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 a40bea1f..a8f41652 100644
Binary files a/bin/windows/contrib/4.3/InterpretMSSpectrum_1.3.3.zip and b/bin/windows/contrib/4.3/InterpretMSSpectrum_1.3.3.zip differ
diff --git a/bin/windows/contrib/4.3/PACKAGES b/bin/windows/contrib/4.3/PACKAGES
index 03550a9c..9bd0339b 100644
--- a/bin/windows/contrib/4.3/PACKAGES
+++ b/bin/windows/contrib/4.3/PACKAGES
@@ -288,7 +288,7 @@ License: GPL (>= 2)
 Archs: x64
 
 Package: cli
-Version: 3.6.2
+Version: 3.6.3
 Depends: R (>= 3.4)
 Imports: utils
 Suggests: callr, covr, crayon, digest, glue (>= 1.6.0), grDevices,
@@ -390,7 +390,7 @@ Suggests: bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,
 License: MIT + file LICENSE
 
 Package: crayon
-Version: 1.5.2
+Version: 1.5.3
 Imports: grDevices, methods, utils
 Suggests: mockery, rstudioapi, testthat, withr
 License: MIT + file LICENSE
@@ -499,7 +499,7 @@ Imports: stats, graphics
 License: GPL (>= 2)
 
 Package: digest
-Version: 0.6.35
+Version: 0.6.36
 Depends: R (>= 3.3.0)
 Imports: utils
 Suggests: tinytest, simplermarkdown
@@ -1721,7 +1721,7 @@ License: MIT + file LICENSE
 Archs: x64
 
 Package: prodlim
-Version: 2023.08.28
+Version: 2024.06.25
 Depends: R (>= 2.9.0)
 Imports: Rcpp (>= 0.11.5), stats, data.table, grDevices, graphics,
         diagram, survival, KernSmooth, lava
@@ -2696,7 +2696,7 @@ License: Apache License (== 2.0) | file LICENSE
 Archs: x64
 
