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index 2a8f0f0f..00000000 Binary files a/bin/windows/contrib/4.2/MASS_7.3-60.zip and /dev/null differ diff --git a/bin/windows/contrib/4.2/Matrix_1.6-4.zip b/bin/windows/contrib/4.2/Matrix_1.6-4.zip deleted file mode 100644 index b37c9103..00000000 Binary files a/bin/windows/contrib/4.2/Matrix_1.6-4.zip and /dev/null differ diff --git a/bin/windows/contrib/4.2/Matrix_1.6-5.zip b/bin/windows/contrib/4.2/Matrix_1.6-5.zip new file mode 100644 index 00000000..804596b5 Binary files /dev/null and b/bin/windows/contrib/4.2/Matrix_1.6-5.zip differ diff --git a/bin/windows/contrib/4.2/PACKAGES b/bin/windows/contrib/4.2/PACKAGES index efaf5bb8..39dfc378 100644 --- a/bin/windows/contrib/4.2/PACKAGES +++ b/bin/windows/contrib/4.2/PACKAGES @@ -42,7 +42,7 @@ License: GPL-2 | GPL-3 Archs: x64 Package: BH -Version: 1.81.0-1 +Version: 1.84.0-0 License: BSL-1.0 Package: Biobase @@ -481,7 +481,7 @@ Imports: stats, graphics License: GPL (>= 2) Package: digest -Version: 0.6.33 +Version: 0.6.34 Depends: R (>= 3.3.0) Imports: utils Suggests: tinytest, simplermarkdown @@ -609,7 +609,7 @@ License: MIT + file LICENSE Archs: x64 Package: fastcluster -Version: 1.2.3 +Version: 1.2.6 Depends: R (>= 3.0.0) Enhances: stats, flashClust License: FreeBSD | GPL-2 | file LICENSE @@ -622,7 +622,7 @@ License: MIT + file LICENSE Archs: x64 Package: ff -Version: 4.0.9 +Version: 4.0.12 Depends: R (>= 2.10.1), bit (>= 4.0.0), utils Suggests: biglm, testthat (>= 0.11.0) License: GPL-2 | GPL-3 | file LICENSE @@ -833,14 +833,14 @@ Enhances: sp License: MIT + file LICENSE Package: ggrepel -Version: 0.9.4 +Version: 0.9.5 Depends: R (>= 3.0.0), ggplot2 (>= 2.2.0) Imports: grid, Rcpp, rlang (>= 0.3.0), scales (>= 0.5.0), withr (>= 2.5.0) LinkingTo: Rcpp -Suggests: knitr, rmarkdown, testthat, svglite, vdiffr, gridExtra, - devtools, prettydoc, ggbeeswarm, dplyr, magrittr, readr, - stringr +Suggests: knitr, rmarkdown, testthat, svglite, vdiffr, gridExtra, ggpp, + patchwork, devtools, prettydoc, ggbeeswarm, dplyr, magrittr, + readr, stringr License: GPL-3 | file LICENSE Archs: x64 @@ -858,12 +858,12 @@ Imports: codetools License: LGPL (>= 2.1) Package: glue -Version: 1.6.2 -Depends: R (>= 3.4) +Version: 1.7.0 +Depends: R (>= 3.6) Imports: methods -Suggests: covr, crayon, DBI, dplyr, forcats, ggplot2, knitr, magrittr, - microbenchmark, R.utils, rmarkdown, rprintf, RSQLite, stringr, - testthat (>= 3.0.0), vctrs (>= 0.3.0), waldo (>= 0.3.0), withr +Suggests: crayon, DBI (>= 1.2.0), dplyr, knitr, magrittr, rlang, + rmarkdown, RSQLite, testthat (>= 3.2.0), vctrs (>= 0.3.0), + waldo (>= 0.3.0), withr License: MIT + file LICENSE Archs: x64 @@ -1301,7 +1301,7 @@ License: GPL (>= 3) Archs: x64 Package: MASS -Version: 7.3-60 +Version: 7.3-60.0.1 Priority: recommended Depends: R (>= 4.0), grDevices, graphics, stats, utils Imports: methods @@ -1316,7 +1316,7 @@ License: LGPL (>= 2) Archs: x64 Package: Matrix -Version: 1.6-4 +Version: 1.6-5 Priority: recommended Depends: R (>= 3.5.0), methods Imports: grDevices, graphics, grid, lattice, stats, utils @@ -1608,7 +1608,7 @@ Suggests: Rcpp License: MIT + file LICENSE Package: plotly -Version: 4.10.3 +Version: 4.10.4 Depends: R (>= 3.2.0), ggplot2 (>= 3.0.0) Imports: tools, scales, httr (>= 1.3.0), jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), @@ -1726,7 +1726,7 @@ License: GPL-2 Archs: x64 Package: ps -Version: 1.7.5 +Version: 1.7.6 Depends: R (>= 3.4) Imports: utils Suggests: callr, covr, curl, pillar, pingr, processx (>= 3.1.0), R6, @@ -1886,7 +1886,7 @@ Depends: R (>= 2.0.0) License: Apache License 2.0 Package: Rcpp -Version: 1.0.11 +Version: 1.0.12 Imports: methods, utils Suggests: tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2) License: GPL (>= 2) @@ -1902,7 +1902,7 @@ License: GPL (>= 2) Archs: x64 Package: RCurl -Version: 1.98-1.13 +Version: 1.98-1.14 Depends: R (>= 3.4.0), methods Imports: bitops Suggests: XML @@ -1953,13 +1953,13 @@ Imports: base64enc, digest, XML License: GPL (>= 3) Package: readr -Version: 2.1.4 -Depends: R (>= 3.5) +Version: 2.1.5 +Depends: R (>= 3.6) Imports: cli (>= 3.2.0), clipr, crayon, hms (>= 0.4.1), lifecycle (>= 0.2.0), methods, R6, rlang, tibble, utils, vroom (>= 1.6.0) LinkingTo: cpp11, tzdb (>= 0.1.1) Suggests: covr, curl, datasets, knitr, rmarkdown, spelling, stringi, - testthat (>= 3.1.2), tzdb (>= 0.1.1), waldo, withr, xml2 + testthat (>= 3.2.0), tzdb (>= 0.1.1), waldo, withr, xml2 License: MIT + file LICENSE Archs: x64 @@ -2004,12 +2004,12 @@ Suggests: covr, testthat License: MIT + file LICENSE Package: reprex -Version: 2.0.2 -Depends: R (>= 3.4) +Version: 2.1.0 +Depends: R (>= 3.6) Imports: callr (>= 3.6.0), cli (>= 3.2.0), clipr (>= 0.4.0), fs, glue, knitr (>= 1.23), lifecycle, rlang (>= 1.0.0), rmarkdown, rstudioapi, utils, withr (>= 2.3.0) -Suggests: covr, fortunes, miniUI, mockr, rprojroot, sessioninfo, shiny, +Suggests: covr, fortunes, miniUI, rprojroot, sessioninfo, shiny, spelling, styler (>= 1.2.0), testthat (>= 3.0.2) License: MIT + file LICENSE @@ -2051,7 +2051,7 @@ License: LGPL-2.1 Archs: x64 Package: rlang -Version: 1.1.2 +Version: 1.1.3 Depends: R (>= 3.5.0) Imports: utils Suggests: cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr, @@ -2129,13 +2129,13 @@ Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2 License: GPL (>= 2) Package: RSQLite -Version: 2.3.4 +Version: 2.3.5 Depends: R (>= 3.1.0) -Imports: bit64, blob (>= 1.2.0), DBI (>= 1.1.0), memoise, methods, +Imports: bit64, blob (>= 1.2.0), DBI (>= 1.2.0), memoise, methods, pkgconfig, rlang LinkingTo: plogr (>= 0.2.0), cpp11 (>= 0.4.0) -Suggests: callr, DBItest (>= 1.7.2.9001), gert, gh, hms, knitr, - magrittr, rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2 +Suggests: callr, DBItest (>= 1.8.0), gert, gh, hms, knitr, magrittr, + rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2 License: LGPL (>= 2.1) Archs: x64 @@ -2402,11 +2402,11 @@ Suggests: covr (>= 3.6.1), feather (>= 0.3.5), glue (>= 1.6.2), mockr License: MIT + file LICENSE Package: timechange -Version: 0.2.0 +Version: 0.3.0 Depends: R (>= 3.3) LinkingTo: cpp11 (>= 0.2.7) Suggests: testthat (>= 0.7.1.99), knitr -License: GPL-3 +License: GPL (>= 3) Archs: x64 Package: timeDate @@ -2455,7 +2455,7 @@ License: Apache License (== 2.0) | file LICENSE Archs: x64 Package: uuid -Version: 1.1-1 +Version: 1.2-0 Depends: R (>= 2.9.0) License: MIT + file LICENSE Archs: x64 @@ -2551,9 +2551,9 @@ Suggests: httpuv, knitr, rmarkdown, shiny, testthat (>= 3.0.0) License: GPL-2 Package: withr -Version: 2.5.2 -Depends: R (>= 3.2.0) -Imports: graphics, grDevices, stats +Version: 3.0.0 +Depends: R (>= 3.5.0) +Imports: graphics, grDevices, Suggests: callr, covr, DBI, knitr, lattice, methods, rlang, rmarkdown (>= 2.12), RSQLite, testthat (>= 3.0.0) License: MIT + file LICENSE diff --git a/bin/windows/contrib/4.2/PACKAGES.gz b/bin/windows/contrib/4.2/PACKAGES.gz index 493c3c8f..670fa5f0 100644 Binary files a/bin/windows/contrib/4.2/PACKAGES.gz and 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+Version: 1.84.0-0 License: BSL-1.0 Package: Biobase @@ -496,7 +496,7 @@ Imports: stats, graphics License: GPL (>= 2) Package: digest -Version: 0.6.33 +Version: 0.6.34 Depends: R (>= 3.3.0) Imports: utils Suggests: tinytest, simplermarkdown @@ -624,7 +624,7 @@ License: MIT + file LICENSE Archs: x64 Package: fastcluster -Version: 1.2.3 +Version: 1.2.6 Depends: R (>= 3.0.0) Enhances: stats, flashClust License: FreeBSD | GPL-2 | file LICENSE @@ -637,7 +637,7 @@ License: MIT + file LICENSE Archs: x64 Package: ff -Version: 4.0.9 +Version: 4.0.12 Depends: R (>= 2.10.1), bit (>= 4.0.0), utils Suggests: biglm, testthat (>= 0.11.0) License: GPL-2 | GPL-3 | file LICENSE @@ -849,14 +849,14 @@ Enhances: sp License: MIT + file LICENSE Package: ggrepel -Version: 0.9.4 +Version: 0.9.5 Depends: R (>= 3.0.0), ggplot2 (>= 2.2.0) Imports: grid, Rcpp, rlang (>= 0.3.0), scales (>= 0.5.0), withr (>= 2.5.0) LinkingTo: Rcpp -Suggests: knitr, rmarkdown, testthat, svglite, vdiffr, gridExtra, - devtools, prettydoc, ggbeeswarm, dplyr, magrittr, readr, - stringr +Suggests: knitr, rmarkdown, testthat, svglite, vdiffr, gridExtra, ggpp, + patchwork, devtools, prettydoc, ggbeeswarm, dplyr, magrittr, + readr, stringr License: GPL-3 | file LICENSE Archs: x64 @@ -874,12 +874,12 @@ Imports: codetools License: LGPL (>= 2.1) Package: glue -Version: 1.6.2 -Depends: R (>= 3.4) +Version: 1.7.0 +Depends: R (>= 3.6) Imports: methods -Suggests: covr, crayon, DBI, dplyr, forcats, ggplot2, knitr, magrittr, - microbenchmark, R.utils, rmarkdown, rprintf, RSQLite, stringr, - testthat (>= 3.0.0), vctrs (>= 0.3.0), waldo (>= 0.3.0), withr +Suggests: crayon, DBI (>= 1.2.0), dplyr, knitr, magrittr, rlang, + rmarkdown, RSQLite, testthat (>= 3.2.0), vctrs (>= 0.3.0), + waldo (>= 0.3.0), withr License: MIT + file LICENSE Archs: x64 @@ -1309,7 +1309,7 @@ License: MIT + file LICENSE Archs: x64 Package: MALDIquant -Version: 1.22.1 +Version: 1.22.2 Depends: R (>= 4.0.0), methods Imports: parallel Suggests: knitr, testthat (>= 0.8) @@ -1317,7 +1317,7 @@ License: GPL (>= 3) Archs: x64 Package: MASS -Version: 7.3-60 +Version: 7.3-60.0.1 Priority: recommended Depends: R (>= 4.0), grDevices, graphics, stats, utils Imports: methods @@ -1332,7 +1332,7 @@ License: LGPL (>= 2) Archs: x64 Package: Matrix -Version: 1.6-4 +Version: 1.6-5 Priority: recommended Depends: R (>= 3.5.0), methods Imports: grDevices, graphics, grid, lattice, stats, utils @@ -1648,7 +1648,7 @@ Suggests: Rcpp License: MIT + file LICENSE Package: plotly -Version: 4.10.3 +Version: 4.10.4 Depends: R (>= 3.2.0), ggplot2 (>= 3.0.0) Imports: tools, scales, httr (>= 1.3.0), jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), @@ -1766,7 +1766,7 @@ License: GPL-2 Archs: x64 Package: ps -Version: 1.7.5 +Version: 1.7.6 Depends: R (>= 