diff --git a/bin/windows/contrib/4.3/DEoptimR_1.1-3-1.zip b/bin/windows/contrib/4.3/DEoptimR_1.1-3-1.zip new file mode 100644 index 00000000..61dcd097 Binary files /dev/null and b/bin/windows/contrib/4.3/DEoptimR_1.1-3-1.zip differ diff --git a/bin/windows/contrib/4.3/DEoptimR_1.1-3.zip b/bin/windows/contrib/4.3/DEoptimR_1.1-3.zip deleted file mode 100644 index 265fceb7..00000000 Binary files a/bin/windows/contrib/4.3/DEoptimR_1.1-3.zip and /dev/null differ diff --git a/bin/windows/contrib/4.3/Hmisc_5.2-0.zip b/bin/windows/contrib/4.3/Hmisc_5.2-0.zip deleted file mode 100644 index adae454b..00000000 Binary files a/bin/windows/contrib/4.3/Hmisc_5.2-0.zip and /dev/null differ diff --git a/bin/windows/contrib/4.3/Hmisc_5.2-1.zip b/bin/windows/contrib/4.3/Hmisc_5.2-1.zip new file mode 100644 index 00000000..6aebc9ed Binary files /dev/null and b/bin/windows/contrib/4.3/Hmisc_5.2-1.zip differ diff --git a/bin/windows/contrib/4.3/MS2Tox_0.4.2.zip b/bin/windows/contrib/4.3/MS2Tox_0.4.2.zip index f4f453f9..9b245072 100644 Binary files a/bin/windows/contrib/4.3/MS2Tox_0.4.2.zip and b/bin/windows/contrib/4.3/MS2Tox_0.4.2.zip differ diff --git a/bin/windows/contrib/4.3/PACKAGES b/bin/windows/contrib/4.3/PACKAGES index 9ae27cbf..dfc2f764 100644 --- a/bin/windows/contrib/4.3/PACKAGES +++ b/bin/windows/contrib/4.3/PACKAGES @@ -111,7 +111,7 @@ Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 Package: bit -Version: 4.5.0 +Version: 4.5.0.1 Depends: R (>= 3.4.0) Suggests: testthat (>= 0.11.0), roxygen2, knitr, markdown, rmarkdown, microbenchmark, bit64 (>= 4.0.0), ff (>= 4.0.0) @@ -489,7 +489,7 @@ Enhances: ggdendro, dendroextras, Hmisc, data.table, rpart, WGCNA, License: GPL-2 | GPL-3 Package: DEoptimR -Version: 1.1-3 +Version: 1.1-3-1 Imports: stats Enhances: robustbase License: GPL (>= 2) @@ -985,7 +985,7 @@ Suggests: knitr, markdown, testit License: GPL Package: Hmisc -Version: 5.2-0 +Version: 5.2-1 Depends: R (>= 4.2.0) Imports: methods, ggplot2, cluster, rpart, nnet, foreign, gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis, @@ -1220,10 +1220,10 @@ Suggests: testit License: LGPL-3 Package: later -Version: 1.3.2 +Version: 1.4.1 Imports: Rcpp (>= 0.12.9), rlang LinkingTo: Rcpp -Suggests: knitr, rmarkdown, testthat (>= 2.1.0) +Suggests: knitr, nanonext, R6, rmarkdown, testthat (>= 2.1.0) License: MIT + file LICENSE Archs: x64 @@ -1581,8 +1581,9 @@ License: MIT + file LICENSE Archs: x64 Package: parallelly -Version: 1.39.0 +Version: 1.40.0 Imports: parallel, tools, utils +Suggests: commonmark, base64enc License: LGPL (>= 2.1) Archs: x64 @@ -1732,16 +1733,17 @@ Suggests: Rcpp, testthat (>= 3.0.0), withr License: MIT + file LICENSE Package: progressr -Version: 0.15.0 +Version: 0.15.1 Depends: R (>= 3.5.0) Imports: digest, utils Suggests: graphics, tcltk, beepr, cli, crayon, pbmcapply, progress, purrr, foreach, plyr, doFuture, future, future.apply, furrr, - RPushbullet, rstudioapi, shiny, commonmark, base64enc, tools + ntfy, RPushbullet, rstudioapi, shiny, commonmark, base64enc, + tools