diff --git a/bin/windows/contrib/4.2/DBI_1.1.3.zip b/bin/windows/contrib/4.2/DBI_1.1.3.zip deleted file mode 100644 index d939689b..00000000 Binary files a/bin/windows/contrib/4.2/DBI_1.1.3.zip and /dev/null differ diff --git a/bin/windows/contrib/4.2/DBI_1.2.0.zip b/bin/windows/contrib/4.2/DBI_1.2.0.zip new file mode 100644 index 00000000..3e86ed41 Binary files /dev/null and b/bin/windows/contrib/4.2/DBI_1.2.0.zip differ diff --git a/bin/windows/contrib/4.2/InterpretMSSpectrum_1.3.3.zip b/bin/windows/contrib/4.2/InterpretMSSpectrum_1.3.3.zip index ba9c3070..3b6c9db4 100644 Binary files a/bin/windows/contrib/4.2/InterpretMSSpectrum_1.3.3.zip and b/bin/windows/contrib/4.2/InterpretMSSpectrum_1.3.3.zip differ diff --git a/bin/windows/contrib/4.2/PACKAGES b/bin/windows/contrib/4.2/PACKAGES index b42a6ea9..efaf5bb8 100644 --- a/bin/windows/contrib/4.2/PACKAGES +++ b/bin/windows/contrib/4.2/PACKAGES @@ -413,11 +413,11 @@ Enhances: igraph License: GPL (>= 2) Package: DBI -Version: 1.1.3 +Version: 1.2.0 Depends: methods, R (>= 3.0.0) Suggests: blob, covr, DBItest, dbplyr, downlit, dplyr, glue, hms, - knitr, magrittr, RMariaDB, rmarkdown, rprojroot, RSQLite (>= - 1.1-2), testthat, xml2 + knitr, magrittr, nanoarrow, RMariaDB, rmarkdown, rprojroot, + RSQLite (>= 1.1-2), testthat (>= 3.0.0), vctrs, xml2 License: LGPL (>= 2.1) Package: dbplyr @@ -727,14 +727,14 @@ Depends: R (>= 2.8.0) License: LGPL-3 Package: future.apply -Version: 1.11.0 +Version: 1.11.1 Depends: R (>= 3.2.0), future (>= 1.28.0) Imports: globals (>= 0.16.1), parallel, utils Suggests: datasets, stats, tools, listenv (>= 0.8.0), R.rsp, markdown License: GPL (>= 2) Package: future -Version: 1.33.0 +Version: 1.33.1 Imports: digest, globals (>= 0.16.1), listenv (>= 0.8.0), parallel, parallelly (>= 1.34.0), utils Suggests: methods, RhpcBLASctl, R.rsp, markdown @@ -1276,7 +1276,7 @@ License: GPL (>= 2) Archs: x64 Package: magick -Version: 2.8.1 +Version: 2.8.2 Imports: Rcpp (>= 0.12.12), magrittr, curl LinkingTo: Rcpp Suggests: av (>= 0.3), spelling, jsonlite, methods, knitr, rmarkdown, @@ -1358,7 +1358,7 @@ Suggests: markdown License: GPL-3 Package: mgcv -Version: 1.9-0 +Version: 1.9-1 Priority: recommended Depends: R (>= 3.6.0), nlme (>= 3.1-64) Imports: methods, stats, graphics, Matrix, splines, utils diff --git a/bin/windows/contrib/4.2/PACKAGES.gz b/bin/windows/contrib/4.2/PACKAGES.gz index 8bcb0dec..493c3c8f 100644 Binary files a/bin/windows/contrib/4.2/PACKAGES.gz and b/bin/windows/contrib/4.2/PACKAGES.gz differ diff --git a/bin/windows/contrib/4.2/PACKAGES.rds b/bin/windows/contrib/4.2/PACKAGES.rds index c6177a30..e8f64d23 100644 Binary files a/bin/windows/contrib/4.2/PACKAGES.rds and b/bin/windows/contrib/4.2/PACKAGES.rds differ diff --git a/bin/windows/contrib/4.2/cliqueMS_1.7.1.zip b/bin/windows/contrib/4.2/cliqueMS_1.7.1.zip index 0987bea8..3988e1ab 100644 Binary files a/bin/windows/contrib/4.2/cliqueMS_1.7.1.zip and b/bin/windows/contrib/4.2/cliqueMS_1.7.1.zip