Update Spack Bioconductor packages to Bioconductor 3.15 (#30984)

187 files changed, 256 insertions, 8 deletions

diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py
index da65ee420d..59b004c217 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('1.44.0', commit='5b0fc5a9971d8f3688ad1f88a4f5ee1498e91633')
     version('1.42.0', commit='fc26809e2bce7cd50d99d6f6dd5f85c38342fdea')
     version('1.38.0', commit='5b7a9087bab10c55e24707e96e48046995236c94')
     version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712')
diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py
index c4a8b8c854..2f26bf5147 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('1.44.0', commit='9ae69e03118c7b14df0e6c9e3b25362b09f25bbe')
     version('1.42.0', commit='d7296e2792020e9c5b1c19101104326ee8bebfe6')
     version('1.38.0', commit='4add242fa9c62795aca5b0dfca34a43484c5aa82')
     version('1.32.0', commit='8a1e15d25494c54db8c1de5dbbd69e628569e3d7')
diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py
index 12bfbd27e6..a93c2521d9 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('1.44.0', commit='df0fce781f9bc480a1159d958c9a63c314a9ed01')
     version('1.42.0', commit='820854a7ca9ed0c295479a25b7e3375c6d01d0b5')
     version('1.38.0', commit='c4d058813efb835774813b2d69c52912162f8e75')
     version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88')
diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py
index bd95da50f2..6321e10d37 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('1.44.0', commit='61a7f3a51a41af615bfd4c22984e4c4a82874e8c')
     version('1.42.0', commit='6985950b72c2a0f20ec44fe2067d8864e004bfaa')
     version('1.38.0', commit='a027dcd3486c64950815ec7c7271f1f65ba3d8a1')
     version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce')
diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py
index e7a063ef89..e1e4016910 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('1.44.0', commit='252381265b96b83803a93e0c2014dd6b0574e57f')
     version('1.42.0', commit='773a91e884d2ada16fe9cf57d5ed53c0155e3fa2')
     version('1.38.0', commit='c93c223bd531bff090531a109b51f8dcd710d0cb')
     version('1.32.0', commit='0da742e500892b682feeb39256906282ad20c558')
diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py
index fd6629bf75..fa91076c6f 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('1.44.0', commit='bfe83507daf53e2e327474ea3012f0dc920efac1')
     version('1.42.0', commit='b0d715b9cdac80bc412f0a9a6b33941c4a7582bb')
     version('1.38.0', commit='cd3cf244e7a299b2485684ed15519cbbda1c590f')
     version('1.32.0', commit='8d781899c625892080eb50f322694dd640d5f792')
diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
index c5ec3cbefa..70b8c8e7d8 100644
--- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py
+++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
@@ -24,6 +24,7 @@ class RAbaenrichment(RPackage):
 
     bioc = "ABAEnrichment"
 
+    version('1.26.0', commit='33df9e162aec07e2aae92cc058cbfb33720ba4b4')
     version('1.24.0', commit='5d20752263ae8f18ea5f5a6cfbdd5921a0f236d7')
     version('1.20.0', commit='608433a0b07e6dd99915dc536a038d960f1be1d5')
     version('1.14.1', commit='e1ebfb5de816b924af16675a5ba9ed1a6b527b23')
diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py
index 63ba9a8a69..758c85e211 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('1.50.0', commit='4f384d04ebaae6ea0b56e5cff9a9dcdcb6c8afb0')
     version('1.48.0', commit='b237c967d44d075ca306c35e92df8b66a60ce72d')
     version('1.44.0', commit='c202b4a059021ed1228ccee7303c69b0aa4ca1ee')
     version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce')
diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py
index be9ad2e438..89a855a456 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('1.26.0', commit='dfef9a435062e948efd5eda22942a0d500baa992')
     version('1.24.0', commit='0c3c4d47af7eaff37420032ea5245743a65124cf')
     version('1.20.0', commit='cefb4f2e2b0ef3c5f51944c0ece7a71294020350')
     version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417')
diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py
index b6f3ac516f..ea7ffd3c23 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('1.74.0', commit='e7ba380af0da138788eb6c86f5dbe453269c0810')
     version('1.72.0', commit='b5d4022ac487125194d3913f1b8c2948db6e2792')
     version('1.68.0', commit='91f41a3917ddce43eb05e11c90eb99c467ba2247')
     version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f')
diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py
index 764c9b0665..e98196b156 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('2.52.0', commit='14a97c722d0201654af9e583e7e462b458c28a77')
     version('2.50.0', commit='d55a19a8c091e8ea5fd35041520107a7f7603e14')
     version('2.46.0', commit='68f45c9f7d34c28adf6a0fc4245fdf63881109de')
     version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a')
diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py
index 2fde71da20..67984d1dac 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('1.66.0', commit='64580a6f7a9bc6b16334267c90df48fbb839cc16')
     version('1.64.0', commit='32f150eb51c66b867301dceeb527de5b97f9f490')
     version('1.60.0', commit='de5abccfe652cbc5b5f49fb6ed77cdd15cc760cd')
     version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652')
diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py
index 5087844228..98e5b0e176 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('1.68.1', commit='821a01a2df18115a3b7864b3f45418255b7123eb')
     version('1.66.0', commit='2ea72d4c924ac14bdd807b23563c8501c226ce3a')
     version('1.62.0', commit='b3e988e5c136c3f1a064e1da13730b403c8704c0')
     version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056')
diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py
index 38c50e73e9..b03133e7e3 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('1.74.0', commit='2266c4a46eda7e5b64f7f3e17e8b61e7b85579ff')
     version('1.72.0', commit='3750b4eb8e5224b19100f6c881b67e568d8968a2')
     version('1.68.0', commit='1664399610c9aa519399445a2ef8bb9ea2233eac')
     version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605')
@@ -24,7 +25,6 @@ class RAffy(RPackage):
     version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
 
     depends_on('r@2.8.0:4.0', type=('build', 'run'), when='@:1.68.0')
-    depends_on('r@: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'))
     depends_on('r-affyio@1.13.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py
index 7f4ff5826e..22c32f2047 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('1.72.0', commit='c52baea98b80abd4a99380ac9d4b68ef91869d40')
     version('1.70.0', commit='487f6775975092475581a6c02ddb27590559cf07')
     version('1.66.0', commit='388d01af8b1e6ab11051407f77d0206512df8424')
     version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c')
diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py
index cc027634f5..875de9489a 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('1.56.0', commit='37ea4bb885c791fb989f40092f3d0d2c57d35641')
     version('1.54.0', commit='fde7d86ccdb03c13c4838c18ac25477ffe6e0fe5')
     version('1.50.0', commit='3b12d12bd6d1a9f0d45e012817231d137d47089e')
     version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476')
diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py
index 4366c70c88..4e806983b5 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('1.54.0', commit='c5208b48b8881983ff53a4713244327e8ad13b78')
     version('1.52.0', commit='47c1d86da330f157d3ece0e26b0657d66a5ca0c9')
     version('1.48.0', commit='88387a2ad4be4234d36710c65f2ca3a5b06b67da')
     version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe')
diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py
index 99e281e2ad..b189360e20 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('1.68.1', commit='69546b1fe5edd71eca130d53d33f0fb0fcf62c97')
     version('1.66.0', commit='6bf769d70e196634097f465ed2fa85cce5312a6d')
     version('1.62.0', commit='c9779e4da648fd174c9bd575c6020be1c03047c4')
     version('1.56.0', commit='71eab04056a8d696470420a600b14900186be898')
diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py
index 6ba098872a..dac3f12256 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('1.44.0', commit='f18304a356cee8cd7297bab362b13c40e50439df')
     version('1.42.0', commit='4b54c1206bedd27ff9be32affc999a279f4e96f0')
     version('1.38.0', commit='b5e843b2514789d0d87bea44d762c89a95314ee7')
     version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd')
diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py
index b247e347ed..b1afc7a946 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('1.48.0', commit='4603a4c4d6c2330a8a56a7bb657dc56c51a9393a')
     version('1.46.0', commit='67ffbfa6c881ed83d15604bf4463fe5dba81036b')
     version('1.42.0', commit='b97b29786b866de38802ebbb995169be91e90942')
     version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132')
diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py
index 5c03f50aac..60c3cc08c4 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('1.66.0', commit='3a0b90704fc46cddd99a72b985a6bdb348f69b50')
     version('1.64.0', commit='aa7ce48f3f4110431f6f488d45961fde4019ffb0')
     version('1.60.0', commit='ee20528b32700e99768da48143d6d45c9a7bbe91')
     version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f')
diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py
index 8d3780ad28..80d3841fe7 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('1.72.0', commit='394c0a8e213f188d0b1d01e20516df8bf1bc5c09')
     version('1.70.0', commit='64abfec92b347aa340b54a8c7b2fbd524fe9c312')
     version('1.66.0', commit='f0780c3d0e9dccaff83861b98beb5c1d324c4399')
     version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d')
diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
index 4b677ebd37..1ecbd12d55 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('1.42.0', commit='5775f41f538b3c8ee4d07d38cec1b49c548cebe6')
     version('1.40.0', commit='8539a91ee464d692a267bb17c91dc1ef9a231f41')
     version('1.36.0', commit='89662b93076659db2967a526899184c12c156bc5')
     version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1')
diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py
index 67f85872a3..5e667ca6da 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('1.44.0', commit='9d3eb90eaf7bf093c7fa73facb3df89506a85185')
     version('1.42.0', commit='175cf1b384b0942103d841b1feb9e4f7d141ba06')
     version('1.38.0', commit='7e2c1f5f27ccbea6a7157f5122212e40408b74da')
     version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf')
diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py
index b473cfe260..456cc429e9 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('3.28.0', commit='2c6dfccc76473b5bef13b75fa59adf46b3381f55')
     version('3.26.0', commit='3170fe2b1cc459d5e2ca7f61a127aac17cd66a96')
     version('3.22.0', commit='7d089d576752e0526f15a1007e94436089954313')
     version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47')
diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
index a4f6a5412b..536433875f 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('2.46.0', commit='8c6d73e1c3f1f9cc019bdb219b19e6179bb1efe4')
     version('2.44.0', commit='8b308baa3b1b0afc0855ea263630a288689e3864')
     version('2.40.0', commit='cfa4acb2215da44767ab3a45845bcd587c309e74')
     version('2.34.0', commit='aaa8cdd70ed2696c313f6240ffbfa044f0d97a7a')
diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py
index 7e9c962ccf..dc484b6984 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('1.28.0', commit='84608df638b5694c08158ed77ad2c8a64c4e594b')
     version('1.26.0', commit='5dcf60eb4cdcf563ea848482c9c488f465c27bbd')
     version('1.22.0', commit='34a38978b24377abb864eff7683bb36344ff171d')
     version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84')
diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py
index 3eb61fe76c..04928a7e16 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('1.28.1', commit='f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6')
     version('1.26.0', commit='0876a2eac08d3f1c01df7414d97d391c80182ada')
     version('1.22.0', commit='ac7f0ab3f094ec52713da7620a27058b14c7181d')
     version('1.16.0', commit='bd698a896a5bea91187e3060e56a147bad1d586f')
diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
index 55061c4064..2b87c67ece 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('1.34.0', commit='290708ccc4ceae1fbb9e9257cb254916449d389b')
     version('1.32.0', commit='428ab8c96bb15fab45e4084da25f98b01b9d60b6')
     version('1.28.0', commit='ac5d13c9ee0935bf9500ee542792644e752a1fde')
     version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a')
diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py
index baae8f4a09..aef774b950 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('1.22.0', commit='6107a82962f07e0434e93f261cd375eaaa171d91')
     version('1.20.0', commit='9348ef14128aa6be10cca1987736ddbc385df7e9')
     version('1.16.0', commit='aee397774ac6cd17ad45dc05be14c526647f3c13')
     version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c')
diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
index a6fa1ca9e7..3e545be934 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('2.58.0', commit='08255a777ffa1e1414d3dd3062d95bfdd3dfd47c')
     version('2.56.0', commit='941e00b97a33662a8230991e387070324b2e76bf')
     version('2.52.0', commit='21329abf82eae26f84b7c0270e81c8e089c548ce')
     version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b')
diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py
index 8f01498845..d4c22d2892 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('2.20.0', commit='61598dd3430b09b57f31d7d550ea95126a2d73c8')
     version('2.18.0', commit='c8e3df3e299c32daac0dda23cea59a18673d886b')
     version('2.14.0', commit='d0a34c931a0e72080bff91dacb37dbbe26b45386')
     version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601')
diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py
index ab8e18abe3..83840de9c9 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('1.24.0', commit='4c6906eee514eba3e8ac159654a6953e37a99bba')
     version('1.22.0', commit='ea0beb3d827c2dd4bc56708a839a93c55304918b')
     version('1.18.0', commit='76ec9af947f97212084ca478e8e82f9e0eb79de9')
     version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e')
diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
index 513894094d..5dc964ec54 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('1.24.0', commit='cf6f3852702aab28e3170fc56b695d00b7389666')
     version('1.22.0', commit='ae8eec3b0afdc351dc447aad2024df5b2c75e56b')
     version('1.18.0', commit='1bf1657b28fc8c1425e611980a692da952ce3d1e')
     version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1')
diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py
index 5bee7d7991..aed4dd6f1e 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('1.68.0', commit='fa930c0bbdca9828a130ab06d86c65d451380830')
     version('1.66.0', commit='aa1afa1509754128d27508228c1f39f51a8da043')
     version('1.62.0', commit='ad9c37e0e7e45e0f35c208ce528ba48000b37432')
     version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233')
diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py
index 2d7c97434c..4bf59970d6 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('1.74.0', commit='200c71743417792880f8171d59b2ac0ddd3902a8')
     version('1.72.0', commit='67ac76a9ff6d60dc1620763d3aa98aef39443110')
     version('1.68.0', commit='98cdb12c612b3f3fc06329a89a1ffb0a92b555c0')
     version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd')
diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
index 3345f17b28..0038613892 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('1.58.0', commit='05fcf7a28a6b15b195da23474d7ba89bd0cfd891')
     version('1.56.2', commit='13fdc4a93852199ca6ec120a2fe1078f9f445f67')
     version('1.52.0', commit='c4e0ca9bd65362ae9cad6a98d90f54267b0ae838')
     version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9')
diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
index c0f6fb9c36..62452c16e7 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('1.20.0', commit='2818aff6502fd6fe819521cd8d97695ef6f9198e')
     version('1.18.0', commit='60a9b666d7362d7ed5c357fd4a5d2744d8598c20')
     version('1.14.0', commit='6ee3a13ed93a535ed452cbc8c118151a2cbb732c')
     version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed')
diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py
index 1a2b1e7b88..777f15ca53 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('1.38.0', commit='1f77750562ea3a01f0f1a46c299184fc31196ffd')
     version('1.36.0', commit='523b5f0c3ffb77e59e1568e5f36a5a470bfeeae5')
     version('1.32.0', commit='3d17c2a945951c02fe152e5a8a8e9c6cb41e30f7')
     version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e')
diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py
index bc900f1746..a043454ac4 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('3.4.0', commit='e74e54ca44f50c2c15c60f8620e3d1721f8f5b6d')
     version('3.2.1', commit='ad1dfe86f0b0ea4711cc9cdb89e073e8794ec9aa')
     version('2.22.0', commit='3ab7dceebbc31ac14ca931f66c662cf9538b7d0a')
     version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed')
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 c2c5b029a4..f0b74ae5e8 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('3.26.0', commit='7ead7517a77bc8b4b4b42aace69957a17e8fe016')
     version('3.24.0', commit='3ff48b8f546acc9803b3c652363cac78d3b81ae5')
     version('3.20.0', commit='02cde7fa166259bce73c396a87dca2ecc8249c39')
     version('3.16.0', commit='fc16179fc4bee8954c5415d7cd13e3112b75b4fd')
diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py
index 63eae14a06..78c886169b 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('1.28.0', commit='27b70be6f73747d9d32054da043f4a37ea55b917')
     version('1.26.0', commit='d57643441d04f77db0907637dc9e7cd5bed5842f')
     version('1.22.0', commit='5f533969c84212406bcb3ebf725ebb6d77e9947a')
     version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657')
@@ -25,6 +26,7 @@ class RBamsignals(RPackage):
     version('1.8.0', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
 
