14.0:")
     depends_on("r@4.2.0:", type=("build", "run"), when="@3.15.2:")
     depends_on("r@4.3.0:", type=("build", "run"), when="@3.17.1:")
+    depends_on("r@4.4.0:", type=("build", "run"), when="@3.19.1:")

var/spack/repos/builtin/packages/r-biomart/package.py

@@ -23,6 +23,9 @@ class RBiomart(RPackage):
 
     bioc = "biomaRt"
 
+    version("2.62.0", commit="7a1547e90abea7b5a07016cb2cf80175b0964f4f")
+    version("2.60.1", commit="af135382ba352b3ffc94590f9995fa5b1d1319fc")
+    version("2.58.2", commit="d8a58e6a19a0da0de3f34f8558147c8d1f1ef718")
     version("2.56.0", commit="91ca89eff52e63c225f7e4eb24b765d08faf3ed9")
     version("2.54.0", commit="4fb88fb56c684d5678f8288ba05db193e4881758")
     version("2.52.0", commit="cf4932ac02686da45ea36ff5137fa63cead8860b")
@@ -34,16 +37,18 @@ class RBiomart(RPackage):
     version("2.34.2", commit="a7030915fbc6120cc6812aefdedba423a207459b")
     version("2.32.1", commit="f84d74424fa599f6d08f8db4612ca09914a9087f")
 
-    depends_on("r-xml", type=("build", "run"))
-    depends_on("r-xml@3.99-0.7:", type=("build", "run"), when="@2.52.0:")
     depends_on("r-annotationdbi", type=("build", "run"))
     depends_on("r-progress", type=("build", "run"), when="@2.34.2:")
     depends_on("r-stringr", type=("build", "run"), when="@2.34.2:")
-    depends_on("r-httr", type=("build", "run"), when="@2.34.2:")
+    depends_on("r-httr2", type=("build", "run"), when="@2.57.2:")
     depends_on("r-digest", type=("build", "run"), when="@2.50.3:")
     depends_on("r-biocfilecache", type=("build", "run"), when="@2.46.2:")
     depends_on("r-rappdirs", type=("build", "run"), when="@2.46.2:")
     depends_on("r-xml2", type=("build", "run"), when="@2.46.2:")
+    depends_on("r-curl", type=("build", "run"), when="@2.61.1:")
 
+    depends_on("r-httr", type=("build", "run"), when="@2.34.2:2.57.2")
+    depends_on("r-xml", type=("build", "run"), when="@:2.59.2")
+    depends_on("r-xml@3.99-0.7:", type=("build", "run"), when="@2.52.0:2.59.2")
     depends_on("r-rcurl", type=("build", "run"), when="@:2.40.5")
     depends_on("r-openssl", type=("build", "run"), when="@2.46.2")

var/spack/repos/builtin/packages/r-biomformat/package.py

@@ -20,6 +20,9 @@ class RBiomformat(RPackage):
 
     bioc = "biomformat"
 
+    version("1.34.0", commit="dd89a5361701dc7ec714e4a5b5ac59e4fc5fdeba")
+    version("1.32.0", commit="9df803bb9eead6cf808504f1f713a8d9a851293e")
+    version("1.30.0", commit="40f51ec90f9707f104b292a3c4ece945078668c7")
     version("1.28.0", commit="9240e78dc378abcf6c62ef8dbf2e60f7241232a3")
     version("1.26.0", commit="f851ba2428b57769f6fbb287874bad0dc84dd69c")
     version("1.24.0", commit="4e14692dbcc34c3bd51defd74c728df5de9d0829")

var/spack/repos/builtin/packages/r-biostrings/package.py

@@ -14,6 +14,9 @@ class RBiostrings(RPackage):
 
     bioc = "Biostrings"
 
+    version("2.74.1", commit="b5de57473dd588dbf1e782c98629f8d94ea61b17")
+    version("2.72.1", commit="959b3ba3cc8a36a2119d0b3f15457a8953bfaad8")
+    version("2.70.3", commit="c213e3561e1ad6b390329d32a543b7e9cd324181")
     version("2.68.0", commit="f28b7838fb8321a9956506b3d2f4af2740bca124")
     version("2.66.0", commit="3470ca7da798971e2c3a595d8dc8d0d86f14dc53")
     version("2.64.1", commit="ffe263e958463bd1edb5d5d9316cfd89905be53c")

var/spack/repos/builtin/packages/r-biovizbase/package.py

@@ -15,6 +15,9 @@ class RBiovizbase(RPackage):
 
     bioc = "biovizBase"
 
+    version("1.54.0", commit="6735c2df59f61927c6327b5efe2629f6110e90d7")
+    version("1.52.0", commit="1cfd8c1ae14a7e3a0f71a4f2f825a259daffc3df")
+    version("1.50.0", commit="c961633be8a0c8319b9bf9c76f0f1f9428edaa75")
     version("1.48.0", commit="534db77074710dae57ade81844c769fd35a2fa9c")
     version("1.46.0", commit="a47060cfb68e3f3b4876114af932823aed5d2d57")
     version("1.44.0", commit="a8f05c56c27b278524033cb896a6c97f3ee0081c")

var/spack/repos/builtin/packages/r-bluster/package.py

@@ -15,6 +15,9 @@ class RBluster(RPackage):
 
     bioc = "bluster"
 