License: GPL (>= 3) Package: promises -Version: 1.3.0 +Version: 1.3.2 Imports: fastmap (>= 1.1.0), later, magrittr (>= 1.5), R6, Rcpp, rlang, stats LinkingTo: later, Rcpp @@ -2182,7 +2184,7 @@ Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2, License: GPL (>= 2) Package: RSQLite -Version: 2.3.8 +Version: 2.3.9 Depends: R (>= 3.1.0) Imports: bit64, blob (>= 1.2.0), DBI (>= 1.2.0), memoise, methods, pkgconfig, rlang diff --git a/bin/windows/contrib/4.3/PACKAGES.gz b/bin/windows/contrib/4.3/PACKAGES.gz index 291351b1..69674ea9 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 794368d6..949f2441 100644 Binary files a/bin/windows/contrib/4.3/PACKAGES.rds and b/bin/windows/contrib/4.3/PACKAGES.rds differ diff --git a/bin/windows/contrib/4.3/RSQLite_2.3.8.zip 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da35a0cd..7751e915 100644 Binary files a/bin/windows/contrib/4.4/MS2Tox_0.4.2.zip and b/bin/windows/contrib/4.4/MS2Tox_0.4.2.zip differ diff --git a/bin/windows/contrib/4.4/PACKAGES b/bin/windows/contrib/4.4/PACKAGES index 88c04263..a5c32920 100644 --- a/bin/windows/contrib/4.4/PACKAGES +++ b/bin/windows/contrib/4.4/PACKAGES @@ -783,7 +783,7 @@ Suggests: covr, pkgload, testthat (>= 3.0.0), tibble, withr License: MIT + file LICENSE Package: GenomeInfoDb -Version: 1.42.0 +Version: 1.42.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData @@ -981,7 +981,7 @@ Suggests: knitr, markdown, testit License: GPL Package: Hmisc -Version: 5.2-0 +Version: 5.2-1 Depends: R (>= 4.2.0) Imports: methods, ggplot2, cluster, rpart, nnet, foreign, gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis, @@ -1216,10 +1216,10 @@ Suggests: testit License: LGPL-3 Package: later -Version: 1.3.2 +Version: 1.4.1 Imports: Rcpp (>= 0.12.9), rlang LinkingTo: Rcpp -Suggests: knitr, rmarkdown, testthat (>= 2.1.0) +Suggests: knitr, nanonext, R6, rmarkdown, testthat (>= 2.1.0) License: MIT + file LICENSE Archs: x64 @@ -1719,16 +1719,17 @@ Suggests: Rcpp, testthat (>= 3.0.0), withr License: MIT + file LICENSE Package: progressr -Version: 0.15.0 +Version: 0.15.1 Depends: R (>= 3.5.0) Imports: digest, utils Suggests: graphics, tcltk, beepr, cli, crayon, pbmcapply, progress, purrr, foreach, plyr, doFuture, future, future.apply, furrr, - RPushbullet, rstudioapi, shiny, commonmark, base64enc, tools + ntfy, RPushbullet, rstudioapi, shiny, commonmark, base64enc, + tools License: GPL (>= 3) Package: promises -Version: 1.3.0 +Version: 1.3.2 Imports: fastmap (>= 1.1.0), later, magrittr (>= 1.5), R6, Rcpp, rlang, stats LinkingTo: later, Rcpp diff --git a/bin/windows/contrib/4.4/PACKAGES.gz b/bin/windows/contrib/4.4/PACKAGES.gz index 39baba9e..7fadc18e 100644 Binary files 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a/bin/windows/contrib/4.4/promises_1.3.0.zip and b/bin/windows/contrib/4.4/promises_1.3.2.zip differ diff --git a/patRoonDeps-4.3.tsv b/patRoonDeps-4.3.tsv index 659caf21..9e5fbe5f 100644 --- a/patRoonDeps-4.3.tsv +++ b/patRoonDeps-4.3.tsv @@ -14,7 +14,7 @@ BiocGenerics 0.48.1 BiocManager 