 Package: XML
-Version: 3.99-0.16.1
+Version: 3.99-0.17
 Depends: R (>= 4.0.0), methods, utils
 Suggests: bitops, RCurl
 License: BSD_3_clause + file LICENSE
diff --git a/bin/windows/contrib/4.3/PACKAGES.gz b/bin/windows/contrib/4.3/PACKAGES.gz
index 5008bff1..ff3be97c 100644
Binary files a/bin/windows/contrib/4.3/PACKAGES.gz and b/bin/windows/contrib/4.3/PACKAGES.gz differ
diff --git a/bin/windows/contrib/4.3/PACKAGES.rds b/bin/windows/contrib/4.3/PACKAGES.rds
index c7d63186..82f3a7c1 100644
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diff --git a/bin/windows/contrib/4.3/XML_3.99-0.16.1.zip b/bin/windows/contrib/4.3/XML_3.99-0.16.1.zip
deleted file mode 100644
index c2d5a708..00000000
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diff --git a/bin/windows/contrib/4.3/XML_3.99-0.17.zip b/bin/windows/contrib/4.3/XML_3.99-0.17.zip
new file mode 100644
index 00000000..9b47d7ce
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diff --git a/bin/windows/contrib/4.3/cli_3.6.2.zip b/bin/windows/contrib/4.3/cli_3.6.2.zip
deleted file mode 100644
index 1d36ddb4..00000000
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diff --git a/bin/windows/contrib/4.3/cli_3.6.3.zip b/bin/windows/contrib/4.3/cli_3.6.3.zip
new file mode 100644
index 00000000..fbc8a61e
Binary files /dev/null and b/bin/windows/contrib/4.3/cli_3.6.3.zip differ
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 9c212bb3..732e5315 100644
Binary files a/bin/windows/contrib/4.3/cliqueMS_1.7.1.zip and b/bin/windows/contrib/4.3/cliqueMS_1.7.1.zip differ
diff --git a/bin/windows/contrib/4.3/crayon_1.5.2.zip b/bin/windows/contrib/4.3/crayon_1.5.2.zip
deleted file mode 100644
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diff --git a/bin/windows/contrib/4.3/crayon_1.5.3.zip b/bin/windows/contrib/4.3/crayon_1.5.3.zip
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index 00000000..4a952947
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diff --git a/bin/windows/contrib/4.3/digest_0.6.35.zip b/bin/windows/contrib/4.3/digest_0.6.35.zip
deleted file mode 100644
index 034aa4bf..00000000
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new file mode 100644
index 00000000..c427a5c7
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diff --git a/bin/windows/contrib/4.3/patRoon_2.3.1.zip b/bin/windows/contrib/4.3/patRoon_2.3.1.zip
index e95aa204..a0fb11b1 100644
Binary files a/bin/windows/contrib/4.3/patRoon_2.3.1.zip and b/bin/windows/contrib/4.3/patRoon_2.3.1.zip differ
diff --git a/bin/windows/contrib/4.3/prodlim_2023.08.28.zip b/bin/windows/contrib/4.3/prodlim_2023.08.28.zip
deleted file mode 100644
index 6556934c..00000000
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diff --git a/bin/windows/contrib/4.3/prodlim_2024.06.25.zip b/bin/windows/contrib/4.3/prodlim_2024.06.25.zip
new file mode 100644
index 00000000..bd9e95cf
Binary files /dev/null and b/bin/windows/contrib/4.3/prodlim_2024.06.25.zip differ
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 3b17a47e..4612aaf6 100644
Binary files a/bin/windows/contrib/4.4/InterpretMSSpectrum_1.3.3.zip and b/bin/windows/contrib/4.4/InterpretMSSpectrum_1.3.3.zip differ
diff --git a/bin/windows/contrib/4.4/MASS_7.3-60.2.zip b/bin/windows/contrib/4.4/MASS_7.3-60.2.zip
deleted file mode 100644
index 371388b8..00000000
Binary files a/bin/windows/contrib/4.4/MASS_7.3-60.2.zip and /dev/null differ
diff --git a/bin/windows/contrib/4.4/MASS_7.3-61.zip b/bin/windows/contrib/4.4/MASS_7.3-61.zip
new file mode 100644
index 00000000..18ecbc0c
Binary files /dev/null and b/bin/windows/contrib/4.4/MASS_7.3-61.zip differ
diff --git a/bin/windows/contrib/4.4/PACKAGES b/bin/windows/contrib/4.4/PACKAGES
index 7c72a374..e720ae8a 100644
--- a/bin/windows/contrib/4.4/PACKAGES
+++ b/bin/windows/contrib/4.4/PACKAGES
@@ -289,7 +289,7 @@ License: GPL (>= 2)
 Archs: x64
 
 Package: cli
-Version: 3.6.2
+Version: 3.6.3
 Depends: R (>= 3.4)
 Imports: utils
 Suggests: callr, covr, crayon, digest, glue (>= 1.6.0), grDevices,
@@ -391,7 +391,7 @@ Suggests: bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,
 License: MIT + file LICENSE
 
 Package: crayon
-Version: 1.5.2
+Version: 1.5.3
 Imports: grDevices, methods, utils
 Suggests: mockery, rstudioapi, testthat, withr
 License: MIT + file LICENSE
@@ -494,7 +494,7 @@ Imports: stats, graphics
 License: GPL (>= 2)
 
 Package: digest
-Version: 0.6.35
+Version: 0.6.36
 Depends: R (>= 3.3.0)
 Imports: utils
 Suggests: tinytest, simplermarkdown
@@ -1315,7 +1315,7 @@ License: GPL (>= 3)
 Archs: x64
 
 Package: MASS
-Version: 7.3-60.2
+Version: 7.3-61
 Priority: recommended
 Depends: R (>= 4.4.0), grDevices, graphics, stats, utils
 Imports: methods
@@ -1531,11 +1531,11 @@ License: GPL (>= 3)
 Archs: x64
 
 Package: nlme
-Version: 3.1-164
+Version: 3.1-165
 Priority: recommended
-Depends: R (>= 3.5.0)
+Depends: R (>= 3.6.0)
 Imports: graphics, stats, utils, lattice
-Suggests: Hmisc, MASS, SASmixed
+Suggests: MASS, SASmixed
 License: GPL (>= 2)
 Archs: x64
 