+    version("1.16.0", commit="32aa5ea9e7595959119e555e26034a4e95338b32")
+    version("1.14.0", commit="5b73704f633882a8f4e26ccd8b516c719361d9f2")
+    version("1.12.0", commit="efc4220a8062cab433a89d3d742880128cdcaad2")
     version("1.10.0", commit="32340420e67a184e39238e46143c00151057924c")
     version("1.8.0", commit="156115c8960c0b66b2c588d9fd8bbdfe56e5f0be")
     version("1.6.0", commit="ff86c7d8d36233e838d4f00e6a4e173e7bf16816")
@@ -28,3 +31,4 @@ class RBluster(RPackage):
     depends_on("r-s4vectors", type=("build", "run"))
     depends_on("r-biocparallel", type=("build", "run"))
     depends_on("r-biocneighbors", type=("build", "run"))
+    depends_on("r-assorthead", type=("build", "run"), when="@1.15.1:")

var/spack/repos/builtin/packages/r-bsgenome/package.py

@@ -13,6 +13,9 @@ class RBsgenome(RPackage):
 
     bioc = "BSgenome"
 
+    version("1.74.0", commit="7ab2eb4e27431a8ee4698bf2a31940bb29d9851a")
+    version("1.72.0", commit="152815df39c49a0d518c2786c0433a761293257b")
+    version("1.70.2", commit="77b80d5515b4a3b8eba9c014104321454dad9bc0")
     version("1.68.0", commit="c546020750e900377fbdeae015a01a96d5962d09")
     version("1.66.1", commit="d1efdfa8e7242bc0f54cc1c3a9583ea555c924f6")
     version("1.64.0", commit="59cdebde613e9702985c003f699f4aea2b0f0e7b")

var/spack/repos/builtin/packages/r-bsseq/package.py

@@ -13,6 +13,9 @@ class RBsseq(RPackage):
 
     bioc = "bsseq"
 
+    version("1.42.0", commit="851185fbece11fa989b32b7353f6d892858b7ade")
+    version("1.40.0", commit="bfe75119f0ff77335d76011712c9ba6a6b8263c9")
+    version("1.38.0", commit="392e22cb833dba561669a201b5378c6eab093599")
     version("1.36.0", commit="5dd72c5a84e1fcc3389ab2a74f8ca14c399ac128")
     version("1.34.0", commit="98239c07d74e1362c7ba2a3bf4f6119830fc95dc")
     version("1.32.0", commit="a0c1eacbc479c57bd836e885e162c28bbe08e115")

var/spack/repos/builtin/packages/r-bumphunter/package.py

@@ -12,6 +12,9 @@ class RBumphunter(RPackage):
 
     bioc = "bumphunter"
 
+    version("1.48.0", commit="d446b63d931c1edcb96d46e8889c68ef32cf4c9f")
+    version("1.46.0", commit="5a10300a73ec48d34fbcfd015ad8d7c0ae2ac4a7")
+    version("1.44.0", commit="084be68b0cfdefced6fe3ba8d94a840371acf85e")
     version("1.42.0", commit="0eb2808a04920aaba00e1ce3e9dff503596e931f")
     version("1.40.0", commit="3de207a3659859737d4c748fc8023694943da43b")
     version("1.38.0", commit="06e2fa87b342d48793d0d2f1f7d94a95a6613995")

var/spack/repos/builtin/packages/r-cairo/package.py

@@ -44,4 +44,5 @@ class RCairo(RPackage):
     conflicts(
         "^cairo ~fc", when="^cairo +ft", msg="For cairo freetype support, also need fontconfig."
     )
+    depends_on("pkgconfig", type="build")
     depends_on("libxt")

var/spack/repos/builtin/packages/r-category/package.py

@@ -13,6 +13,9 @@ class RCategory(RPackage):
 
     bioc = "Category"
 
+    version("2.72.0", commit="343907a78d700c1bab7f99dd00aff223def153af")
+    version("2.70.0", commit="b4b61618911c66ac87faf848dcbe4d60eeaccfa4")
+    version("2.68.0", commit="17a23f809c9f4bccec2fd0ab15aac9492578f3b2")
     version("2.66.0", commit="404c5e4bebeb91b04ac62a821f9eea5610d98b96")
     version("2.64.0", commit="b512cbeb22fc50a2f6d767a2eef356fb143a974e")
     version("2.62.0", commit="0fe801c0c443aebd5d4cefa8c30e4e7d0931b673")

var/spack/repos/builtin/packages/r-champ/package.py

@@ -15,6 +15,9 @@ class RChamp(RPackage):
 
     bioc = "ChAMP"
 