     depends_on('r@3.2.0:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@1.28.0:')
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-rcpp@0.10.6:', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py
index d9a7421029..3ce3ec04e1 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('2.12.0', commit='3e6af145bdcdf0a0b722d8256ba1a38b8a36b2f5')
     version('2.10.0', commit='b7cc532d4a5b26d9073135cc9945258ea08e5079')
     version('2.6.4', commit='7d9dc6379017d723dda3e8dc9fd1f6de7fd33cdb')
     version('2.0.0', commit='2bdac6ce7b636fd16f78641a0bcc2181670107ab')
diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py
index 4308ffa4fd..1cde45a432 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('2.56.0', commit='3b2dd91b333677c2f27257c7624014a55e73c52b')
     version('2.54.0', commit='8215d76ce44899e6d10fe8a2f503821a94ef6b40')
     version('2.50.0', commit='9927f90d0676382f2f99e099d8d2c8e2e6f1b4de')
     version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3')
diff --git a/var/spack/repos/builtin/packages/r-biocfilecache/package.py b/var/spack/repos/builtin/packages/r-biocfilecache/package.py
index 5a8d03dc7e..b74191ad15 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('2.4.0', commit='2c00eee40d95fddad223f115f959b09e1a14f75d')
     version('2.2.1', commit='cc912123408803193bf37395f4d18baa8dcd6f47')
     version('1.14.0', commit='cdcde4b59ae73dda12aa225948dbd0a058d9be6d')
     version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0')
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index 666898ea6b..37f6a1c350 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('0.42.0', commit='3582d47b836387afc08157f3d6a5013fd64334ed')
     version('0.40.0', commit='0bc1e0ed4d20c7101cd782a14f6373e27478acfc')
     version('0.36.0', commit='0d5d169d7d64d648a22f9043837c93bc784e71ed')
     version('0.34.0', commit='f7c2020')
diff --git a/var/spack/repos/builtin/packages/r-biocio/package.py b/var/spack/repos/builtin/packages/r-biocio/package.py
index 43fb6b7655..59b127844a 100644
--- a/var/spack/repos/builtin/packages/r-biocio/package.py
+++ b/var/spack/repos/builtin/packages/r-biocio/package.py
@@ -22,6 +22,7 @@ class RBiocio(RPackage):
 
     bioc = "BiocIO"
 
+    version('1.6.0', commit='60c8aa1a961e43bf0ee5d563a6d9fcec84f7f8f8')
     version('1.4.0', commit='c335932526a38c75dbfa4970c1d90b8a21466d37')
 
     depends_on('r@4.0.0:', 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 342b0e96c7..890455d5d3 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('1.14.0', commit='670a1bd4d82636d28fbff50cea2157e16bb1a858')
     version('1.12.0', commit='3c8a290f75adc944b408e6e77a36f3a0c1509c4c')
     version('1.8.2', commit='889bc91f8cb45d210b47ae5c0b9cfb86fb071ca2')
     version('1.2.0', commit='f754c6300f835142536a4594ddf750481e0fe273')
diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py
index 519e5a59fb..14ad2c1a50 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('1.30.2', commit='e7e109f7a94dbfbc50f926be030c7ad8c1a053db')
     version('1.28.3', commit='2f9d88ad83659939e7911d49c2d24d2cd599c7cc')
     version('1.24.1', commit='f713caa4314ec0ddeba7fe0eb599ad417efb413f')
     version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e')
diff --git a/var/spack/repos/builtin/packages/r-biocsingular/package.py b/var/spack/repos/builtin/packages/r-biocsingular/package.py
index df221d0b83..c1bd782b07 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('1.12.0', commit='7d1b8f4954e9e6f2c30a5111cdab9aabc8bcc3a6')
     version('1.10.0', commit='6615ae8cb124aba6507447c1081bd2eba655e57d')
     version('1.6.0', commit='11baf1080d6f791439cd5d97357589d6451643d9')
     version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833')
diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py
index d67301b545..42d8a4d67c 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('2.24.0', commit='53095b534b7e6c80a33a67b5f2db0db8f00db902')
     version('2.22.0', commit='86250b637afa3a3463fac939b99c0402b47876ea')
     version('2.18.1', commit='956f0654e8e18882ba09305742401128c9c7d47d')
     version('2.12.0', commit='0fba3fe6e6a38504f9aadcd3dc95bb83d7e92498')
diff --git a/var/spack/repos/builtin/packages/r-biocversion/package.py b/var/spack/repos/builtin/packages/r-biocversion/package.py
index d7f3f6e097..89b214f947 100644
--- a/var/spack/repos/builtin/packages/r-biocversion/package.py
+++ b/var/spack/repos/builtin/packages/r-biocversion/package.py
@@ -14,8 +14,10 @@ class RBiocversion(RPackage):
 
     bioc = "BiocVersion"
 