differ 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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 e65c05ad..be9b2657 100644 --- a/bin/windows/contrib/4.3/PACKAGES +++ b/bin/windows/contrib/4.3/PACKAGES @@ -427,11 +427,11 @@ Enhances: igraph License: GPL (>= 2) Package: DBI -Version: 1.1.3 +Version: 1.2.0 Depends: methods, R (>= 3.0.0) Suggests: blob, covr, DBItest, dbplyr, downlit, dplyr, glue, hms, - knitr, magrittr, RMariaDB, rmarkdown, rprojroot, RSQLite (>= - 1.1-2), testthat, xml2 + knitr, magrittr, nanoarrow, RMariaDB, rmarkdown, rprojroot, + RSQLite (>= 1.1-2), testthat (>= 3.0.0), vctrs, xml2 License: LGPL (>= 2.1) Package: dbplyr @@ -742,14 +742,14 @@ Depends: R (>= 2.8.0) License: LGPL-3 Package: future.apply -Version: 1.11.0 +Version: 1.11.1 Depends: R (>= 3.2.0), future (>= 1.28.0) Imports: globals (>= 0.16.1), parallel, utils Suggests: datasets, stats, tools, listenv (>= 0.8.0), R.rsp, markdown License: GPL (>= 2) Package: future -Version: 1.33.0 +Version: 1.33.1 Imports: digest, globals (>= 0.16.1), listenv (>= 0.8.0), parallel, parallelly (>= 1.34.0), utils Suggests: methods, RhpcBLASctl, R.rsp, markdown @@ -789,12 +789,13 @@ Suggests: covr, pkgload, testthat (>= 3.0.0), tibble, withr License: MIT + file LICENSE Package: GenomeInfoDb -Version: 1.38.2 +Version: 1.38.5 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData -Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, - TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, +Suggests: R.utils, data.table, GenomicRanges, Rsamtools, + GenomicAlignments, GenomicFeatures, BSgenome, + TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 @@ -1291,7 +1292,7 @@ License: GPL (>= 2) Archs: x64 Package: magick -Version: 2.8.1 +Version: 2.8.2 Imports: Rcpp (>= 0.12.12), magrittr, curl LinkingTo: Rcpp Suggests: av (>= 0.3), spelling, jsonlite, methods, knitr, rmarkdown, @@ -1380,7 +1381,7 @@ Suggests: markdown License: GPL-3 Package: mgcv -Version: 1.9-0 +Version: 1.9-1 Priority: recommended Depends: R (>= 3.6.0), nlme (>= 3.1-64) Imports: methods, stats, graphics, Matrix, splines, utils @@ -2311,7 +2312,7 @@ License: MIT + file LICENSE Archs: x64 Package: SparseArray -Version: 1.2.2 +Version: 1.2.3 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors, S4Arrays (>= 1.1.6) Imports: stats, matrixStats, IRanges, XVector diff --git a/bin/windows/contrib/4.3/PACKAGES.gz b/bin/windows/contrib/4.3/PACKAGES.gz index 52b40fe8..9ab886d8 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 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from bin/windows/contrib/4.3/magick_2.8.1.zip rename to bin/windows/contrib/4.3/magick_2.8.2.zip index 6502181f..8ef1917e 100644 Binary files a/bin/windows/contrib/4.3/magick_2.8.1.zip and b/bin/windows/contrib/4.3/magick_2.8.2.zip differ diff --git a/bin/windows/contrib/4.3/mgcv_1.9-0.zip b/bin/windows/contrib/4.3/mgcv_1.9-0.zip deleted file mode 100644 index b2fbcd66..00000000 Binary files