+    version("2.36.0", commit="f75307638d3387624c91406e958a98a60ce5dff6")
+    version("2.34.0", commit="fd26db198c2af3a8265fa33276e406a7a1e55454")
+    version("2.32.0", commit="95ac9464c74bbb3ca1f8ff24ab11aea2384c2b68")
     version("2.30.0", commit="b6ff6670d239c2517aa57144a793ea93da3c7b42")
     version("2.28.0", commit="3d27ac67a738afea8cc9ece6ea1301120e4b48f7")
     version("2.26.0", commit="1548910bf53e1e5f7a8d80c83b742a94297d8a34")

var/spack/repos/builtin/packages/r-champdata/package.py

@@ -13,6 +13,9 @@ class RChampdata(RPackage):
 
     bioc = "ChAMPdata"
 
+    version("2.38.0", commit="373fee54eda7048bbd4e5046c1fb4c33c4620397")
+    version("2.36.0", commit="f3d7acf36c1613dd55dc51d3ec5d23633c71b662")
+    version("2.34.0", commit="debac652f0e001883c3c26b2f66efcea42ef633d")
     version("2.32.0", commit="98a94978001b6a28543257e72a036c43d61e67ef")
     version("2.30.0", commit="6e05b8f7b004b1a5185ec4b387c32725e8bd95cb")
     version("2.28.0", commit="601555bf599828b6cfa125beffa51aebccdc8503")

var/spack/repos/builtin/packages/r-chipseq/package.py

@@ -14,6 +14,9 @@ class RChipseq(RPackage):
 
     maintainers("dorton21")
 
+    version("1.56.0", commit="bb61f21dd88ea2f3608da52d9262efa8b0d2ce46")
+    version("1.54.0", commit="c02cb58cc93255349e55ad3103747446c2afc37f")
+    version("1.52.0", commit="1092f8c908056d9271224940846127355d7ef2e9")
     version("1.50.0", commit="0bdfa25828b1d65f629e96c8e832061fd7ff7935")
     version("1.48.0", commit="9c78296001b6dd4102318879c8504dac70015822")
     version("1.46.0", commit="76b00397cd117d5432158f50fc1032d50485bd24")

var/spack/repos/builtin/packages/r-clusterprofiler/package.py

@@ -14,6 +14,9 @@ class RClusterprofiler(RPackage):
 
     bioc = "clusterProfiler"
 
+    version("4.14.4", commit="0be6e3bf12d42c0769653c44a1dce9f4e8a02b84")
+    version("4.12.6", commit="af7bbecdf62de32033a114602add1736676dfa4f")
+    version("4.10.1", commit="072a273e06ca98f2c6a2c60a549fe3df97d99d38")
     version("4.8.0", commit="35a69cf05855b01775658def2f3f26596902f5db")
     version("4.6.0", commit="2644118c36a3aa14408bc0c97ac20a545e40344d")
     version("4.4.4", commit="9fca9a45ca1793884d8dcfd0f077353dbf75df29")

var/spack/repos/builtin/packages/r-cner/package.py

@@ -13,6 +13,9 @@ class RCner(RPackage):
 
     bioc = "CNEr"
 
+    version("1.42.0", commit="d83a1b6299d27b0553c13f23f62f31840ec904d3")
+    version("1.40.0", commit="e967f8432f3a006e3c7a86e48194ef1fce8cc6e4")
+    version("1.38.0", commit="50955a03b8ff2827b47b70341437ba1da1297013")
     version("1.36.0", commit="4f2feeb395cfc071ed97ba8b6327425dfd42d6b5")
     version("1.34.0", commit="878de98d18f6f959ad5e014ecd8165d3105d8b48")
     version("1.32.0", commit="1c92f3d7f3dccf76ab7d54f286117b09bc470b8f")

var/spack/repos/builtin/packages/r-codex/package.py

@@ -21,6 +21,9 @@ class RCodex(RPackage):
 
     bioc = "CODEX"
 
+    version("1.38.0", commit="30a58de81f6986db1d77745a7f980f94f7631d3f")
+    version("1.36.0", commit="10cf2cbc3e86d239cc752954e9d7bf390da5184f")
+    version("1.34.0", commit="f59d9cf447d746cd6bef1f1895e0cd645d4a4151")
     version("1.32.0", commit="83926238fb49b0e95d989612a98356d20e7caf57")
     version("1.30.0", commit="0694f11be9e0b02ab15047d01db2afce943f92d8")
     version("1.28.0", commit="c707497bd93aa4a0516fcf3671a64997c28c9f67")

var/spack/repos/builtin/packages/r-complexheatmap/package.py

@@ -17,6 +17,9 @@ class RComplexheatmap(RPackage):
 
     license("MIT")
 
+    version("2.22.0", commit="bf351d6dc95d692217019b3aeda53f8ce56f5e1e")
+    version("2.20.0", commit="d9e4bb2ab50c32e555055590020d9d36331c71c5")
+    version("2.18.0", commit="d3c15b6eb7889cec2a705e81a3a2b761b8ea9ea0")
     version("2.16.0", commit="01eb55ca9b783c6d99bdfe88aa131cc102bae5b3")
     version("2.14.0", commit="57fcaa040b08917c97fb66b963eb240d5fd5a8c7")
     version("2.12.1", commit="2c5fe70724219008174d4e6f83189cddbd895ec6")

var/spack/repos/builtin/packages/r-ctc/package.py

@@ -13,6 +13,9 @@ class RCtc(RPackage):
 
     bioc = "ctc"
 