+    version('3.15.2', commit='818ab03b6a3551993b712e3702126040f9fb7600')
     version('3.14.0', commit='aa56d93d0ea5dcdbf301f120502981740fd91e1e')
     version('3.12.0', commit='23b971963c6b73550a7e330dab5a046d58ce0223')
 
     depends_on('r@4.0.0:', type=('build', 'run'))
     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:')
diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py
index 67286cf3ef..c06c1ef1a2 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('2.52.0', commit='cf4932ac02686da45ea36ff5137fa63cead8860b')
     version('2.50.3', commit='83a519ac13d73dc545cb6aafde5f4b5001e9e08f')
     version('2.46.2', commit='90d6abfdfa04259006f7b47efb10271ada76aec1')
     version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68')
@@ -33,6 +34,7 @@ class RBiomart(RPackage):
     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:')
diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py
index 0080b1980d..e156ad6c19 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('1.24.0', commit='4e14692dbcc34c3bd51defd74c728df5de9d0829')
     version('1.22.0', commit='ab7c6411a038fec010baa72e663f362fd972cb34')
     version('1.18.0', commit='dc18859c139f4d76805adb6f01e199573cdd5a8b')
     version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a')
diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py
index e7a341eefe..a51fce5437 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('2.64.0', commit='c7ad3c7af607bc8fe4a5e1c37f09e6c9bf70b4f6')
     version('2.62.0', commit='53ed287e03d16fa523789af3131c60375ccf587f')
     version('2.58.0', commit='0ec1a5455d5e9eebd14b26228906bb04e2abb197')
     version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5')
@@ -26,6 +27,8 @@ class RBiostrings(RPackage):
     depends_on('r@2.8.0:', type=('build', 'run'))
     depends_on('r@3.5.0:', type=('build', 'run'), when='@2.50.2:')
     depends_on('r@4.0.0:', type=('build', 'run'), when='@2.62.0:')
+    # Older versions do not build with r@4.2:
+    depends_on('r@:4.1', type=('build', 'run'), when='@:2.62.0')
     depends_on('r-biocgenerics@0.15.6:', type=('build', 'run'))
     depends_on('r-biocgenerics@0.31.5:', type=('build', 'run'), when='@2.58.0:')
     depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@2.62.0:')
diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py
index eb16fed1b0..b30e734a65 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('1.44.0', commit='a8f05c56c27b278524033cb896a6c97f3ee0081c')
     version('1.42.0', commit='f1627b2b567471837daca6e763acfc3e13937461')
     version('1.38.0', commit='d0f3362e0ad0e90b4b1d3e47b13ed57907d03403')
     version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8')
diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py
index b510460deb..e1fafb94c4 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('1.64.0', commit='59cdebde613e9702985c003f699f4aea2b0f0e7b')
     version('1.62.0', commit='9b1859e11ffa082833f035a45274af6e4e83e863')
     version('1.58.0', commit='3a4926e03a7a1d7140a10c1b2bf6090808470145')
     version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b')
diff --git a/var/spack/repos/builtin/packages/r-bsseq/package.py b/var/spack/repos/builtin/packages/r-bsseq/package.py
index e636accfe9..c814ecf79c 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('1.32.0', commit='a0c1eacbc479c57bd836e885e162c28bbe08e115')
     version('1.30.0', commit='7eb5223e9ee02fd08a52be56eaa9316a67c0d66b')
     version('1.26.0', commit='fae32292687625012a2938a48c93df55ad4257b5')
     version('1.24.4', commit='8fe7a03')
diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py
index 674ffa2100..fd014d50bd 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('1.38.0', commit='06e2fa87b342d48793d0d2f1f7d94a95a6613995')
     version('1.36.0', commit='db50fcf7798c2eddfe48fd510d081dda82f2ee4e')
     version('1.32.0', commit='b7d39c2a6385ca217dceefc918b3ccd5c31bbaa0')
     version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa')
diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py
index 5d964d838f..0aae98c8be 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('2.62.0', commit='0fe801c0c443aebd5d4cefa8c30e4e7d0931b673')
     version('2.60.0', commit='55210d8c539474954d18cf913a219dce883eac2e')
     version('2.56.0', commit='ad478caa9d693dbc2770608e79dd852375b9a223')
     version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9')
diff --git a/var/spack/repos/builtin/packages/r-champ/package.py b/var/spack/repos/builtin/packages/r-champ/package.py
index ec9ed5724e..88f1679c19 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('2.26.0', 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 95ea37c1ef..686ed6c048 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('2.28.0', 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 fcda046de5..0604632139 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('1.46.0', 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 3f3a0e0f51..fb732f1423 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('4.4.1', commit='daad11fb80be2dd9b825e0b484815a0a2b1592a4')
     version('4.2.2', commit='4ebb9de8e03eedc971f54a57cf5bf1b250ed43d5')
     version('3.18.0', commit='064a6e612ce27e260e33af78b907bee4065ff821')
     version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2')
diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py
index 220bbd8ea7..e42b806c9b 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('1.32.0', commit='1c92f3d7f3dccf76ab7d54f286117b09bc470b8f')
     version('1.30.0', commit='e682f2a7c8ebb561c872cf51a58ba36eed341187')
     version('1.26.0', commit='e5e582da6feeae0618c4460f16ece724215e3b20')
     version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5')
diff --git a/var/spack/repos/builtin/packages/r-codex/package.py b/var/spack/repos/builtin/packages/r-codex/package.py
index 602af52c61..1f0c363080 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('1.28.0', commit='c707497bd93aa4a0516fcf3671a64997c28c9f67')
     version('1.26.0', commit='729fd10bd42d12edcedd65b5a8fb1579e5949718')
     version('1.22.0', commit='aa0ee4278111a46e0c790312b0526ba07aab22eb')
     version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc')
diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
index 59d902e7dc..f054149546 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('2.12.0', commit='8a5f060b06646f9d6a5032832ea72e3f183ca5d7')
     version('2.10.0', commit='170df82a1568e879e4019e0ff6feb0047851684f')
     version('2.6.2', commit='0383bada2c76dc3dde71cf6a625016b619aec4d3')
     version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4')
@@ -29,6 +30,7 @@ class RComplexheatmap(RPackage):
     depends_on('r-circlize@0.3.4:', type=('build', 'run'))
     depends_on('r-circlize@0.4.1:', type=('build', 'run'), when='@1.17.1:')
     depends_on('r-circlize@0.4.5:', type=('build', 'run'), when='@2.0.0:')
+    depends_on('r-circlize@0.4.14:', type=('build', 'run'), when='@2.12.0:')
     depends_on('r-getoptlong', type=('build', 'run'))
     depends_on('r-colorspace', type=('build', 'run'))
     depends_on('r-clue', type=('build', 'run'), when='@2.0.0:')
@@ -41,6 +43,7 @@ class RComplexheatmap(RPackage):
     depends_on('r-matrixstats', type=('build', 'run'), when='@2.6.2:')
     depends_on('r-foreach', type=('build', 'run'), when='@2.10.0:')
     depends_on('r-doparallel', type=('build', 'run'), when='@2.10.0:')
+    depends_on('r-codetools', type=('build', 'run'), when='@2.12.0:')
 
     depends_on('r-dendextend@1.0.1:', type=('build', 'run'), when='@1.14.0:1.17.1')
     depends_on('r-s4vectors@0.26.1:', type=('build', 'run'), when='@2.6.2')
diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py
index 6d0e585c46..4ade350e0f 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('1.70.0', commit='05dc046ecfddbc1eeadf77e8f3ec0ce054794437')
     version('1.68.0', commit='c2733534ef9d948e07ea654d1998a67ed8f7a98a')
     version('1.64.0', commit='35dbe620a21056b8f69890e6f9a7c320528d8621')
     version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb')
diff --git a/var/spack/repos/builtin/packages/r-decipher/package.py b/var/spack/repos/builtin/packages/r-decipher/package.py
index 03a6d2429d..35438953bc 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('2.24.0', commit='437e60005ab281bd836f47756a367795bc16755d')
     version('2.22.0', commit='45da5cab5869d83af797aa82b08ebcd24f5bdab3')
     version('2.18.1', commit='6a708421550e6705d05e2fb50a0f5ab4f9041cb0')
     version('2.12.0', commit='658ae23870383b25b96a03a18d4ecac228a2650f')
diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py
index 51a3a65e88..6817044ef5 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('0.22.0', commit='4a5afd117b189b40bd409c7aff60e09d41797472')
     version('0.20.0', commit='829b52916ec54bb4f1a3c6f06c9955f3e28b3592')
     version('0.16.1', commit='c95eba771ad3fee1b49ec38c51cd8fd1486feadc')
     version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a')
diff --git a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
index 767b9b2d2d..e9d7fea6c4 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('1.18.0', commit='50c9aab259b6e8f68abf44b78122662a41c8bf47')
     version('1.16.0', commit='d44a3d765769cb022193428a77af25bf19916be7')
     version('1.12.3', commit='2b3091dfa9b3bab914e3a4157182063714ba86ae')
     version('1.6.1', commit='4378d1898a403305a94b122c4f36d1215fa7708d')
diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py
index 22a0608a48..b5aebafcc6 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('1.36.0', commit='2800b78ae52c0600f7e603c54af59beed3a2ed17')
     version('1.34.0', commit='25d4f74be59548122ccfbe8687d30c0bae5cf49a')
     version('1.30.0', commit='f4b47b208ee26ab23fe65c345f907fcfe70b3f77')
     version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf')
diff --git a/var/spack/repos/builtin/packages/r-dexseq/package.py b/var/spack/repos/builtin/packages/r-dexseq/package.py
index c04d14a68a..b9579b459f 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('1.42.0', 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 b436ebc408..3a12379edd 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('1.38.0', commit='b4de83d354e974fdb7cb3526d029487f24aab670')
     version('1.36.0', commit='926baff6c75cb498945c5895f25cc143c907a357')
     version('1.32.0', commit='6949abab2462b2c09f7a0ca5b5cbf0c95a40ad16')
     version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f')
diff --git a/var/spack/repos/builtin/packages/r-dmrcate/package.py b/var/spack/repos/builtin/packages/r-dmrcate/package.py
index a1ee79369b..8b8050d8db 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('2.10.0', 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 5802a82266..c44ef069d3 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('1.70.0', commit='9595d0ad7c78af4ed568cbd210b894d3350eae0a')
     version('1.68.0', commit='08f039f58bc2f5ed2cc3117ae817dbac333002a6')
     version('1.64.0', commit='01650266ea7a4e5c600de545fe70a1103e79b2d8')
     version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23')
diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py
index 4e11126611..38d67408d6 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('3.22.0', commit='242ac1b746c44fbbf281fbe6e5e4424a8dc74375')
     version('3.20.1', commit='bf434f24d035217822cb1b0ab08a486b9a53edb4')
     version('3.16.0', commit='a534a4f2ef1e54e8b92079cf1bbedb5042fd90cd')
     version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3')
diff --git a/var/spack/repos/builtin/packages/r-dss/package.py b/var/spack/repos/builtin/packages/r-dss/package.py
index 266571a0b1..d0d8eb92ae 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('2.44.0', commit='b9f44106f139c93564dfb4afab50555d24a657ba')
     version('2.42.0', commit='33e87450fbb64bb3e321688ff613e83cd40efe48')
     version('2.38.0', commit='82e65b92e6e227f1f99620362db8b03059e07e98')
     version('2.36.0', commit='841c7ed')
@@ -25,7 +26,10 @@ class RDss(RPackage):
     version('2.32.0', commit='ffb502d')
 
     depends_on('r@3.3:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.44.0:')
     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-delayedarray', type=('build', 'run'), when='@2.36.0:')
+    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')
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index 0b04cabdef..8556b1c129 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('3.38.1', commit='e58bf52f34ec451096f593126922ad7e5d517f7e')
     version('3.36.0', commit='c7db03addfc42138a1901834409c02da9d873026')
     version('3.32.1', commit='b881d801d60e5b38413d27f149384c218621c55a')
     version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f')
diff --git a/var/spack/repos/builtin/packages/r-enrichplot/package.py b/var/spack/repos/builtin/packages/r-enrichplot/package.py
index 01adf64e87..cd3ef6df4b 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('1.16.1', commit='cff77b622b2312be546714ec437aa4bc585bac87')
     version('1.14.1', commit='ccf3a6d9b7cd9cffd8de6d6263efdffe59d2ec36')
     version('1.10.2', commit='77ee04f60a07cc31151f8f47f8ee64f3a43c9760')
     version('1.4.0', commit='6ffe5d9c5dbe5cbea29f2e0941595475bbbcea0e')
diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py
index 2de8e6a9e4..92876b5a4c 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('2.20.1', commit='e547d184730cfe5e65f59e4f3512395fb1cdba1a')
     version('2.18.3', commit='e2fcfc0c7700110df070a171d2d542b37ec098f3')
     version('2.14.0', commit='c7150519ed4ef38e5eac1043209863dbc7be43a1')
     version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0')
@@ -32,6 +33,7 @@ class REnsembldb(RPackage):
     version('2.2.2', commit='d71610e58aed88dbbe6a74e7a8ddfb7451398060')
     version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
 