a/bin/windows/contrib/4.3/mgcv_1.9-0.zip and /dev/null differ diff --git a/bin/windows/contrib/4.3/mgcv_1.9-1.zip b/bin/windows/contrib/4.3/mgcv_1.9-1.zip new file mode 100644 index 00000000..a00ab5b3 Binary files /dev/null and b/bin/windows/contrib/4.3/mgcv_1.9-1.zip differ 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 f094b8d3..9d34ca0e 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/patRoonDeps-4.2.tsv b/patRoonDeps-4.2.tsv index 52292cd5..e614099d 100644 --- a/patRoonDeps-4.2.tsv +++ b/patRoonDeps-4.2.tsv @@ -49,7 +49,7 @@ crosstalk 1.2.1 curl 5.2.0 data.table 1.14.10 data.tree 1.1.0 -DBI 1.1.3 +DBI 1.2.0 dbplyr 2.4.0 dbscan 1.1-12 DelayedArray 0.23.2 @@ -89,8 +89,8 @@ fst 0.9.8 fstcore 0.9.18 futile.logger 1.4.3 futile.options 1.0.1 -future 1.33.0 -future.apply 1.11.0 +future 1.33.1 +future.apply 1.11.1 GA 3.2.3 gargle 1.5.2 gclus 1.3.2 @@ -152,7 +152,7 @@ lifecycle 1.0.4 limma 3.54.2 listenv 0.9.0 lubridate 1.9.3 -magick 2.8.1 +magick 2.8.2 magrittr 2.0.3 MALDIquant 1.22.1 MASS 7.3-60 @@ -162,7 +162,7 @@ MatrixGenerics 1.10.0 matrixStats 1.2.0 memoise 2.0.1 MetaClean 1.0.1 d0ce1bc0b2fe4d17e7e047c8c07c75b81c4e5833 -mgcv 1.9-0 +mgcv 1.9-1 mime 0.12 miniUI 0.1.1.1 MLmetrics 1.1.1 @@ -186,7 +186,7 @@ nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4 numDeriv 2016.8-1.1 openssl 2.1.1 parallelly 1.36.0 -patRoon 2.3.1 336bc1625e69b4ff6444f52d861b459ef8d10e5b +patRoon 2.3.1 44da5141fd5bdb3565ad42720514f158ed96d939 pcaMethods 1.90.0 permute 0.9-7 pillar 1.9.0 diff --git a/patRoonDeps-4.3.tsv b/patRoonDeps-4.3.tsv index 6a36bcec..f5cc66ab 100644 --- a/patRoonDeps-4.3.tsv +++ b/patRoonDeps-4.3.tsv @@ -51,7 +51,7 @@ crosstalk 1.2.1 curl 5.2.0 data.table 1.14.10 data.tree 1.1.0 -DBI 1.1.3 +DBI 1.2.0 dbplyr 2.4.0 dbscan 1.1-12 DelayedArray 0.28.0 @@ -91,13 +91,13 @@ fst 0.9.8 fstcore 0.9.18 futile.logger 1.4.3 futile.options 1.0.1 -future 1.33.0 -future.apply 1.11.0 +future 1.33.1 +future.apply 1.11.1 GA 3.2.3 gargle 1.5.2 gclus 1.3.2 generics 0.1.3 -GenomeInfoDb 1.38.2 +GenomeInfoDb 1.38.5 GenomeInfoDbData 1.2.11 f3111730888a3d83e9465ffa2552003de153bbf2 GenomicRanges 1.54.1 getPass 0.2-4 @@ -154,7 +154,7 @@ lifecycle 1.0.4 limma 3.58.1 listenv 0.9.0 lubridate 1.9.3 -magick 2.8.1 +magick 2.8.2 magrittr 2.0.3 MALDIquant 1.22.1 MASS 7.3-60 @@ -165,7 +165,7 @@ matrixStats 1.2.0 memoise 2.0.1 MetaboCoreUtils 1.10.0 MetaClean 1.0.1 d0ce1bc0b2fe4d17e7e047c8c07c75b81c4e5833 -mgcv 1.9-0 +mgcv 1.9-1 mime 0.12 miniUI 0.1.1.1 MLmetrics 1.1.1 @@ -191,7 +191,7 @@ nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4 numDeriv 2016.8-1.1 openssl 2.1.1 parallelly 1.36.0 -patRoon 2.3.1 336bc1625e69b4ff6444f52d861b459ef8d10e5b +patRoon 2.3.1 44da5141fd5bdb3565ad42720514f158ed96d939 pcaMethods 1.94.0 permute 0.9-7 pillar 1.9.0 @@ -279,7 +279,7 @@ shinyjs 2.1.0 slam 0.1-50 snow 0.4-4 sourcetools 0.1.7-1 -SparseArray 1.2.2 +SparseArray 1.2.3 sparsesvd 0.2-2 Spectra 1.12.0 splashR 0.0.4 174fbf289a0357535f9bacda282b9a2dbb7807cc