@@ -1707,7 +1707,7 @@ License: MIT + file LICENSE
 Archs: x64
 
 Package: prodlim
-Version: 2023.08.28
+Version: 2024.06.25
 Depends: R (>= 2.9.0)
 Imports: Rcpp (>= 0.11.5), stats, data.table, grDevices, graphics,
         diagram, survival, KernSmooth, lava
@@ -2377,7 +2377,7 @@ Suggests: HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db,
 License: Artistic-2.0
 
 Package: survival
-Version: 3.6-4
+Version: 3.7-0
 Priority: recommended
 Depends: R (>= 3.5.0)
 Imports: graphics, Matrix, methods, splines, stats, utils
@@ -2654,10 +2654,10 @@ License: GPL (>= 2) + file LICENSE
 Archs: x64
 
 Package: xfun
-Version: 0.44
+Version: 0.45
 Imports: grDevices, stats, tools
 Suggests: testit, parallel, codetools, methods, rstudioapi, tinytex (>=
-        0.30), mime, markdown (>= 1.5), knitr (>= 1.42), htmltools,
+        0.30), mime, markdown (>= 1.5), knitr (>= 1.47), htmltools,
         remotes, pak, rhub, renv, curl, xml2, jsonlite, magick, yaml,
         qs, rmarkdown
 License: MIT + file LICENSE
diff --git a/bin/windows/contrib/4.4/PACKAGES.gz b/bin/windows/contrib/4.4/PACKAGES.gz
index cd5e4e54..71027b20 100644
Binary files a/bin/windows/contrib/4.4/PACKAGES.gz and b/bin/windows/contrib/4.4/PACKAGES.gz differ
diff --git a/bin/windows/contrib/4.4/PACKAGES.rds b/bin/windows/contrib/4.4/PACKAGES.rds
index 1a918ebb..55d5e7c6 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/cli_3.6.2.zip b/bin/windows/contrib/4.4/cli_3.6.2.zip
deleted file mode 100644
index 522172dc..00000000
Binary files a/bin/windows/contrib/4.4/cli_3.6.2.zip and /dev/null differ
diff --git a/bin/windows/contrib/4.4/cli_3.6.3.zip b/bin/windows/contrib/4.4/cli_3.6.3.zip
new file mode 100644
index 00000000..6bbdfe4b
Binary files /dev/null and b/bin/windows/contrib/4.4/cli_3.6.3.zip differ
diff --git a/bin/windows/contrib/4.4/crayon_1.5.2.zip b/bin/windows/contrib/4.4/crayon_1.5.2.zip
deleted file mode 100644
index 2fe80e7b..00000000
Binary files a/bin/windows/contrib/4.4/crayon_1.5.2.zip and /dev/null differ
diff --git a/bin/windows/contrib/4.4/crayon_1.5.3.zip b/bin/windows/contrib/4.4/crayon_1.5.3.zip
new file mode 100644
index 00000000..71d277b6
Binary files /dev/null and b/bin/windows/contrib/4.4/crayon_1.5.3.zip differ
diff --git a/bin/windows/contrib/4.4/digest_0.6.35.zip b/bin/windows/contrib/4.4/digest_0.6.35.zip
deleted file mode 100644
index c56ff3ff..00000000
Binary files a/bin/windows/contrib/4.4/digest_0.6.35.zip and /dev/null differ
diff --git a/bin/windows/contrib/4.4/digest_0.6.36.zip b/bin/windows/contrib/4.4/digest_0.6.36.zip
new file mode 100644
index 00000000..1e0acc5a