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.20.1:')
     depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
     depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
     depends_on('r-genomicranges@1.31.18:', type=('build', 'run'), when='@2.4.1:')
diff --git a/var/spack/repos/builtin/packages/r-exomecopy/package.py b/var/spack/repos/builtin/packages/r-exomecopy/package.py
index dc6ee42e82..4f287ae29f 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('1.42.0', commit='ba0979cf5fbdefed841022f2dc0604941315c1b8')
     version('1.40.0', commit='ebde39be67baace2c326359421fd17f4a02fd4fe')
     version('1.36.0', commit='cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26')
     version('1.32.0', commit='c9a884427d91b6d62ddc16a939bd808e389d3ea6')
diff --git a/var/spack/repos/builtin/packages/r-experimenthub/package.py b/var/spack/repos/builtin/packages/r-experimenthub/package.py
index 0ec999a5c0..7bc44a9722 100644
--- a/var/spack/repos/builtin/packages/r-experimenthub/package.py
+++ b/var/spack/repos/builtin/packages/r-experimenthub/package.py
@@ -18,11 +18,13 @@ class RExperimenthub(RPackage):
 
     bioc = "ExperimentHub"
 
+    version('2.4.0', commit='bdce35d3a89e8633cc395f28991e6b5d1eccbe8e')
     version('2.2.1', commit='4e10686fa72baefef5d2990f41a7c44c527a7a7d')
     version('1.16.1', commit='61d51b7ca968d6cc1befe299e0784d9a19ca51f6')
 
     depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
     depends_on('r-annotationhub@2.19.3:', type=('build', 'run'))
+    depends_on('r-annotationhub@3.3.6:', type=('build', 'run'), when='@2.4.0:')
     depends_on('r-biocfilecache@1.5.1:', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-biocmanager', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py
index 3bf7e9248b..3e14210373 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('1.22.0', commit='e4e203aa64faa984e0406fed5d87a422d9df92f2')
     version('1.20.0', commit='b704f81687dc16afdaafc6d30108c62a067856b2')
     version('1.16.0', commit='9d9df596c7e160afa18e067b7637cfc465494318')
     version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3')
diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py
index edc10e7b84..653450eb51 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('2.68.0', commit='c14063ff5490fac8d60530826613d728e68b3d66')
     version('2.66.0', commit='ba134b392def89d36b5639a187e0c25a4353457b')
     version('2.62.0', commit='b91bdf5bf4e875defedb4d4e3e1e75867773287a')
     version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224')
diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
index 1bfe72c824..f6f964d58c 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('1.32.0', commit='06f2097cc10b1888739f86e635383a0f2ee7e208')
     version('1.30.0', commit='d27dde6a70bb2295f5bbc8961152b45ccee7a652')
     version('1.26.1', commit='bd180b21b1ace120035f0da255cbf6f13088f069')
     version('1.20.0', commit='b1fbaba0a5ace3dc45daecc85168651cd85dce00')
diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py
index 306752ba8a..bd2f0f2adf 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('1.78.0', commit='2f574388971641d3a71858f5c34606c04fcd2ba2')
     version('1.76.0', commit='8d630fd25f0d2a4101e05e123c3959591203a7ea')
     version('1.72.1', commit='b01b00a766982ef7d80b90a252085c8c4f085e1b')
     version('1.72.0', commit='8cb0b2e73531a417d53e5625bcf436265cdbe101')
@@ -22,6 +23,7 @@ class RGenefilter(RPackage):
     version('1.60.0', commit='c98f695253c330a9380b2b4ffa27f3b7d66773e4')
     version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2')
 
+    depends_on('r-biocgenerics', type=('build', 'run'), when='@1.78.0:')
     depends_on('r-biocgenerics@0.31.2:', type=('build', 'run'), when='@1.68.0:')
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-annotate', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py
index 330fa300e4..f91a8b0472 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('1.32.0', commit='eaa193a2c6d502c6d59113fd42f66761b8730594')
     version('1.30.0', commit='b3cc755f1ffcbb2eacd9ea45e11f39f1639782b1')
     version('1.26.0', commit='2724715ae23a6647d1c0c6e934720aad9377d65e')
     version('1.20.0', commit='70a1abed00ee68f7bfa07c42c011f9edae9915e4')
diff --git a/var/spack/repos/builtin/packages/r-genemeta/package.py b/var/spack/repos/builtin/packages/r-genemeta/package.py
index 25b8b7a24d..cdb597022c 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('1.68.0', commit='4213c0205d477660195300a0aa9751972f86bf91')
     version('1.66.0', commit='c16eb09492f08f6cc0f253fafa3fa5dce35dcdba')
     version('1.62.0', commit='eb4273ff5867e39592f50b97b454fa5e32b4a9bf')
     version('1.56.0', commit='cb2c9e353d34ea9f3db06cb236c7a89674f2682d')
diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py
index e1266658f3..f3d146dab0 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('1.74.0', commit='ca819565829eac7a9a98e3cafafd6c06a466fddf')
     version('1.72.0', commit='57a1d830ba7844fda5236af0153d5b5587634f96')
     version('1.68.0', commit='f1fea7e468fb24fdfa93ef4493600a4d8d183f69')
     version('1.62.0', commit='1fbaddde11014b453b131860409f89cd784e8e48')
diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py
index 002fddc333..5959844b36 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('1.18.0', commit='f16b25ef50978a4a497eb2f911e21f2e839fa33c')
     version('1.16.0', commit='5543b1b883d3a1c92e955de6668444278edc2bdf')
     version('1.12.0', commit='14289cee9bed113ab35ba03bcaac4a30e5784497')
     version('1.6.0', commit='d6a49182e098342afe77f01c322dfc7b72450502')
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index 85a1218690..667ad29936 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('1.32.2', commit='2e40af38f00ee86d2c83d140e234c1349baa27de')
     version('1.30.1', commit='bf8b385a2ffcecf9b41e581794056f267895863d')
     version('1.26.2', commit='96dd27a7e3ef476790b1475aab50dbbed7df67a2')
     version('1.20.0', commit='ea771e3b429ef17fb912fb37333556c6f77f2265')
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
index 8b3d2d86b9..f7a00311b8 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
@@ -13,6 +13,9 @@ class RGenomeinfodbdata(RPackage):
     bioc = "GenomeInfoDbData"
     url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz"
 
+    version('1.2.8',
+            url='https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz',
+            sha256='576750330a011c1eccb47c7154ca1b40ae4cd473fd7973f6c2955237a0729eb4')
     version('1.2.7',
             url='https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz',
             sha256='217cbad0dd3ed8f0da6b21c7d35df5737bcbd21e317ca71d2fb6ec4c316b1987')
diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
index a186f8308a..785c0ac4f1 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('1.32.0', commit='7a660a914a04e2eb0758082b6f64c4124a887ef3')
     version('1.30.0', commit='2d2c5fce3529c2962fdcefd736d8b7f7c0ec2d54')
     version('1.26.0', commit='6c74c74ee53efcd880171126366fee4bd72357bc')
     version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd')
diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
index 344645024f..089df084dc 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('1.48.3', commit='b0ddea0e101e3861928f3ad353348df047d90382')
     version('1.46.4', commit='d3ab6fd069624904ce7fcdf75dad884473f97975')
     version('1.42.1', commit='2e82891974138b0e976799d64a8938f0be61284d')
     version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555')
@@ -28,6 +29,7 @@ class RGenomicfeatures(RPackage):
     version('1.30.3', commit='496bbf81beebd7c934b8d3dcea001e3e4a7d7dee')
     version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
 
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@1.48.3:')
     depends_on('r-biocgenerics@0.1.0:', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
     depends_on('r-s4vectors@0.17.29:', 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 e40d4257d6..7b49c83ec8 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('1.48.0', commit='2bce60814db7c20949892587740fb484aa435978')
     version('1.46.1', commit='e422642f64815cdfee8fc340681ad87a7eafc3bb')
     version('1.42.0', commit='32baca734b599d60fa13bdbe31c5712e648f538d')
     version('1.36.1', commit='418e7e5647dd54d81b804455ddfcbc027fd0164a')
diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py
index 46a034475c..5504ff463d 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('2.64.2', commit='e9b7f075a4a6a952660443ca93ed392d7a4fd6d7')
     version('2.62.2', commit='1966c108fe8a58ac39ef53c3c452fd160efa526e')
     version('2.58.0', commit='6332ca3791ddcfb233b9ad75b5904b3d60f49b93')
     version('2.52.0', commit='3059331eb82ad4947c2d1bef86ff9526e70af643')
@@ -25,7 +26,6 @@ class RGeoquery(RPackage):
     version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
 
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r-httr', type=('build', 'run'))
     depends_on('r-readr', type=('build', 'run'), when='@2.46.15:')
     depends_on('r-readr@1.3.1:', type=('build', 'run'), when='@2.50.5:')
     depends_on('r-xml2', type=('build', 'run'), when='@2.46.15:')
@@ -33,8 +33,10 @@ class RGeoquery(RPackage):
     depends_on('r-data-table', type=('build', 'run'), when='@2.62.2:')
     depends_on('r-tidyr', type=('build', 'run'), when='@2.46.15:')
     depends_on('r-magrittr', type=('build', 'run'), when='@2.46.15:')
-    depends_on('r-r-utils', type=('build', 'run'), when='@2.62.2:')
     depends_on('r-limma', type=('build', 'run'), when='@2.46.15:')
+    depends_on('r-curl', type=('build', 'run'), when='@2.64.2:')
+    depends_on('r-r-utils', type=('build', 'run'), when='@2.62.2:')
 
     depends_on('r-xml', type=('build', 'run'), when='@2.42.0')
     depends_on('r-rcurl', type=('build', 'run'), when='@2.42.0')
+    depends_on('r-httr', type=('build', 'run'), when='@:2.62.2')
diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py
index 8352efdc57..30287b9f77 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('1.44.0', commit='cb21284a9803917fa76e116adfc456525c95f660')
     version('1.42.0', commit='3540047ef018957d59fba8af7d3c58e4659f8e26')
     version('1.38.0', commit='c39c51993f419cfc2f094e664477f25f5212a242')
     version('1.32.0', commit='04bd12fbe0b1c5c6b721a5f927e1352765f9bf88')
diff --git a/var/spack/repos/builtin/packages/r-ggtree/package.py b/var/spack/repos/builtin/packages/r-ggtree/package.py
index 244d49bf1a..9a6db88855 100644
--- a/var/spack/repos/builtin/packages/r-ggtree/package.py
+++ b/var/spack/repos/builtin/packages/r-ggtree/package.py
@@ -16,19 +16,23 @@ class RGgtree(RPackage):
 
     bioc = "ggtree"
 
