diff --git a/bin/windows/contrib/4.3/InterpretMSSpectrum_1.3.3.zip b/bin/windows/contrib/4.3/InterpretMSSpectrum_1.3.3.zip
index 40f7bd12..3f3ade9d 100644
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diff --git a/bin/windows/contrib/4.3/cliqueMS_1.7.1.zip b/bin/windows/contrib/4.3/cliqueMS_1.7.1.zip
index bbf96256..daa32fd6 100644
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diff --git a/bin/windows/contrib/4.3/patRoon_2.3.2.zip b/bin/windows/contrib/4.3/patRoon_2.3.2.zip
index 934270fb..6ce776f1 100644
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diff --git a/bin/windows/contrib/4.4/InterpretMSSpectrum_1.3.3.zip b/bin/windows/contrib/4.4/InterpretMSSpectrum_1.3.3.zip
index 9295eb2b..d8c89d76 100644
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diff --git a/bin/windows/contrib/4.4/MultiAssayExperiment_1.30.2.zip b/bin/windows/contrib/4.4/MultiAssayExperiment_1.30.2.zip
deleted file mode 100644
index 96095833..00000000
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diff --git a/bin/windows/contrib/4.4/MultiAssayExperiment_1.30.3.zip b/bin/windows/contrib/4.4/MultiAssayExperiment_1.30.3.zip
new file mode 100644
index 00000000..c2177c2d
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diff --git a/bin/windows/contrib/4.4/PACKAGES b/bin/windows/contrib/4.4/PACKAGES
index fbec0070..e45cbba2 100644
--- a/bin/windows/contrib/4.4/PACKAGES
+++ b/bin/windows/contrib/4.4/PACKAGES
@@ -1258,7 +1258,7 @@ Suggests: covr, crayon, knitr, lintr, rmarkdown, testthat (>= 3.0.1),
 License: MIT + file LICENSE
 
 Package: limma
-Version: 3.60.3
+Version: 3.60.4
 Depends: R (>= 3.6.0)
 Imports: grDevices, graphics, stats, utils, methods, statmod
 Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines,
@@ -1473,7 +1473,7 @@ License: Artistic-2.0
 Archs: x64
 
 Package: MultiAssayExperiment
-Version: 1.30.2
+Version: 1.30.3
 Depends: SummarizedExperiment (>= 1.3.81), R (>= 3.5.0)
 Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray,
         GenomicRanges, IRanges, methods, S4Vectors, tidyr, utils
diff --git a/bin/windows/contrib/4.4/PACKAGES.gz b/bin/windows/contrib/4.4/PACKAGES.gz
index 42498279..abae01f2 100644
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diff --git a/bin/windows/contrib/4.4/PACKAGES.rds b/bin/windows/contrib/4.4/PACKAGES.rds
index 1431bf45..6bed2044 100644
Binary files a/bin/windows/contrib/4.4/PACKAGES.rds and b/bin/windows/contrib/4.4/PACKAGES.rds differ
diff --git a/bin/windows/contrib/4.4/limma_3.60.3.zip b/bin/windows/contrib/4.4/limma_3.60.4.zip
similarity index 54%
rename from bin/windows/contrib/4.4/limma_3.60.3.zip
rename to bin/windows/contrib/4.4/limma_3.60.4.zip
index 350b04c7..5aea50eb 100644
Binary files a/bin/windows/contrib/4.4/limma_3.60.3.zip and b/bin/windows/contrib/4.4/limma_3.60.4.zip differ
diff --git a/bin/windows/contrib/4.4/patRoon_2.3.2.zip b/bin/windows/contrib/4.4/patRoon_2.3.2.zip
index 5f7ef403..caf18fd3 100644
Binary files a/bin/windows/contrib/4.4/patRoon_2.3.2.zip and b/bin/windows/contrib/4.4/patRoon_2.3.2.zip differ
diff --git a/patRoonDeps-4.3.tsv b/patRoonDeps-4.3.tsv
index 5a5490cb..b810fbf3 100644
--- a/patRoonDeps-4.3.tsv
+++ b/patRoonDeps-4.3.tsv
@@ -190,7 +190,7 @@ nontargetData	1.1	75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
 numDeriv	2016.8-1.1	
 openssl	2.2.0	
 parallelly	1.37.1	
-patRoon	2.3.2	c3f5c4968c026c54ef4134728dc135be635ef532
+patRoon	2.3.2	3bd25abac934ad6cfabb259a0d52a0d5c33f10b2
 pcaMethods	1.94.0	
 permute	0.9-7	
 pillar	1.9.0	
diff --git a/patRoonDeps-4.4.tsv b/patRoonDeps-4.4.tsv
index 71bb54dc..bee78e0b 100644
--- a/patRoonDeps-4.4.tsv
+++ b/patRoonDeps-4.4.tsv
@@ -149,7 +149,7 @@ lattice	0.22-6
 lava	1.8.0	
 lazyeval	0.2.2	
 lifecycle	1.0.4	
-limma	3.60.3	
+limma	3.60.4	
 listenv	0.9.1	
 lubridate	1.9.3	
 magick	2.8.4	
@@ -175,7 +175,7 @@ MsCoreUtils	1.16.0
 MsExperiment	1.6.0	
 MsFeatures	1.12.0	
 MSnbase	2.30.1	
-MultiAssayExperiment	1.30.2	
+MultiAssayExperiment	1.30.3	
 MultiDataSet	1.32.0	
 munsell	0.5.1	
 mzID	1.42.0	
@@ -188,7 +188,7 @@ nontargetData	1.1	75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
 numDeriv	2016.8-1.1	
 openssl	2.2.0	
 parallelly	1.37.1	
-patRoon	2.3.2	c3f5c4968c026c54ef4134728dc135be635ef532
+patRoon	2.3.2	3bd25abac934ad6cfabb259a0d52a0d5c33f10b2
 pcaMethods	1.96.0	
 permute	0.9-7	
 pillar	1.9.0