Binary files /dev/null and b/bin/windows/contrib/4.4/digest_0.6.36.zip differ
diff --git a/bin/windows/contrib/4.4/nlme_3.1-164.zip b/bin/windows/contrib/4.4/nlme_3.1-164.zip
deleted file mode 100644
index 31407ba3..00000000
Binary files a/bin/windows/contrib/4.4/nlme_3.1-164.zip and /dev/null differ
diff --git a/bin/windows/contrib/4.4/nlme_3.1-165.zip b/bin/windows/contrib/4.4/nlme_3.1-165.zip
new file mode 100644
index 00000000..b711a3f6
Binary files /dev/null and b/bin/windows/contrib/4.4/nlme_3.1-165.zip differ
diff --git a/bin/windows/contrib/4.4/patRoon_2.3.1.zip b/bin/windows/contrib/4.4/patRoon_2.3.1.zip
index bd6309dc..db49b5a5 100644
Binary files a/bin/windows/contrib/4.4/patRoon_2.3.1.zip and b/bin/windows/contrib/4.4/patRoon_2.3.1.zip differ
diff --git a/bin/windows/contrib/4.4/prodlim_2023.08.28.zip b/bin/windows/contrib/4.4/prodlim_2023.08.28.zip
deleted file mode 100644
index 338c5ccb..00000000
Binary files a/bin/windows/contrib/4.4/prodlim_2023.08.28.zip and /dev/null differ
diff --git a/bin/windows/contrib/4.4/prodlim_2024.06.25.zip b/bin/windows/contrib/4.4/prodlim_2024.06.25.zip
new file mode 100644
index 00000000..b1d2c267
Binary files /dev/null and b/bin/windows/contrib/4.4/prodlim_2024.06.25.zip differ
diff --git a/bin/windows/contrib/4.4/survival_3.6-4.zip b/bin/windows/contrib/4.4/survival_3.7-0.zip
similarity index 52%
rename from bin/windows/contrib/4.4/survival_3.6-4.zip
rename to bin/windows/contrib/4.4/survival_3.7-0.zip
index 138e642f..26c9a324 100644
Binary files a/bin/windows/contrib/4.4/survival_3.6-4.zip and b/bin/windows/contrib/4.4/survival_3.7-0.zip differ
diff --git a/bin/windows/contrib/4.4/xfun_0.44.zip b/bin/windows/contrib/4.4/xfun_0.44.zip
deleted file mode 100644
index 3cdbf7cf..00000000
Binary files a/bin/windows/contrib/4.4/xfun_0.44.zip and /dev/null differ
diff --git a/bin/windows/contrib/4.4/xfun_0.45.zip b/bin/windows/contrib/4.4/xfun_0.45.zip
new file mode 100644
index 00000000..6b4289e7
Binary files /dev/null and b/bin/windows/contrib/4.4/xfun_0.45.zip differ
diff --git a/patRoonDeps-4.3.tsv b/patRoonDeps-4.3.tsv
index 6fb49615..fee4bbbd 100644
--- a/patRoonDeps-4.3.tsv
+++ b/patRoonDeps-4.3.tsv
@@ -34,7 +34,7 @@ circlize	0.4.16
 Ckmeans.1d.dp	4.3.5	
 class	7.3-22	
 classInt	0.4-10	
-cli	3.6.2	
+cli	3.6.3	
 clipr	0.8.0	
 cliqueMS	1.7.1	cb569e0b78ce0fa4254f1393874762bed08fa855
 clock	0.7.0	
@@ -46,7 +46,7 @@ combinat	0.0-8
 commonmark	1.9.1	
 conflicted	1.2.0	
 cpp11	0.4.7	
-crayon	1.5.2	
+crayon	1.5.3	
 crosstalk	1.2.1	
 curl	5.2.1	
 data.table	1.15.4	
@@ -58,7 +58,7 @@ DelayedArray	0.28.0
 dendextend	1.17.1	