+    version('3.4.0', commit='23f08a3da1829d1bbb6827ed1c4cf878daa4b539')
     version('3.2.1', commit='d3747e636fe1a6a9e09b56a3a3899208ebd05547')
 
     depends_on('r@3.5.0:', type=('build', 'run'))
     depends_on('r-ape', type=('build', 'run'))
     depends_on('r-aplot@0.0.4:', type=('build', 'run'))
+    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-magrittr', type=('build', 'run'))
     depends_on('r-purrr', type=('build', 'run'))
     depends_on('r-rlang', type=('build', 'run'))
     depends_on('r-ggfun', type=('build', 'run'))
+    depends_on('r-ggfun@0.0.6:', type=('build', 'run'), when='@3.4.0:')
     depends_on('r-yulab-utils', type=('build', 'run'))
     depends_on('r-tidyr', type=('build', 'run'))
     depends_on('r-tidytree@0.2.6:', type=('build', 'run'))
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py
index e631d220a6..22e3c8b4e3 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('2.6.0', commit='23220d9b90476059aab035b5de11b7ce04b331c8')
     version('2.4.0', commit='caa270e44ec6994035d2e915c0f68a14ccbb58db')
     version('2.0.0', commit='40bebaa79e8c87c5686cff7285def4461c11bca9')
     version('1.12.0', commit='d02174239fe0b47983d6947ed42a1a53b24caecb')
diff --git a/var/spack/repos/builtin/packages/r-globaltest/package.py b/var/spack/repos/builtin/packages/r-globaltest/package.py
index ef67d0e2b9..e3d9ee61e0 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('5.50.0', 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 bdc61b8e4c..accc8a7f67 100644
--- a/var/spack/repos/builtin/packages/r-go-db/package.py
+++ b/var/spack/repos/builtin/packages/r-go-db/package.py
@@ -13,8 +13,11 @@ class RGoDb(RPackage):
     Ontology assembled using data from GO."""
 
     bioc = "GO.db"
-    url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz"
+    url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz"
 
+    version('3.15.0',
+            sha256='bac91d73c57f206fa5bc4a501a2aaf61b365cf411181ce44353370cdbc132d99',
+            url='https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GO.db_3.15.0.tar.gz')
     version('3.14.0',
             sha256='45d0a681a662667d45b2472d160b72f7058ad0a28dd0ca24742e11ddfd87d8e7',
             url='https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GO.db_3.14.0.tar.gz')
@@ -29,3 +32,4 @@ class RGoDb(RPackage):
     depends_on('r-annotationdbi@1.37.4:', type=('build', 'run'))
     depends_on('r-annotationdbi@1.51.3:', type=('build', 'run'), when='@3.12.1:')
     depends_on('r-annotationdbi@1.55.1:', type=('build', 'run'), when='@3.14.0:')
+    depends_on('r-annotationdbi@1.57.1:', type=('build', 'run'), when='@3.15.0:')
diff --git a/var/spack/repos/builtin/packages/r-gofuncr/package.py b/var/spack/repos/builtin/packages/r-gofuncr/package.py
index 62921ac64d..62c0d992b2 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('1.16.0', commit='603fc79e13b58ec4612b6092f37d2450078dbfe1')
     version('1.14.0', commit='b3d445acf95851241d1fdb673d108ee115bdc17b')
     version('1.10.0', commit='51b01a2b9afa03fde2e1628036096cbeafaa2ef4')
     version('1.4.0', commit='2f633dc28e3faeddc5346fcdcadf1c29e3fcf709')
diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py
index 394fc244aa..b21842c3b9 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('2.22.0', commit='fd74aeba2371ebf9db0595cf18674441bdac9618')
     version('2.20.0', commit='fa82442aaa4ad1a8dacc05ee2c54f5e5e770a794')
     version('2.16.1', commit='92f1d567f3584fe488f434abce87c2e1950081c0')
     version('2.10.0', commit='5db1ecbf2f8d870430d6e587609327d05ba3ad7b')
diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py
index 87eaa1bcdf..af50ec9778 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('1.48.0', commit='d077fda56986cc7218a88f7db37a42412b227025')
     version('1.46.0', commit='1fb5626cc80f595499af511a830322ed12bbe144')
     version('1.42.0', commit='8164b90e7505bbc1035105fdc15219c764ef8b8d')
     version('1.36.0', commit='26c9f7de18889afeee1b571ca1c4ab4d2877ab80')
diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py
index b3fd2e9e64..0f50b56c24 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('2.62.0', commit='217db032272010ebb8fe3af4647153428f42cd47')
     version('2.60.0', commit='a20055cc1c04a91b0291a918dadd9ea912c187ce')
     version('2.56.0', commit='8f988c3b4b1ce7e05626aae8956004c7bbdd6f3a')
     version('2.50.0', commit='ee13f84341988d537a5485dcdcfb71f69e6e4930')
diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py
index 815b00fec1..6ed3d59c4f 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('1.74.0', commit='4af608a5d9e1de33fda6ae28fb73bff9272ee296')
     version('1.72.0', commit='7afbd26ecd76e55e6bbd74915a561d7a9b15f907')
     version('1.68.0', commit='03ad9ed088095605e317510b8234501318994e94')
     version('1.62.0', commit='95223bd63ceb66cfe8d881f992a441de8b8c89a3')
diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py
index 9d7e00c56e..e85980e0bf 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('1.58.0', commit='7de04442fb1ab63ffde29f4e3daf13ad32e90bdb')
     version('1.56.0', commit='ee7c3ca4ad0f1f3e9b9162db1515413802860ecc')
     version('1.52.1', commit='257dfccbc5b507d82099fac6b06bb03825e995e8')
     version('1.46.0', commit='edce83a9256a0c03206c2bce7c90ada0d90f6622')
diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py
index 044027e4cc..e1c4b5afc9 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('1.28.0', commit='d770a7b3441e4003869c88cfd8e21fd6508b86c4')
     version('1.26.0', commit='f2c3121b31ad1b422e2cf503435d0590e903ff3f')
     version('1.22.0', commit='c071c5631f3dedda212aed87d9c02954b5ed6611')
     version('1.16.1', commit='a9003ededc8f2a48c78d4545e2f214023c13a7da')
diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py
index 0678ee0391..71007a95c4 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('1.40.1', commit='d21843710cd05135353de5cd4ce4d35cdd333b7c')
     version('1.38.3', commit='c4b352a16455a5744533c511e59354977814cb9e')
     version('1.34.0', commit='445fadff2aedd8734580fa908aa47ff1216a8182')
     version('1.28.3', commit='20b9825af144cfc888629c34aa980b5bbd65bf86')
@@ -29,6 +30,7 @@ class RGviz(RPackage):
     depends_on('r@2.10.0:', type=('build', 'run'))
     depends_on('r@4.0:', type=('build', 'run'), when='@1.34.0:')
     depends_on('r@4.1:', type=('build', 'run'), when='@1.38.3:')
+    depends_on('r@4.2:', type=('build', 'run'), when='@1.40.1:')
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
     depends_on('r-iranges@1.99.18:', type=('build', 'run'))
     depends_on('r-genomicranges@1.17.20:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py
index 4d671c682a..f32891fa09 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('1.24.1', commit='d002fe70c84baaadb62058ce467d6c1ea032d8f5')
     version('1.22.1', commit='b3f091fbc159609e8e0792d2bf9fbef52c6ceede')
     version('1.18.0', commit='d5bd55d170cb384fdebdf60751e1e28483782caa')
     version('1.12.3', commit='21c6077f3f789748a18f2e579110576c5522e975')
diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py
index e924415f7e..c6ce4f4124 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('1.68.0', commit='7d53b5050f4ebe0a7007c02b76e93498195da3a4')
     version('1.66.0', commit='e9c47336df6409006622818f541f258103163a39')
     version('1.62.0', commit='a286bbb70289e9f3cdf41407d52e5976bd6ed11e')
     version('1.56.0', commit='f8b977fe068f15ecea49d30e77a871a35afcb97b')
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 417bb29cbf..2da13d126c 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('1.32.0', commit='a15602253e675a104303627957653a08876d8d7c')
     version('1.30.0', commit='ba1296b4aafc287dea61f5f37c6c99fd553e52a2')
     version('1.26.0', commit='fffe6033cc8d87354078c14de1e29976eaedd611')
 
diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py
index f0be63afc3..48b0703a57 100644
--- a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py
@@ -16,7 +16,13 @@ class RIlluminahumanmethylation450kannoIlmn12Hg19(RPackage):
     bioc = "IlluminaHumanMethylation450kanno.ilmn12.hg19"
     url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz"
 
-    version('0.6.0', sha256='249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15')
+    version('0.6.1',
+            url="https://bioconductor.org/packages/3.15/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1.tar.gz",
+            sha256='3627d75a6303f4d307fa6daf0c5afd57649c60a268b3d4be7e8ac8edc4b1e288')
+    version('0.6.0',
+            url="https://bioconductor.org/packages/3.4/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz",
+            sha256='249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15')
 
     depends_on('r@3.3.0:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@0.6.1:')
     depends_on('r-minfi@1.19.15:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py
index 97a036f4d8..0f377b6573 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('0.38.0', commit='b16231b7417b4d6e9cff1e2724ed3529871dff92')
     version('0.36.0', commit='c5b6e9164b73c650c0a9f055f4fd0580ac64fae7')
     version('0.32.0', commit='e1322c781dd475a5e8ff6c0422bebb3deb47fa80')
     version('0.26.0', commit='40c2f94df2ea64d745d25aadd2bfb33ac3e02f81')
diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py
index 3b99037c58..796d30eb3d 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('1.70.0', commit='970b2c28d908e26369b01dddf36dab2f8916d4af')
     version('1.68.0', commit='fa4e4d883e609633c49d865a44acd6a79954eaac')
     version('1.64.0', commit='31a5636f4dfbb1fd61386738786a0de048a620c2')
     version('1.58.0', commit='dc17173df08d965a0d0aac9fa4ad519bd99d127e')
diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
index 7a34e88252..b7c855e138 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('1.34.0', commit='fafbb13a42bb7549f17aa08cdb0e51728c5e825e')
     version('1.32.0', commit='0f88b2ac3689d51abb6ac0045b3207ca77963a5a')
     version('1.28.0', commit='a74c02c971c4f9c7086e14abd23f1a4190da4599')
     version('1.22.0', commit='4ce3cde1dabc01375c153ad614d77a5e28b96916')
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
index d9d9e25d77..e3bfccb6ff 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('2.30.0', commit='9b5f3ca12812fb76c23b1550aa3a794384384d9b')
     version('2.28.0', commit='d85ee908a379e12d1e32599e999c71ab37c25e57')
     version('2.24.1', commit='6c61fddf4c5830f69a0f7f108888c67cd0a12b19')
     version('2.22.2', commit='8c5e991')
@@ -42,3 +43,4 @@ class RIranges(RPackage):
     depends_on('r-s4vectors@0.25.14:', type=('build', 'run'), when='@2.22.2:')
     depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@2.24.1:')
     depends_on('r-s4vectors@0.29.19:', type=('build', 'run'), when='@2.28.0:')
+    depends_on('r-s4vectors@0.33.3:', type=('build', 'run'), when='@2.30.0:')
diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py
index 0ce55ae88e..b11208a35a 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('1.56.0', commit='e95cbf9f8a095d59b78a053463191b89c00d5ded')
     version('1.54.0', commit='135ee3dad30ca208e21acd0a2d81120b74b64079')
     version('1.50.0', commit='3335e85cdba264c04e6e36378578cf6c83a30eb8')
     version('1.44.0', commit='2c24e8ec53fe34c72ea65f34e3c09905ab2e5c62')
diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py
index 3967797795..27e292de8f 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('1.36.0', commit='591818bbc9195bfd0657cf4f5c7c771ea7f86830')
     version('1.34.0', commit='2056750dc202fa04a34b84c6c712e884c7cad2bd')
     version('1.30.1', commit='fd9970ea9df117d625257b8c6351cf85098cfbc1')
     version('1.24.1', commit='bbc3ef476e02147aad8e1f33178136cc797c1b3f')
diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py
index 82e25741da..b391aadee3 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('3.52.1', commit='c81c539a217ac1cf46e850f8a20266cecfafed50')
     version('3.50.0', commit='657b19bbc33c5c941af79aeb68967bf42ea40e23')
     version('3.46.0', commit='ff03542231827f39ebde6464cdbba0110e24364e')
     version('3.40.6', commit='3ae0767ecf7a764030e7b7d0b1d0f292c0b24055')
diff --git a/var/spack/repos/builtin/packages/r-lumi/package.py b/var/spack/repos/builtin/packages/r-lumi/package.py
index c557ec0364..dfb86edf30 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('2.48.0', commit='1f988ffe04d2c0707b2202d2074d02b679a3204b')
     version('2.46.0', commit='a68932c17a61c99e58ebbd8008d078bec6adb4e7')
     version('2.42.0', commit='a643b3ba46fee951b8566ddd8216af7e6c92f6f6')
     version('2.38.0', commit='321d480d44ce9a0c02ce5af1bddc1f549abdea59')
diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
index 9756aea25d..9fa7443e4c 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('1.72.0', commit='85c89688e6b6e8bff46b92cbeba49e38c510492e')
     version('1.70.0', commit='82ecd0fa8ac401e4ac8f1e9139556d2be4a3c4f3')
     version('1.66.0', commit='02aa975d543089f5495cb3b4e8edbcf0ff05148a')
     version('1.60.0', commit='900ece3ecd7a0ade9f8a0374e5a03def4e079cb3')
diff --git a/var/spack/repos/builtin/packages/r-marray/package.py b/var/spack/repos/builtin/packages/r-marray/package.py
index 6b911753a2..05a78e529c 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('1.74.0', 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 845f5b4187..35a87b57b6 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('1.8.0', commit='e4cc34d53bcfb9a5914afd79fda31ecd5037a47a')
     version('1.6.0', commit='4588a60e5cc691424c17faa281bdd7d99d83ec34')
     version('1.2.1', commit='abcc9ca0504e0b915cd7933a3169a8e9e5bd2fe9')
 