+    version("1.80.0", commit="00f4fb67b54e3412a4944bdb73d8d6036cd3608d")
+    version("1.78.0", commit="ba922348637c4d59e9b76ecfd54acd728e431848")
+    version("1.76.0", commit="3e581adbcabf67a8bed878ff0e411df6196341af")
     version("1.74.0", commit="00be85633de7d71ca3dc6fe6c634cf0bde6188fd")
     version("1.72.0", commit="0a4b464e1768e6407c1c2ce64ec4ae5a4577be65")
     version("1.70.0", commit="05dc046ecfddbc1eeadf77e8f3ec0ce054794437")

var/spack/repos/builtin/packages/r-decipher/package.py

@@ -12,6 +12,9 @@ class RDecipher(RPackage):
 
     bioc = "DECIPHER"
 
+    version("3.2.0", commit="7d5caa259d743538544af34680e4138c9aa3914d")
+    version("3.0.0", commit="1b13c4ea08ece7a46b2675c8ae88f2bbb738561c")
+    version("2.30.0", commit="e33ea83bf5ef398b214f5bd3dca41101badafbe9")
     version("2.28.0", commit="9be570c9fd812139d6bf9cd0851821fe54d4d3fa")
     version("2.26.0", commit="7de99ec5e79f1f645f29dfbe24d2a106c2b0e69a")
     version("2.24.0", commit="437e60005ab281bd836f47756a367795bc16755d")

var/spack/repos/builtin/packages/r-delayedarray/package.py

@@ -19,6 +19,9 @@ class RDelayedarray(RPackage):
 
     bioc = "DelayedArray"
 
+    version("0.32.0", commit="980c34ea2e6b6f6c6e7a6da7e709f90ef2335f96")
+    version("0.30.1", commit="099a64332ede8db85d4150adba76c8126c3d4d3a")
+    version("0.28.0", commit="4f6387772799bcddd49f71b65604486876629949")
     version("0.26.0", commit="e3bdae96838a8ed45f18697f072f3c4ec011aa03")
     version("0.24.0", commit="68ee3d0626c234ee1e9248a6cb95b901e4b3ad90")
     version("0.22.0", commit="4a5afd117b189b40bd409c7aff60e09d41797472")
@@ -41,6 +44,7 @@ class RDelayedarray(RPackage):
     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-biocgenerics@0.51.3:", type=("build", "run"), when="@0.31.13:")
     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:")
@@ -51,6 +55,8 @@ class RDelayedarray(RPackage):
     depends_on("r-iranges", type=("build", "run"))
     depends_on("r-iranges@2.11.17:", type=("build", "run"), when="@0.4.1:")
     depends_on("r-iranges@2.17.3:", type=("build", "run"), when="@0.10.0:")
+    depends_on("r-s4arrays@1.5.4:", type=("build", "run"), when="@0.31.14:")
+    depends_on("r-sparsearray@1.5.42:", type=("build", "run"), when="@0.31.14:")
 
     depends_on("r-matrixstats", type=("build", "run"), when="@:0.10.0")
     depends_on("r-biocparallel", type=("build", "run"), when="@0.6.6:0.10.0")

var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py

@@ -17,6 +17,9 @@ class RDelayedmatrixstats(RPackage):
 
     bioc = "DelayedMatrixStats"
 
+    version("1.28.0", commit="1cf7f742f11d93def7de82977b9a0e542f756804")
+    version("1.26.0", commit="57747783b3fdc5819b5deba51b1b70efad76eab9")
+    version("1.24.0", commit="8fb9c6e38cda6d9637a1aa662a7c83c0c02928a1")
     version("1.22.0", commit="e820ab9a72963badc539e38fa79dbaeab95b2d2c")
     version("1.20.0", commit="1ed14250e8731e60bccb44946cafad4c2b3ac5b0")
     version("1.18.1", commit="9c4658d11fc20b7d88e05b9c52140c2ca8a65768")
@@ -30,24 +33,28 @@ class RDelayedmatrixstats(RPackage):
 
     depends_on("r-matrixgenerics", type=("build", "run"), when="@1.12.2:")
     depends_on("r-matrixgenerics@1.5.3:", type=("build", "run"), when="@1.16.0:")
+    depends_on("r-matrixgenerics@1.15.1:", type=("build", "run"), when="@1.25.3:")
     depends_on("r-delayedarray", type=("build", "run"))
     depends_on("r-delayedarray@0.5.27:", type=("build", "run"), when="@1.2.0:")
     depends_on("r-delayedarray@0.7.37:", type=("build", "run"), when="@1.4.0:")
     depends_on("r-delayedarray@0.9.8:", type=("build", "run"), when="@1.6.1:")
     depends_on("r-delayedarray@0.15.3:", type=("build", "run"), when="@1.12.2:")
     depends_on("r-delayedarray@0.17.6:", type=("build", "run"), when="@1.16.0:")
-    depends_on("r-matrixstats@0.53.1:", type=("build", "run"))
-    depends_on("r-matrixstats@0.55.0:", type=("build", "run"), when="@1.6.1:")
-    depends_on("r-matrixstats@0.56.0:", type=("build", "run"), when="@1.12.2:")
-    depends_on("r-matrixstats@0.60.0:", type=("build", "run"), when="@1.16.0:")
+    depends_on("r-delayedarray@0.31.7:", type=("build", "run"), when="@1.27.2:")
     depends_on("r-sparsematrixstats", type=("build", "run"), when="@1.12.2:")
+    depends_on("r-sparsematrixstats@1.13.2:", type=("build", "run"), when="@1.23.1:")
     depends_on("r-matrix", type=("build", "run"))
     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"))
     depends_on("r-iranges@2.25.10:", type=("build", "run"), when="@1.16.0:")
+    depends_on("r-sparsearray@1.5.19:", type=("build", "run"), when="@1.27.2:")
 