 DEoptimR	1.1-3	
 diagram	1.6.5	
-digest	0.6.35	
+digest	0.6.36	
 docopt	0.7.1	
 doParallel	1.0.17	
 dplyr	1.1.4	
@@ -191,7 +191,7 @@ nontargetData	1.1	75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
 numDeriv	2016.8-1.1	
 openssl	2.2.0	
 parallelly	1.37.1	
-patRoon	2.3.1	02e71665cb9c53ef1e89a17f26560d45ae5419d8
+patRoon	2.3.1	f0f8aa2b888eea31ee89226b98e17ce9af81e707
 pcaMethods	1.94.0	
 permute	0.9-7	
 pillar	1.9.0	
@@ -205,7 +205,7 @@ preprocessCore	1.64.0
 prettyunits	1.2.0	
 pROC	1.18.5	
 processx	3.8.4	
-prodlim	2023.08.28	
+prodlim	2024.06.25	
 progress	1.2.3	
 progressr	0.14.0	
 promises	1.3.0	
@@ -320,7 +320,7 @@ withr	3.0.0
 xcms	4.0.2	
 xfun	0.45	
 xgboost	1.7.7.1	
-XML	3.99-0.16.1	
+XML	3.99-0.17	
 xml2	1.3.6	
 xtable	1.8-4	
 XVector	0.42.0	
diff --git a/patRoonDeps-4.4.tsv b/patRoonDeps-4.4.tsv
index 8b701fb8..d155971e 100644
--- a/patRoonDeps-4.4.tsv
+++ b/patRoonDeps-4.4.tsv
@@ -34,7 +34,7 @@ circlize	0.4.16
 Ckmeans.1d.dp	4.3.5	
 class	7.3-22	
 classInt	0.4-10	
-cli	3.6.2	
+cli	3.6.3	
 clipr	0.8.0	
 cliqueMS	1.7.1	cb569e0b78ce0fa4254f1393874762bed08fa855
 clock	0.7.0	
@@ -46,7 +46,7 @@ combinat	0.0-8
 commonmark	1.9.1	
 conflicted	1.2.0	
 cpp11	0.4.7	
-crayon	1.5.2	
+crayon	1.5.3	
 crosstalk	1.2.1	
 curl	5.2.1	
 data.table	1.15.4	
@@ -57,7 +57,7 @@ dbscan	1.1-12
 DelayedArray	0.30.1	
 dendextend	1.17.1	
 diagram	1.6.5	
-digest	0.6.35	
+digest	0.6.36	
 docopt	0.7.1	
 doParallel	1.0.17	
 dplyr	1.1.4	
@@ -156,7 +156,7 @@ lubridate	1.9.3
 magick	2.8.3	
 magrittr	2.0.3	
 MALDIquant	1.22.2	
-MASS	7.3-60.2	
+MASS	7.3-61	
 MassSpecWavelet	1.70.0	
 Matrix	1.7-0	
 MatrixGenerics	1.16.0	
@@ -182,14 +182,14 @@ munsell	0.5.1
 mzID	1.42.0	
 mzR	2.38.0	
 ncdf4	1.22	
-nlme	3.1-164	
+nlme	3.1-165	
 nnet	7.3-19	
 nontarget	2.2	e30221585182bc66e1f8e1113b2c1103a0f2cb56
 nontargetData	1.1	75b2a92cd549f72cc71dfe7b86bd42947d62f2c4
 numDeriv	2016.8-1.1	
 openssl	2.2.0	
 parallelly	1.37.1	
-patRoon	2.3.1	02e71665cb9c53ef1e89a17f26560d45ae5419d8
+patRoon	2.3.1	f0f8aa2b888eea31ee89226b98e17ce9af81e707
 pcaMethods	1.96.0	
 permute	0.9-7	
 pillar	1.9.0	
@@ -203,7 +203,7 @@ preprocessCore	1.66.0
 prettyunits	1.2.0	
 pROC	1.18.5	
 processx	3.8.4	
-prodlim	2023.08.28	
+prodlim	2024.06.25	
 progress	1.2.3	
 progressr	0.14.0	
 promises	1.3.0	
@@ -285,7 +285,7 @@ stringi	1.8.4
 stringr	1.5.1	
 styler	1.10.3	
 SummarizedExperiment	1.34.0	
-survival	3.6-4	
+survival	3.7-0	
 svglite	2.1.3	
 sys	3.4.2	
 systemfonts	1.1.0	
@@ -315,7 +315,7 @@ webchem	1.3.0
 webshot	0.5.5	
 withr	3.0.0	
 xcms	4.2.2	
-xfun	0.44	
+xfun	0.45	
 xgboost	1.7.7.1	
 XML	3.99-0.16.1	
 xml2	1.3.6