diff --git a/var/spack/repos/builtin/packages/r-methylumi/package.py b/var/spack/repos/builtin/packages/r-methylumi/package.py
index c69aa2df5b..c0cf02bc69 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('2.42.0', commit='73e9c7fe1252c4ca20dc7b4e58decf04bf22d5e0')
     version('2.40.1', commit='211039225ca6fca9af75b8266f656161912ce10f')
     version('2.36.0', commit='5fb0b609f9c9181ac99f902745958774e5489606')
     version('2.32.0', commit='e2a29c1b214c0d43c7325d176f9ce41dcf8e2f9d')
diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py
index cf361e76b3..268073e1aa 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('1.42.0', commit='30fc7059460a9ec0be734fc26e608426ca9f5614')
     version('1.40.0', commit='17fa2b5d6cdbef6cbfb690242bd3f660731431f1')
     version('1.36.0', commit='94301da343226be7cd878c2a6c1bb529564785d6')
     version('1.30.0', commit='a4c28e9388fe3b35e7d21a9669e39250ed6dcbcd')
diff --git a/var/spack/repos/builtin/packages/r-missmethyl/package.py b/var/spack/repos/builtin/packages/r-missmethyl/package.py
index 848c6c2519..025524f04a 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('1.30.0', 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 30c2f02c5a..cb903d0cb6 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('1.76.0', commit='935323d8ce1e4bbf41844a1f9b6c946c5a30c673')
     version('1.74.0', commit='5ee73b6491b1d68d7b49ddce6483df98ad880946')
     version('1.70.0', commit='7b076c3e85314dd5fd5bd8a98e8123d08d9acd3b')
     version('1.64.1', commit='0b081112d87771248bc33b3b82d5ca4685f986a1')
diff --git a/var/spack/repos/builtin/packages/r-mscoreutils/package.py b/var/spack/repos/builtin/packages/r-mscoreutils/package.py
index 7138fc5f21..b91d59dd61 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('1.8.0', commit='8b7e2c31009276aad0b418ba5cdfc94d03e1973e')
     version('1.6.0', commit='9ed95b2d20dacaa83567fadd04349c81db9127ef')
 
     depends_on('r@3.6.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py
index 72c90f7603..01869ef1c4 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('2.22.0', commit='4f6e5767eee91b2105781b494fcabcfed16eba2d')
     version('2.20.4', commit='c86ac8b341832f2b577f2153258c1abf064e6448')
     version('2.16.1', commit='4d88b4edd1af59474462b1b06ad0ec5831f3a878')
     version('2.10.1', commit='4d5899bc9c714f0b1a70cddd537cd4621b2b53b0')
@@ -33,10 +34,12 @@ class RMsnbase(RPackage):
     depends_on('r-mzr@2.15.1:', type=('build', 'run'), when='@2.8.3:')
     depends_on('r-mzr@2.17.3:', type=('build', 'run'), when='@2.10.1:')
     depends_on('r-mzr@2.19.6:', type=('build', 'run'), when='@2.16.1:')
+    depends_on('r-mzr@2.29.3:', type=('build', 'run'), when='@2.22.0:')
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-protgenerics@1.5.1:', type=('build', 'run'))
     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-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 97ab070efe..db507f1dc6 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('2.52.0', commit='00cfc9beb6d063c2b04fc83495a76824f8a33a64')
     version('2.50.0', commit='1de96649a942b115d3d554394514745e86eb3fd3')
     version('2.46.0', commit='c4dd27b333c80313a88668b59d0299988c6478a2')
     version('2.40.0', commit='5f00017c2d3a31e05e1cfe06d9f7afdee19f8473')
diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py
index 85973c0101..e68992ac45 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('1.34.0', commit='bef64db159a0a4d241ba2ba271f70266c1522b2b')
     version('1.32.0', commit='d4146385b54f4d8361e23fc2c2aef79e952f4730')
     version('1.28.0', commit='cd006631c8222ce5b4af0577a7401b39cc58fd9c')
     version('1.22.0', commit='382d9cf11f0cba996911a9d79e193d28f3ac6042')
diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py
index d7a1c9cb65..91c48b2a8f 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('2.30.0', commit='563ae755cfc7de1ac8862247779182b7b3aebdcc')
     version('2.28.0', commit='bee7d6fb5f99e1fab5444ae1ad27b0bc6e83be9e')
     version('2.24.1', commit='e1d4de8761e6729fd45320d842691c8fe9116b7b')
     version('2.18.1', commit='13f9f9b1149859c3e29cfce941d958cc4f680546')
@@ -27,6 +28,7 @@ class RMzr(RPackage):
     version('2.12.0', commit='f05eb27ae31c3d019cca10fc3b9ee513cbcdfc5a')
     version('2.10.0', commit='a6168b68e48c281e88de9647254a8db1e21df388')
 
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@2.30.0:')
     depends_on('r-rcpp@0.10.1:', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics@0.13.6:', type=('build', 'run'))
@@ -34,6 +36,7 @@ class RMzr(RPackage):
     depends_on('r-protgenerics@1.9.1:', type=('build', 'run'), when='@2.12.0:')
     depends_on('r-protgenerics@1.17.3:', type=('build', 'run'), when='@2.24.1:')
     depends_on('r-ncdf4', type=('build', 'run'), when='@2.16.2:')
-    depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-rhdf5lib@1.1.4:', type=('build', 'run'), when='@2.14.0:')
     depends_on('gmake', type='build')
+
+    depends_on('r-zlibbioc', type=('build', 'run'), when='@:2.28.0')
diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
index 6d5f532881..cd3d1365e3 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('1.58.0', commit='5544e937913bb0df54c66d738d279c38efeb30cd')
     version('1.56.0', commit='6e6c7b4ba54095d1d3c44c081839f57af9261cbf')
     version('1.52.0', commit='7995efbd2d26b8fa950830d62db92bdaf5cbeeea')
     version('1.46.0', commit='325684f66fc92f778098f24bcfbef0ce3da9717c')
diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py
index a853cda294..0e1f6b0b6f 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('1.38.0', commit='2ca01830a6ffcd0c0018d2bdbd3de8b4df716771')
     version('1.36.0', commit='3e7a90d248ff09f05ccd381ff921e12373a4b330')
     version('1.32.0', commit='c8100c4fea17bf1b10d4efacc73a7e2866d649e3')
     version('1.26.0', commit='495b4a8f8264d06d827537d43b3c6cc705244bb5')
diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py
index 95d647a073..ab507d1320 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('1.36.0', commit='4f6be090a4089b5259d8e796d62f9830e2d63943')
     version('1.34.0', commit='a8788902a3bb047f8ee785966e57f84596076bbd')
     version('1.30.1', commit='a6a32395db408798cb076894678e90148bae6bf4')
     version('1.24.0', commit='e4401c1425c980ce2e6e478a4602a9f6d36ccd8d')
diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py
index e130a9fcf3..1a7334565a 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('1.88.0', commit='02fb58d6fe35579b86fb2ebd2eaf92e6b53444d2')
     version('1.86.0', commit='9419cfa18c18dfbd1e1194127fd120ab456c3657')
     version('1.82.0', commit='d500b3363308f1f8ca70625c5cd10cce59b27641')
     version('1.76.0', commit='5db995330ced37dfd5ddad6ad1d90b4815d3127a')
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 623956c46f..f540cd371e 100644
--- a/var/spack/repos/builtin/packages/r-pfam-db/package.py
+++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py
@@ -13,8 +13,11 @@ class RPfamDb(RPackage):
     public repositories."""
 
     bioc = "PFAM.db"
-    url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz"
+    url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz"
 