+    depends_on("r-matrixstats@0.53.1:", type=("build", "run"), when="@:1.23.7")
+    depends_on("r-matrixstats@0.55.0:", type=("build", "run"), when="@1.6.1:1.23.7")
+    depends_on("r-matrixstats@0.56.0:", type=("build", "run"), when="@1.12.2:1.23.7")
+    depends_on("r-matrixstats@0.60.0:", type=("build", "run"), when="@1.16.0:1.23.7")
     depends_on("r-hdf5array@1.7.10:", type=("build", "run"), when="@1.4.0:1.12.3")
     depends_on("r-hdf5array@1.17.2:", type=("build", "run"), when="@1.12.2:1.12.3")
     depends_on("r-biocparallel", type=("build", "run"), when="@1.4.0:1.12.3")

var/spack/repos/builtin/packages/r-densvis/package.py

@@ -34,6 +34,9 @@ class RDensvis(RPackage):
 
     license("MIT")
 
+    version("1.16.0", commit="c6a55af619d0959ac29e41f246d51fd6f56fc322")
+    version("1.14.1", commit="a74b17e33e2f4212506bb3694078b061ae7c4d49")
+    version("1.12.1", commit="052bd25b5cc8f7ed041e103488d8cafc484ad4a5")
     version("1.10.0", commit="833db1fb7b2a5667575cc2e7c2fefc8360c8d7fb")
 
     depends_on("cxx", type="build")  # generated
@@ -43,3 +46,4 @@ class RDensvis(RPackage):
     depends_on("r-assertthat", type=("build", "run"))
     depends_on("r-reticulate", type=("build", "run"))
     depends_on("r-irlba", type=("build", "run"))
+    depends_on("r-rtsne", type=("build", "run"), when="@1.12.0:")

var/spack/repos/builtin/packages/r-dexseq/package.py

@@ -20,6 +20,9 @@ class RDexseq(RPackage):
 
     maintainers("dorton21")
 
+    version("1.52.0", commit="02d945a2b79f2a0af6ae39e183cac54b2e5cb044")
+    version("1.50.0", commit="d831c0f9004ae1d6aefd0cb8b21405958e348c52")
+    version("1.48.0", commit="40ec7aefb489082b2f3f43c2a03846319a4a9f66")
     version("1.46.0", commit="074c0bf6776eea69e58a788a0f6904dd632a1b74")
     version("1.44.0", commit="9660d7372d5ced1a7e324ed9a61b935023b7d135")
     version("1.42.0", commit="d91de62a27d0cab2ef12ef1a5f23dc2f7a0cfadd")

var/spack/repos/builtin/packages/r-dir-expiry/package.py

@@ -15,6 +15,9 @@ class RDirExpiry(RPackage):
 
     bioc = "dir.expiry"
 
+    version("1.14.0", commit="350a482fb2acc124f5115babfbd06b7d32fd1f6f")
+    version("1.12.0", commit="141ea0d286e6851ac844216734f7ceb40c8c5fe7")
+    version("1.10.0", commit="58c7811e19baa99d9f58dc65845fa6cb26f52009")
     version("1.8.0", commit="271f76cb2e8565817400e85fcc2c595923af4af6")
 
     depends_on("r-filelock", type=("build", "run"))

var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py

@@ -17,6 +17,9 @@ class RDirichletmultinomial(RPackage):
 
     bioc = "DirichletMultinomial"
 
+    version("1.48.0", commit="37dd5f306196b87d6fca041f9260761e5f56781e")
+    version("1.46.0", commit="40e13c6ef8510de840eda2e33d0b8a621526ec38")
+    version("1.44.0", commit="dbea7cfb6e45128a13244fd0d6daecdc249a70b2")
     version("1.42.0", commit="c388536bed4bdc57724b704edec04b28acbf48db")
     version("1.40.0", commit="200176f8c72ff127788c500629b71872bc6b1f83")
     version("1.38.0", commit="b4de83d354e974fdb7cb3526d029487f24aab670")

var/spack/repos/builtin/packages/r-dmrcate/package.py

@@ -16,8 +16,12 @@ class RDmrcate(RPackage):
 
     bioc = "DMRcate"
 