1.30.25 BiocParallel 1.36.0 BiocStyle 2.30.0 -bit 4.5.0 +bit 4.5.0.1 bit64 4.5.2 bitops 1.0-9 blob 1.2.4 @@ -56,7 +56,7 @@ dbplyr 2.5.0 dbscan 1.2-0 DelayedArray 0.28.0 dendextend 1.19.0 -DEoptimR 1.1-3 +DEoptimR 1.1-3-1 diagram 1.6.5 digest 0.6.37 docopt 0.7.1 @@ -117,7 +117,7 @@ hardhat 1.4.0 haven 2.5.4 heatmaply 1.5.0 highr 0.11 -Hmisc 5.2-0 +Hmisc 5.2-1 hms 1.1.3 htmlTable 2.4.3 htmltools 0.5.8.1 @@ -145,7 +145,7 @@ KPIC 2.4.0 dd0dddb0cac9bc7882eb1a420c82c9713a8aa0ce labeling 0.4.3 labelled 2.13.0 lambda.r 1.2.4 -later 1.3.2 +later 1.4.1 lattice 0.22-6 lava 1.8.0 lazyeval 0.2.2 @@ -171,7 +171,7 @@ MLmetrics 1.1.3 ModelMetrics 1.2.2.2 modelr 0.1.11 MS2Quant 1.1.0 e2cd1868cfe2cdb085899a7cf3edb145d2820f01 -MS2Tox 0.4.2 42c9747ba7cffc61e4e9a28f676b85cc2e1cd8df +MS2Tox 0.4.2 27fb0805a6bcc3b41634dc5d636079390b62173d MsCoreUtils 1.14.1 MsExperiment 1.4.0 MsFeatures 1.10.0 @@ -189,8 +189,8 @@ nontarget 2.2 e30221585182bc66e1f8e1113b2c1103a0f2cb56 nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4 numDeriv 2016.8-1.1 openssl 2.2.2 -parallelly 1.39.0 -patRoon 2.3.3 cbc12002ac7fc40d2478dd86d83a0c690f3dff2a +parallelly 1.40.0 +patRoon 2.3.3 0e811b3836ae3004a98b67d11ed59c7c68843016 pcaMethods 1.94.0 permute 0.9-7 pillar 1.9.0 @@ -206,8 +206,8 @@ pROC 1.18.5 processx 3.8.4 prodlim 2024.06.25 progress 1.2.3 -progressr 0.15.0 -promises 1.3.0 +progressr 0.15.1 +promises 1.3.2 ProtGenerics 1.34.0 proxy 0.4-27 ps 1.8.1 @@ -263,7 +263,7 @@ ropls 1.34.0 rpart 4.1.23 rprojroot 2.0.4 rsm 2.10.5 -RSQLite 2.3.8 +RSQLite 2.3.9 rstudioapi 0.17.1 rvest 1.0.4 S4Arrays 1.2.1 diff --git a/patRoonDeps-4.4.tsv b/patRoonDeps-4.4.tsv index 83ed4029..6cdc4e56 100644 --- a/patRoonDeps-4.4.tsv +++ b/patRoonDeps-4.4.tsv @@ -95,7 +95,7 @@ GA 3.2.4 gargle 1.5.2 gclus 1.3.2 generics 0.1.3 -GenomeInfoDb 1.42.0 +GenomeInfoDb 1.42.1 GenomeInfoDbData 1.2.13 b9d26daeee8f21f198372e59b6d712b44348a915 GenomicRanges 1.58.0 getPass 0.2-4 @@ -116,7 +116,7 @@ hardhat 1.4.0 haven 2.5.4 heatmaply 1.5.0 highr 0.11 -Hmisc 5.2-0 +Hmisc 5.2-1 hms 1.1.3 htmlTable 2.4.3 htmltools 0.5.8.1 @@ -144,7 +144,7 @@ KPIC 2.4.0 dd0dddb0cac9bc7882eb1a420c82c9713a8aa0ce labeling 0.4.3 labelled 2.13.0 lambda.r 1.2.4 -later 1.3.2 +later 1.4.1 lattice 0.22-6 lava 1.8.0 lazyeval 0.2.2 @@ -170,7 +170,7 @@ MLmetrics 1.1.3 ModelMetrics 1.2.2.2 modelr 0.1.11 MS2Quant 1.1.0 e2cd1868cfe2cdb085899a7cf3edb145d2820f01 -MS2Tox 0.4.2 42c9747ba7cffc61e4e9a28f676b85cc2e1cd8df +MS2Tox 0.4.2 27fb0805a6bcc3b41634dc5d636079390b62173d MsCoreUtils 1.18.0 MsExperiment 1.8.0 MsFeatures 1.14.0 @@ -188,7 +188,7 @@ nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4 numDeriv 2016.8-1.1 openssl 2.2.2 parallelly 1.39.0 -patRoon 2.3.3 cbc12002ac7fc40d2478dd86d83a0c690f3dff2a +patRoon 2.3.3 0e811b3836ae3004a98b67d11ed59c7c68843016 pcaMethods 1.98.0 permute 0.9-7 pillar 1.9.0 @@ -204,8 +204,8 @@ pROC 1.18.5 processx 3.8.4 prodlim 2024.06.25 progress 1.2.3 -progressr 0.15.0 -promises 1.3.0 +progressr 0.15.1 +promises 1.3.2 ProtGenerics 1.38.0 proxy 0.4-27 ps 1.8.1