+    version('3.15.0',
+            sha256='e7036a5f76779ab6e8a32eb659c54f52426c4824dee02903cffd85bed372720f',
+            url='https://bioconductor.org/packages/3.15/data/annotation/src/contrib/PFAM.db_3.15.0.tar.gz')
     version('3.14.0',
             sha256='25c1915079e8f93d04e2cc1ab791f7f47813aaab5ac394feaf57520bb292d616',
             url='https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PFAM.db_3.14.0.tar.gz')
@@ -33,3 +36,4 @@ class RPfamDb(RPackage):
     depends_on('r-annotationdbi@1.47.1:', type=('build', 'run'), when='@3.10.0:')
     depends_on('r-annotationdbi@1.51.3:', type=('build', 'run'), when='@3.12.0:')
     depends_on('r-annotationdbi@1.55.1:', type=('build', 'run'), when='@3.14.0:')
+    depends_on('r-annotationdbi@1.57.1:', type=('build', 'run'), when='@3.15.0:')
diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py
index 5be8fd3421..8cec6beea8 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('1.40.0', commit='20bb27d5e6e0d4368978a15671b829990b1f4568')
     version('1.38.0', commit='1e2409a6ed3c23e308275098c2dc9fdba9d5e5f6')
     version('1.34.0', commit='cbed93ead5528fe9024d646c597dab9fc95952d3')
     version('1.28.0', commit='a86ed1e0a650fdf80bee5a0a5a82aaa5a276178d')
diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
index f7a4619b7e..f18061212c 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('1.58.0', commit='2995e3e1a8f428a80aee200db42ee44743d893f6')
     version('1.56.0', commit='8f3272219507aa85e0c876fb434dc3b926c22c5d')
     version('1.52.1', commit='91de4ab67315dc2af68554ae3c48823f4b1ea8ac')
     version('1.46.0', commit='8cfc3938c1b08424587f437ed6cd2ec43512500e')
diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py
index 29d96a0617..c30542230c 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('1.28.0', commit='cfcd0a9ebd642515764ba70c5c4e9c2a0f2f07ac')
     version('1.26.0', commit='2033289ab928034b86c321e56c37e502e557c7a1')
     version('1.22.0', commit='2bb3011fb0d79536e1c50251084a7057004449c6')
     version('1.16.0', commit='960a5fdc586898513b5ae9c48fffba5c5d703723')
diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py
index 713e129f4b..72e171c501 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('1.30.0', commit='e756c439cdc5a6fb4d7879aff56a8368475513b5')
     version('1.28.0', commit='109e7452a349f273e10d2ffb79d5624260b67dd5')
     version('1.24.0', commit='c7c0180292156a01722d91b353da44324e72d68f')
     version('1.18.0', commit='f6553c2296289eed31e4b2f32a082e990bdb8359')
diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py
index a8f63c3e3c..e9837c0abd 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('2.28.0', commit='aaa62d5ab5a960e0a626928abaf5b3a5c5f73374')
     version('2.26.0', commit='6d7410d4b8673bcf9065e054670c1fbcb917a27e')
     version('2.22.0', commit='b4bde8198252737b287fd7f9a4ed697f57fad92c')
     version('2.16.0', commit='5efbe20ef522a45a7a04b681f72bb9a12e2747ae')
diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py
index 0a55c3d7a4..d699f24ac8 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('1.72.0', commit='a86f3102f2795e1ffb530bb061247e3a42ca22f7')
     version('1.70.0', commit='9cfd5fdad4f1f438ff748317f32e822aede8921b')
     version('1.66.0', commit='bf0c111dbc231de6d3423c28e115b54fb010e1ea')
     version('1.60.0', commit='ef24c17c411659b8f030602bd9781c534d6ec93b')
diff --git a/var/spack/repos/builtin/packages/r-rcppml/package.py b/var/spack/repos/builtin/packages/r-rcppml/package.py
new file mode 100644
index 0000000000..3a0577a725
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppml/package.py
@@ -0,0 +1,21 @@
+# 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 RRcppml(RPackage):
+    """Rcpp Machine Learning Library
+
+    Fast machine learning algorithms including matrix factorization and
+    divisive clustering for large sparse and dense matrices."""
+
+    cran     = "RcppML"
+
+    version('0.3.7', sha256='325c6515085527eb9123cc5e87e028547065771ed4d623048f41886ae28908c6')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-rcppeigen', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py
index 6b0b22f023..718e67cc93 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('2.36.0', commit='34122d4bde5ce43415f63f2e39e3a088c55282cc')
     version('2.34.0', commit='fb5aef0b6e1c6166d0f025d9e6ca60e54c68dbaf')
     version('2.30.0', commit='fb9aee416f38cfd308d6d7264ccbcda0467642a7')
     version('2.24.0', commit='d114c658affba9b682a37b4e2caf4341cf8da6cf')
diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
index c5c9732b08..c4a62b6b3b 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('2.40.0', commit='d864c9741c9177bc627cca1198673be2b1bfbc3e')
     version('2.38.0', commit='004de09a5b171211aff6cbaa1969ab8e3a5d6c61')
     version('2.34.0', commit='9746623211be794226258631992dfcccccfd7487')
     version('2.28.0', commit='c1f57c11f037c977f1d17f227f12a09a999e8c0b')
diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py
index f144ec4dc6..a38a917537 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('2.40.0', commit='fb6c15a3199f3ffd746fb9a381d574d17fef45a2')
     version('2.38.0', commit='f6fdfa807f5cd5a4d11d4aa6ebfaa81c118b4c3f')
     version('2.34.0', commit='ec861b81fc6962e844bf56b7549ba565a7e4c69c')
     version('2.28.1', commit='e230fa34d6f3e97dd4e6065115675baf5e8213bb')
diff --git a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py
index e1651aed73..8d27d93a00 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('1.8.0', 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 b91b98deae..0333226745 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('1.18.2', commit='d104bbfdb91ac5ec7db3c453f23e4d1d6feb671f')
     version('1.16.0', commit='534c49705dbdb27ae0c564acff2c72df2b27b3f1')
     version('1.12.1', commit='cf464f40fd95274d0d351cf28b586c49307c4f0b')
     version('1.6.3', commit='11ac3069f28b0068002db9c645817401f6c5b3c4')
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py
index 8ce11d6277..dbda5783df 100644
--- a/var/spack/repos/builtin/packages/r-rhtslib/package.py
+++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py
@@ -17,6 +17,7 @@ class RRhtslib(RPackage):
 
     bioc = "Rhtslib"
 
+    version('1.99.5', commit='a5335e1fea92ea06c33d42c7e290b6d8b4245ad3')
     version('1.26.0', commit='f5b20e97b283942877529f750b28398782552655')
     version('1.22.0', commit='899b79faa54d42c7c9b9a2bc49972109637d367f')
     version('1.18.1', commit='751a2ebaed43b7991204b27bd6c7870645001d82')
diff --git a/var/spack/repos/builtin/packages/r-roc/package.py b/var/spack/repos/builtin/packages/r-roc/package.py
index b0ccd2b7b3..b420d344d8 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('1.72.0', commit='c5d083b01314280dd43eb4cddd8a7fde8b5dce18')
     version('1.70.0', commit='44fd639958b9b1be4f8f731dc2be9dd91b2fa632')
     version('1.66.0', commit='62701ee41f48f99d15344127384fa032db69486f')
     version('1.62.0', commit='60250fdb091f6a938709b8a2cffe6442ee22a9a2')
diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py
index f3ba1ebfee..de89f41df1 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('1.24.0', commit='372e4623b39f585d4196d21164436c1ba013173f')
     version('1.22.0', commit='a53ec77c40ed3b3c84e91d794c1602dd509cad83')
     version('1.18.0', commit='1d4e206a8ce68d5a1417ff51c26174ed9d0ba7d2')
     version('1.12.0', commit='7e2c96fd8fd36710321498745f24cc6b59ac02f0')
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
index 938c29382d..af672b60f3 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('2.12.0', commit='d6a65dd57c5a17e4c441a27492e92072f69b175e')
     version('2.10.0', commit='b19738e85a467f9032fc7903be3ba10e655e7061')
     version('2.6.0', commit='f2aea061517c5a55e314c039251ece9831c7fad2')
     version('2.2.1', commit='f10084658b4c9744961fcacd79c0ae9a7a40cd30')
diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index aa5892dd04..24fc1955b1 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('1.56.0', commit='1d70f7dc464ad87a1fde61588cd9ae0cb86b6e86')
     version('1.54.0', commit='04cdd75521a8364e67a49d7352500dd4a3e83c55')
     version('1.50.0', commit='d2e61f72ff5d5a94c2c487ba108a37f23bfcc1e6')
     version('1.44.4', commit='aec96e85daf53b5c5eb2e89250d2755352be4de3')
diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py
index dabf9fdb54..3f892b58e0 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('0.34.0', commit='f590de3ec4d896a63351d0c1925d3856c0bd5292')
     version('0.32.3', commit='ad90e78fd3a4059cfcf2846498fb0748b4394e1a')
     version('0.28.1', commit='994cb7ef830e76f8b43169cc72b553869fafb2ed')
     version('0.26.1', commit='935769c')
diff --git a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py
index 389086d890..7f2cf3618f 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('1.4.0', commit='32e6e918bc7bb64bbf75613d353ca268c7d04292')
     version('1.2.0', commit='d0573e14ca537b40ade7dd1c9cf0cadae60d4349')
 
     depends_on('r-matrix', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-scater/package.py b/var/spack/repos/builtin/packages/r-scater/package.py
index ab6bbf27d2..7e5909c8a1 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('1.24.0', commit='013f0935a1a225139986ca5a3f0e9d08a1558153')
     version('1.22.0', commit='ea2c95c53adb8c6fab558c1cb869e2eab36aa9f8')
     version('1.18.3', commit='a94e7f413bf0f5f527b41b0b34e7a8e5c947ae37')
     version('1.12.2', commit='1518dc27a87c79181c34107d639e95fe55e55092')
@@ -46,6 +47,7 @@ class RScater(RPackage):
     depends_on('r-viridis', type=('build', 'run'))
     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-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-scuttle/package.py b/var/spack/repos/builtin/packages/r-scuttle/package.py
index cf640c841c..339f756cd7 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('1.6.2', commit='afdfc555151d84cc332757b4ec0b97cb7f39d2d5')
     version('1.4.0', commit='b335263dd56bb859b5dd3ea27ee00dffa0215313')
     version('1.0.4', commit='a827e2759d80e6c3510e2f8fd4bd680274206d9f')
 
diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py
index 9984ad18aa..58aa6609cd 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('1.62.0', commit='f2d0b53b1411ea98299201a8125a85f4cbf7c9cd')
     version('1.60.0', commit='4115c8e1d01accb8c8cc1cf96f23359466827e16')
     version('1.56.0', commit='169260c43fc58dc75becb3b7842cac3d0038a8d5')
     version('1.50.0', commit='57986221c90c3920f9829756c4b3ee566dc1e14d')
@@ -22,3 +23,5 @@ class RSeqlogo(RPackage):
     version('1.46.0', commit='e78be03db5f6a516138aeea6aa9512685633a4a2')
     version('1.44.0', commit='4cac14ff29f413d6de1a9944eb5d21bfe5045fac')
     version('1.42.0', commit='d7e04726c813282aa3f47a9ee98c5e1cec9bdddd')
+
+    depends_on('r@4.2:', type=('build', 'run'), when='@1.62.0:')
diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py
index 1faf2a0018..3cd154c345 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('1.54.0', commit='a1082a335120860d019aa0065a975d41890351f7')
     version('1.52.0', commit='4d7304d7b5a0ca5c904c0b919d6c95599db72a39')
     version('1.48.0', commit='ba44cd2517bc0e6f46d2cfcfce393f86eec814d0')
     version('1.42.0', commit='daa2576a48278460caf87f42c022c796652f4908')
diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py
index b701acaaef..4cc2d957bf 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('1.70.0', commit='c263daa14cf87c61b41e3a9e88573ba339c66179')
     version('1.68.0', commit='a29bf02b19cc9003c8401608831232b7c2af26e7')
     version('1.64.0', commit='3b528d37c16fc41bbc5c98165f606394313aa050')
     version('1.58.0', commit='69500158d69942cf7c62f583830933cf8baf89a1')
diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py
index 2501f8380c..226db0e4b3 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('1.18.0', commit='3a72dcd97e628055b2d02294eaecca9a41aba604')
     version('1.16.0', commit='bb27609ba08052607fc08529ffbbbcf1eab265cb')
     version('1.12.0', commit='66063b74c8b0bd0fd1277c7ad425ad11823ab356')
     version('1.6.0', commit='baa51d77a8dacd2a22e7293095a8cffaaa3293b4')
diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py
index 6bd0d5910d..48aac0b886 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('1.30.1', commit='baef8a71d3908287a2307768348c02db0720d125')
     version('1.28.0', commit='8fcd837f4627a3bb77cb8d992b2baedd0589d123')
     version('1.24.0', commit='419b13b761ea39a8b1b9bc73097fb0359c59f1c2')
     version('1.18.1', commit='81c581bf76392efdc8ba237ca2e42ca1dba788ca')
diff --git a/var/spack/repos/builtin/packages/r-snpstats/package.py b/var/spack/repos/builtin/packages/r-snpstats/package.py
index 4d2c1085ce..db43464c53 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('1.46.0', commit='1e70784b113eaca231bc5f91fc8ae5aadb151ddb')
     version('1.44.0', commit='72392dab4e75de2da459b1e95f1d48947811597b')
     version('1.40.0', commit='5fcac6f3b4bb6f45c19dff8f3089b693b74a56ce')
     version('1.34.0', commit='e31cdfb18a9e12d70d6a3e8e6fbf7cf8faa3ea5b')
diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
index 1c1be5becd..df3709e29a 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('2.32.0', commit='444d37661d147618f6830fd5de01a83ddf2a694d')
     version('2.30.0', commit='03f7ad707f6530fa7f62093f808884b6e83b0526')
     version('2.26.0', commit='9d4bed6e118ac76755ffb7abd058b09bac58a9d7')
     version('2.20.0', commit='dbedc30d92b600b3a17de596ebe38d15982c70c6')
diff --git a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py
index 5a65b01d35..49aa313ee6 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('1.8.0', 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 09d8ee08d5..32b4d0e48c 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('1.36.0', commit='75832966ba3e2bae6b56aa138764f7a98c7ba9b1')
     version('1.34.0', commit='53fd404638a04ec8e2e826e55c3f2d91d8b28e3d')
     version('1.30.0', commit='6b2eb64bfe6287846b1408297dd46dc772431031')
     version('1.24.0', commit='537ed19e466008f2972a246479b327c95177a99e')
diff --git a/var/spack/repos/builtin/packages/r-sseq/package.py b/var/spack/repos/builtin/packages/r-sseq/package.py
index aadcfb95f9..438a1665f6 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('1.34.0', commit='882bea1664f55d85550a7185cbd4a0108c35df36')
     version('1.32.0', commit='c0d3c305755d888f64d334a4ab5fa54c623054cf')
     version('1.28.0', commit='401f6805628bdf6579cc0e643b7ed54319f024be')
     version('1.22.0', commit='fa3895c9578edddca17b5d13a2678ee5830b85cc')
diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
index 52a14a0709..f54ee29f13 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('1.26.1', commit='c8cbd3b4f0fa1d686c4d7ce5b8614a24c74b2074')
     version('1.24.0', commit='d37f19383d03c107a8a41c0df2326e28efe46b28')
     version('1.20.0', commit='874aa87a481e4076a0ec3369f55c9c0a1ab8025e')
     version('1.18.2', commit='e22fafe')
@@ -40,6 +41,7 @@ class RSummarizedexperiment(RPackage):
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
     depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.10.1:')
     depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.20.0:')
+    depends_on('r-s4vectors@0.33.7:', type=('build', 'run'), when='@1.26.1:')
     depends_on('r-iranges@2.7.2:', type=('build', 'run'))
     depends_on('r-iranges@2.11.17:', type=('build', 'run'), when='@1.8.1:')
     depends_on('r-iranges@2.13.16:', type=('build', 'run'), when='@1.10.1:')
diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py
index ab135b7342..473ff95d53 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('3.44.0', commit='45ab2c1d6643bcda4de2d95a81b9b28d33a1a8a1')
     version('3.42.0', commit='54c843cc46437be233ecb43b6aa868e968d71138')
     version('3.38.0', commit='5ded8ba649200ec4829051f86a59e1a2548a7ab8')
     version('3.32.1', commit='1b8286734d00533b49d9f1456b6523cc778bb744')
diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py
index 3d7f8725f2..583d1db7e4 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('1.34.0', commit='7f8d0cb58a527a5d7ba94a773279f13aedca6ec7')
     version('1.32.0', commit='235505626b910de29156a07e1f990daa3b5d57d9')
     version('1.28.0', commit='15e7cf76f39ee3280a27284d58f7adef1c33f193')
     version('1.22.0', commit='613d3567fd662b65269bd200c5aa5f87ac6a4612')
diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py
index 20ecaf2751..80ea59a497 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('1.18.0', commit='71f80a7ace481f46471f36c91223effb85e17186')
     version('1.16.0', commit='e525cfd9c729a73a1964c243e5c34c37343f7bfa')
     version('1.12.0', commit='982b31bd7e22a3dc638bbda0336546220444f0c2')
     version('1.6.0', commit='9f5f78e52538d15f402c8f6e4c60f7212c7bc548')
diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py
index 1125de4034..bb948deb71 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('2.48.0', commit='a47f0079319c7d74db4aeda6399e06f12a34b585')
     version('2.46.0', commit='2bfa9dff41fff261aa6188f8368aebd6e8250b18')
     version('2.42.0', commit='3a33cf53883de45bda506953303e1809ab982adc')
     version('2.36.0', commit='c2f6c187b41c4aa44cc92ac781fdd878491a4019')
diff --git a/var/spack/repos/builtin/packages/r-treeio/package.py b/var/spack/repos/builtin/packages/r-treeio/package.py
index c94f5290dc..a1e3a0e1af 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('1.20.0', commit='5f7c3704fc8202c52451d092148fdcfe683f026a')
     version('1.18.1', commit='a06b6b3d2a64f1b22c6c8c5f97c08f5863349c83')
 
     depends_on('r@3.6.0:', type=('build', 'run'))
@@ -28,3 +29,4 @@ class RTreeio(RPackage):
     depends_on('r-rlang', type=('build', 'run'))
     depends_on('r-tibble', type=('build', 'run'))
     depends_on('r-tidytree@0.3.0:', type=('build', 'run'))
+    depends_on('r-tidytree@0.3.9:', type=('build', 'run'), when='@1.20.0:')
diff --git a/var/spack/repos/builtin/packages/r-tximport/package.py b/var/spack/repos/builtin/packages/r-tximport/package.py
index 9e68fd31f3..091dcbd1e1 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('1.24.0', commit='58524f39bdd55299cfe80a726f99b714b724be20')
     version('1.22.0', commit='335213baee3492fbf6baaa8b4e067ac0ef384684')
     version('1.18.0', commit='58b20cbc566648586b6990b30ebc70bef308cb05')
     version('1.12.3', commit='acbdead961471c3b910d720f73bd0af1b7a07c57')
diff --git a/var/spack/repos/builtin/packages/r-tximportdata/package.py b/var/spack/repos/builtin/packages/r-tximportdata/package.py
index 02cf762fb7..e55e8da421 100644
--- a/var/spack/repos/builtin/packages/r-tximportdata/package.py
+++ b/var/spack/repos/builtin/packages/r-tximportdata/package.py
@@ -18,5 +18,6 @@ class RTximportdata(RPackage):
 
     bioc = "tximportData"
 
+    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 f283881775..5e0136c610 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('1.42.1', commit='d1121696c76c189d6b4df9914806bf585a495845')
     version('1.40.0', commit='50ead7cb60cedf3c053853fab92d9f104f9f85bd')
     version('1.36.0', commit='9918bd19a2e6f89e5edc5fe03c8812f500bb3e19')
     version('1.30.1', commit='fb1ab00872570afb280522c4663e347dafc07a9e')
diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py
index a5b87eb059..f45c220ac0 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('3.64.0', commit='1f09f20ee7f81100fb0bf66288c4caf0049b5508')
     version('3.62.0', commit='6ae7f4e07ec1a5a9482cab892d98175983bfcd50')
     version('3.58.0', commit='a451e6ae989623750feacf26d99683a7955adf85')
     version('3.52.0', commit='e80642d850ae93bc141654200a8970b561a94fbe')
diff --git a/var/spack/repos/builtin/packages/r-watermelon/package.py b/var/spack/repos/builtin/packages/r-watermelon/package.py
index f85fdf6c6e..d42937374f 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('2.2.0', commit='6ec49efe98aef31d0789b31ab048eb46edec762c')
     version('2.0.0', commit='f6a331bdf50e0e5c94009fb67be873d996348ade')
     version('1.34.0', commit='3fa2745535c22068a438747b41b9d793196098d4')
     version('1.30.0', commit='66d7579fe49206d965832288df7937c3d43ed578')
diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py
index d056bdf300..04b5a91f70 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('2.42.0', commit='298e83eff7fc5f72a2bb76b559c5115c6cd3ee84')
     version('2.40.0', commit='bfc3c54787aec97b70bef7b99a6adc75d2cf5ed2')
     version('2.36.0', commit='0277f9dffbd7d1880be77cb8581fc614501b3293')
     version('2.30.0', commit='058af6f1e431522778f970bf61f834620d3d7dd7')
diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
index da927d94df..e28b2c5d02 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('1.54.0', commit='a316e2399894191646c229378fa138b7461c75ab')
     version('1.52.0', commit='fe32fcd2a83432c721eb948cb3af73dd187065f6')
     version('1.48.0', commit='1cefe6b56c6dcb1f18028b3b7d6a67d490bc9730')
     version('1.42.0', commit='d79c80dfc1a0ed3fd6d3e7a7c3a4aff778537ca9')
diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py
index 2bab94440d..a1bfab96bb 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('0.36.0', commit='ff6f818ff4357eb9bf00654de9e0f508a5285408')
     version('0.34.0', commit='06adb25ac51c707b90fb8e0637fa06df237a863c')
     version('0.30.0', commit='985e963e0b1c3ff004dd0b07ad7c9ff7ed853ec0')
     version('0.24.0', commit='e5109cb2687724b9fddddf296c07a82bae4c551d')
diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py
index f6bee15e74..a5f0539cbd 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('1.22.0', commit='55c2886874f154c737264ce6843089bf3565fa57')
     version('1.20.1', commit='6c3f437911859df6f6e4a9af5571c3a5aafbffb2')
     version('1.16.0', commit='f344cdb81bb886c633f9325f811912fb59d58eb1')
     version('1.10.0', commit='06af18e424868eb0f0be6c80e90cbab1eabf3d73')
diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py
index ab3fa587a4..c243d6bd56 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('1.22.0', commit='0d94152eee4224bf1ca467fad7f2b35c2e1df6b2')
     version('1.20.0', commit='b41e4ef14f980518af2fc59f202ad8ec148e8b47')
     version('1.16.0', commit='ff5a18cb946ffec3cb773fe32af401c8a72d674a')
     version('1.10.0', commit='36ffe84148eb871e93bc8f9e697475319b5ea472')
diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
index 10eaf33ac5..57b7837bb0 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('1.42.0', commit='aa074d72515df745ad65133ca21d3cad778ccc0e')
     version('1.40.0', commit='3f116b39d104c1ea8288f6b8f0ef94bb95f41f69')
     version('1.36.0', commit='62e888cd7fb482d512c6c31961b657e0b924e357')
     version('1.30.0', commit='99eae5b05968bf6abc9b54b9031afd93517381e0')