+    version("3.3.1", commit="52f38aac5f0a9c6e54a68129e63e7afc9357b742")
+    version("3.2.1", commit="e441ab41214f45bb1a46695ffbecaa3924ab669e")
     version("3.2.0", commit="1f46517bcdea269a2c9726d1156495d6dd172067")
+    version("3.0.10", commit="a04f3c932d222b7a2053d3c4f2ff95e5305569b0")
     version("3.0.0", commit="9cd77dedef76528990487b931ae0cc314423c3b9")
+    version("2.16.1", commit="4cd23978fcc74bc5cd22d48e756f454532a4478f")
     version("2.16.0", commit="9e42d8c8eb26dbd2d36a70bf32be322062ecc850")
     version("2.14.0", commit="6e7bae0917001e7664f01c3f8d261f9fe28c2f4d")
     version("2.12.0", commit="560dd5067b05715631739d0fb58ef9cebdbf7078")

var/spack/repos/builtin/packages/r-dnacopy/package.py

@@ -14,6 +14,9 @@ class RDnacopy(RPackage):
 
     bioc = "DNAcopy"
 
+    version("1.80.0", commit="f89937b306b41c495758e8712dc80046b2a8e791")
+    version("1.78.0", commit="51f8d46999e1b52d2249ad2ed184ac297d2f558c")
+    version("1.76.0", commit="de0b0ade51bf4e37400d0b18d9924202b9dca228")
     version("1.74.0", commit="7d22a81570c0fe76f4b5a5c25d0b8fd3696ec70e")
     version("1.72.0", commit="1a1ae854c3425aee68b060e3e7ab788db5bed08c")
     version("1.70.0", commit="9595d0ad7c78af4ed568cbd210b894d3350eae0a")

var/spack/repos/builtin/packages/r-dose/package.py

@@ -17,6 +17,9 @@ class RDose(RPackage):
 
     bioc = "DOSE"
 
+    version("4.0.0", commit="5c3c2f3669f0dfec9336ffe40053b71b4167a559")
+    version("3.30.5", commit="f2882c1bf60496619a3ff40b434ade673ee0c460")
+    version("3.28.2", commit="9e236d97ad30d3db1b00895815f23c88b17a04fe")
     version("3.26.0", commit="9c91fb45a2ab9a875a6a7259610b7d5bc86933f6")
     version("3.24.1", commit="a78995d3b12bd4baabb69c497102687814cd4c68")
     version("3.22.1", commit="6b711a0f076a9fefcb00ddef66e8f198039e6dfa")

var/spack/repos/builtin/packages/r-dss/package.py

@@ -17,6 +17,9 @@ class RDss(RPackage):
 
     bioc = "DSS"
 
+    version("2.54.0", commit="d18c722c5efb5ae12f42696a7d178c8dff032cf7")
+    version("2.52.0", commit="bc657668f8ac1c645534ca1c57db04b6e23d1339")
+    version("2.50.1", commit="57860cac9bb1aac36e273735201093dcb6c16b90")
     version("2.48.0", commit="03ceee2656e57b717e4fd7f22ff389f118421ae1")
     version("2.46.0", commit="debfbac4bc741961ba57915d4f2d98534f02cc21")
     version("2.44.0", commit="b9f44106f139c93564dfb4afab50555d24a657ba")

var/spack/repos/builtin/packages/r-dupradar/package.py

@@ -14,11 +14,13 @@ class RDupradar(RPackage):
 
     license("GPL-3.0-only")
 
+    version("1.36.0", commit="f219b1dac0aeeca1910bd945a83508df10201dfc")
+    version("1.34.0", commit="8dadc41cfd84943a6e37f7c0764e169e71b88dd9")
     version("1.32.0", commit="7e07fc3a3901f8cae0203759fc24dd7df430a07f")
     version("1.30.3", commit="19e3b13a148c47e69686cd1e872182c564fd4dcd")
     version("1.30.0", commit="3d53d2d2e0c404a25845d78b8df8fee3f6b34eb5")
 
-    depends_on("r@3.2:", type=("build", "run"))
+    depends_on("r@3.2.0:", type=("build", "run"))
     depends_on("r-kernsmooth", type=("build", "run"))
-    depends_on("r-rsubread", type=("build", "run"))
+    depends_on("r-rsubread@1.14.1:", type=("build", "run"))
     depends_on("subread", type=("build", "run"))

var/spack/repos/builtin/packages/r-ebseq/package.py

@@ -20,6 +20,8 @@ class REbseq(RPackage):
 
     bioc = "EBSeq"
 
+    version("2.4.0", commit="6f13304c4034c19a2d37f4c811ac7aea40f631c6")
+    version("2.2.0", commit="95b79f290698ef871baa2744fd24dd3bb61af5ff")
     version("2.0.0", commit="f1d4e4419988ab98540739c9349559fd437cb59f")
     version("1.40.0", commit="7d1d2a2b4ea0df8cddfb5e57d6431f3948c5c4ca")
 

var/spack/repos/builtin/packages/r-edger/package.py

@@ -18,6 +18,9 @@ class REdger(RPackage):
 
     bioc = "edgeR"
 
+    version("4.4.1", commit="797c5353c166a6ea15094f9f36d547187ea81aaa")
+    version("4.2.2", commit="d50e8020f272abdaf612326bf55a1ef7c2123f22")
+    version("4.0.16", commit="1e37a9b4c0660174016925d6294221e9ac9d5ea2")
     version("3.42.0", commit="197b9a8ccc27016611b262c2c31ca22f991661c5")
     version("3.40.0", commit="0b25adcc6b3cb0a8c641964d1274536ee07ee162")
     version("3.38.4", commit="f5a3bb568a23b34146ac66329a95ee4785093536")
@@ -38,5 +41,7 @@ class REdger(RPackage):
     depends_on("r-limma", type=("build", "run"))
     depends_on("r-limma@3.34.5:", type=("build", "run"), when="@3.20.9:")
     depends_on("r-limma@3.41.5:", type=("build", "run"), when="@3.32.1:")
+    depends_on("r-limma@3.61.9:", type=("build", "run"), when="@4.3.8:")
     depends_on("r-locfit", type=("build", "run"))
-    depends_on("r-rcpp", type=("build", "run"), when="@3.20.9:")
+
+    depends_on("r-rcpp", type=("build", "run"), when="@3.20.9:4.3.10")

var/spack/repos/builtin/packages/r-enrichplot/package.py

@@ -15,6 +15,9 @@ class REnrichplot(RPackage):
 
     bioc = "enrichplot"
 
+    version("1.26.5", commit="fcb6e51593cccc45f8cc0bdfa171d5998816946f")
+    version("1.24.4", commit="ae4470158b2c3e423ef997cb2b7e2ae423ac5b01")
+    version("1.22.0", commit="6277b76898e14b6cde758186bb3870632132ab16")
     version("1.20.0", commit="ae72efe5f2ded561958f95bc8b1b41c0fc79840e")
     version("1.18.0", commit="61ea941784a1ed6cc604af1c1cc4532b8b5fcea7")
     version("1.16.2", commit="eeb21345288d96c116ac308649fa772d03760259")

var/spack/repos/builtin/packages/r-ensembldb/package.py

@@ -23,6 +23,9 @@ class REnsembldb(RPackage):
 
     bioc = "ensembldb"
 
+    version("2.30.0", commit="1376f59be5f6d34f9cc8e57632fc27fa58b1dcc0")
+    version("2.28.1", commit="32dfb29152e8f581398dc6893eecc92347a1f2a8")
+    version("2.26.1", commit="acdf57b7e91e5256e63e87a1d0c457e11d8405d1")
     version("2.24.0", commit="45a79a438fde11b0d244b071e6ae2b652100be03")
     version("2.22.0", commit="4dda178a14e080c643bbd8c4dd6378bfe4e6ee9f")
     version("2.20.2", commit="ac1fb8389efd88099600af298d6bb3384206f9ed")

var/spack/repos/builtin/packages/r-exomecopy/package.py

@@ -16,6 +16,7 @@ class RExomecopy(RPackage):
 
     bioc = "exomeCopy"
 
+    version("1.48.0", commit="c418319e721b440272b551be91b965e928b8af65")
     version("1.46.0", commit="b282adb17fb05e1a940d068d27bfd9d4549a53e7")
     version("1.44.0", commit="2dd6598d5fb14d49f7a42e597284c7a929c0cd62")
     version("1.42.0", commit="ba0979cf5fbdefed841022f2dc0604941315c1b8")

var/spack/repos/builtin/packages/r-experimenthub/package.py

@@ -17,6 +17,9 @@ class RExperimenthub(RPackage):
 
     bioc = "ExperimentHub"
 
+    version("2.14.0", commit="2bac493f4fb89cdd562840050631e3d937db949b")
+    version("2.12.0", commit="b9071266793f2857365bc621ddf91d8c5cc8445c")
+    version("2.10.0", commit="f9cb6a0518ece8ff2b5d0708861ad5e5b47b2903")
     version("2.8.0", commit="f25c854c51878844098290a05936cb35b235f30e")
     version("2.6.0", commit="557ba29720bce85902a85445dd0435b7356cdd7f")
     version("2.4.0", commit="bdce35d3a89e8633cc395f28991e6b5d1eccbe8e")

var/spack/repos/builtin/packages/r-fgsea/package.py

@@ -17,6 +17,9 @@ class RFgsea(RPackage):
 
     license("MIT")
 
+    version("1.32.2", commit="46202811bc1b3fb1c40d96b43cc45fb662fd61e0")
+    version("1.30.0", commit="5f634393679cb5556797982f1ee1ba0f5b4c24c6")
+    version("1.28.0", commit="6c19b1edca90ef064c2246d52f3473d18dab0bcc")
     version("1.26.0", commit="102b439e2208ae415dc19d3d1ac8936f9c5999f1")
     version("1.24.0", commit="ac74ccd935c15623b8584caa791835aec514144b")
     version("1.22.0", commit="e4e203aa64faa984e0406fed5d87a422d9df92f2")
@@ -31,6 +34,7 @@ class RFgsea(RPackage):
     depends_on("cxx", type="build")  # generated
 
     depends_on("r@3.3:", type=("build", "run"))
+    depends_on("r@4.1:", type=("build", "run"), when="@1.27.1:")
     depends_on("r-rcpp", type=("build", "run"))
     depends_on("r-data-table", type=("build", "run"))
     depends_on("r-biocparallel", type=("build", "run"))

var/spack/repos/builtin/packages/r-gcrma/package.py

@@ -12,6 +12,9 @@ class RGcrma(RPackage):
 
     bioc = "gcrma"
 
+    version("2.78.0", commit="dc3bef2a17004fdb6d8842c258c2e1b9122f221a")
+    version("2.76.0", commit="01247c38a2f4be1088df02645b9110369f609e91")
+    version("2.74.0", commit="1ceeafef23eec0669759bff675d15385dda22c33")
     version("2.72.0", commit="5cfccc7c684283dc3a82830bad75aad254efcb01")
     version("2.70.0", commit="095f38914525d8812524a3cb38db8075382f8121")
     version("2.68.0", commit="c14063ff5490fac8d60530826613d728e68b3d66")

var/spack/repos/builtin/packages/r-gdsfmt/package.py

@@ -25,6 +25,9 @@ class RGdsfmt(RPackage):
 
     license("BSD-2-Clause")
 
+    version("1.42.1", commit="a1256b83b335aa7db67719a42a8270ea9780c326")
+    version("1.40.2", commit="3e0d00850ddb7480e935bc5b6c906512aac6b7e0")
+    version("1.38.0", commit="47ebf725814d52ff0c42d6fce908dbd11c8b50b3")
     version("1.36.0", commit="39ba0af93d499b0f9ef53f04d4f15e5436616f1a")
     version("1.34.0", commit="ab912c393d8eb6dc26f844a13422a29b9ce7265b")
     version("1.32.0", commit="06f2097cc10b1888739f86e635383a0f2ee7e208")

var/spack/repos/builtin/packages/r-genefilter/package.py

@@ -12,6 +12,9 @@ class RGenefilter(RPackage):
 
     bioc = "genefilter"
 
+    version("1.88.0", commit="f0d698ac73b17b9c845e8778b0a355216eb50c31")
+    version("1.86.0", commit="43d41cbf547ac1cbeddc9b60fab2b8787781d77c")
+    version("1.84.0", commit="94eca03db3d721035df17e32ff369e6a28a9394a")
     version("1.82.0", commit="1ee4bdc65b0144853211354f8fabf8b497d9a565")
     version("1.80.0", commit="14fbc2d776916e572583e3c268ea9ba60ed60a9a")
     version("1.78.0", commit="2f574388971641d3a71858f5c34606c04fcd2ba2")

var/spack/repos/builtin/packages/r-genelendatabase/package.py

@@ -13,6 +13,9 @@ class RGenelendatabase(RPackage):
 
     bioc = "geneLenDataBase"
 
+    version("1.42.0", commit="8eb26117e5e45ac2079162c84f37d233c54e0640")
+    version("1.40.1", commit="f1617949a5586f7668f3d196ea404b0d12e57103")
+    version("1.38.0", commit="cbe2fbdba91a5b8f98242d3164d4564f3329e39e")
     version("1.36.0", commit="e8f37dd2a63cf10ba946958362192909fec64a10")
     version("1.34.0", commit="e26cf8e3fc20b5d183cbd39b7b28a8cc866f6ead")
     version("1.32.0", commit="eaa193a2c6d502c6d59113fd42f66761b8730594")

var/spack/repos/builtin/packages/r-genemeta/package.py

@@ -13,6 +13,9 @@ class RGenemeta(RPackage):
 
     bioc = "GeneMeta"
 
+    version("1.78.0", commit="4d17ec8babebad5b49b007d2791181f95cb39a02")
+    version("1.76.0", commit="2eed8386ee1a40e4ab14594323e4538b7f73f8e9")
+    version("1.74.0", commit="476eb5edef69cc05d4178faaf02ef45293c91f32")
     version("1.72.0", commit="1cb047172f54c12c5dc5a9b39358ea04cbeff8a2")
     version("1.70.0", commit="e5db82e04efc4572358abce7e0c09273f94c9d72")
     version("1.68.0", commit="4213c0205d477660195300a0aa9751972f86bf91")

var/spack/repos/builtin/packages/r-geneplotter/package.py

@@ -12,6 +12,9 @@ class RGeneplotter(RPackage):
 
     bioc = "geneplotter"
 
+    version("1.84.0", commit="199585668e533efce2142fd9ef72e16f9c05e6ff")
+    version("1.82.0", commit="37e374b8f02a9addea35c7908eaa1d9660a1ace4")
+    version("1.80.0", commit="e304c8a6aeff1b37257f8d94c133fb1b3a40b0e5")
     version("1.78.0", commit="a105c51d2f7a097ea33c3aad8f2345e9a51406d3")
     version("1.76.0", commit="4eb6a787d0c66110ec9a7d34fc76b64030fbde5d")
     version("1.74.0", commit="ca819565829eac7a9a98e3cafafd6c06a466fddf")