3.4) Imports: utils Suggests: callr, covr, curl, pillar, pingr, processx (>= 3.1.0), R6, @@ -1939,7 +1939,7 @@ Depends: R (>= 2.0.0) License: Apache License 2.0 Package: Rcpp -Version: 1.0.11 +Version: 1.0.12 Imports: methods, utils Suggests: tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2) License: GPL (>= 2) @@ -1955,7 +1955,7 @@ License: GPL (>= 2) Archs: x64 Package: RCurl -Version: 1.98-1.13 +Version: 1.98-1.14 Depends: R (>= 3.4.0), methods Imports: bitops Suggests: XML @@ -2006,13 +2006,13 @@ Imports: base64enc, digest, XML License: GPL (>= 3) Package: readr -Version: 2.1.4 -Depends: R (>= 3.5) +Version: 2.1.5 +Depends: R (>= 3.6) Imports: cli (>= 3.2.0), clipr, crayon, hms (>= 0.4.1), lifecycle (>= 0.2.0), methods, R6, rlang, tibble, utils, vroom (>= 1.6.0) LinkingTo: cpp11, tzdb (>= 0.1.1) Suggests: covr, curl, datasets, knitr, rmarkdown, spelling, stringi, - testthat (>= 3.1.2), tzdb (>= 0.1.1), waldo, withr, xml2 + testthat (>= 3.2.0), tzdb (>= 0.1.1), waldo, withr, xml2 License: MIT + file LICENSE Archs: x64 @@ -2057,12 +2057,12 @@ Suggests: covr, testthat License: MIT + file LICENSE Package: reprex -Version: 2.0.2 -Depends: R (>= 3.4) +Version: 2.1.0 +Depends: R (>= 3.6) Imports: callr (>= 3.6.0), cli (>= 3.2.0), clipr (>= 0.4.0), fs, glue, knitr (>= 1.23), lifecycle, rlang (>= 1.0.0), rmarkdown, rstudioapi, utils, withr (>= 2.3.0) -Suggests: covr, fortunes, miniUI, mockr, rprojroot, sessioninfo, shiny, +Suggests: covr, fortunes, miniUI, rprojroot, sessioninfo, shiny, spelling, styler (>= 1.2.0), testthat (>= 3.0.2) License: MIT + file LICENSE @@ -2104,7 +2104,7 @@ License: LGPL-2.1 Archs: x64 Package: rlang -Version: 1.1.2 +Version: 1.1.3 Depends: R (>= 3.5.0) Imports: utils Suggests: cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr, @@ -2182,13 +2182,13 @@ Suggests: emmeans (> 1.3.5.1), Vdgraph, conf.design, DoE.base, FrF2 License: GPL (>= 2) Package: RSQLite -Version: 2.3.4 +Version: 2.3.5 Depends: R (>= 3.1.0) -Imports: bit64, blob (>= 1.2.0), DBI (>= 1.1.0), memoise, methods, +Imports: bit64, blob (>= 1.2.0), DBI (>= 1.2.0), memoise, methods, pkgconfig, rlang LinkingTo: plogr (>= 0.2.0), cpp11 (>= 0.4.0) -Suggests: callr, DBItest (>= 1.7.2.9001), gert, gh, hms, knitr, - magrittr, rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2 +Suggests: callr, DBItest (>= 1.8.0), gert, gh, hms, knitr, magrittr, + rmarkdown, rvest, testthat (>= 3.0.0), withr, xml2 License: LGPL (>= 2.1) Archs: x64 @@ -2496,11 +2496,11 @@ Suggests: covr (>= 3.6.1), feather (>= 0.3.5), glue (>= 1.6.2), mockr License: MIT + file LICENSE Package: timechange -Version: 0.2.0 +Version: 0.3.0 Depends: R (>= 3.3) LinkingTo: cpp11 (>= 0.2.7) Suggests: testthat (>= 0.7.1.99), knitr -License: GPL-3 +License: GPL (>= 3) Archs: x64 Package: timeDate @@ -2549,7 +2549,7 @@ License: Apache License (== 2.0) | file LICENSE Archs: x64 Package: uuid -Version: 1.1-1 +Version: 1.2-0 Depends: R (>= 2.9.0) License: MIT + file LICENSE Archs: x64 @@ -2645,15 +2645,15 @@ Suggests: httpuv, knitr, rmarkdown, shiny, testthat (>= 3.0.0) License: GPL-2 Package: withr -Version: 2.5.2 -Depends: R (>= 3.2.0) -Imports: graphics, grDevices, stats +Version: 3.0.0 +Depends: R (>= 3.5.0) +Imports: graphics, grDevices, Suggests: callr, covr, DBI, knitr, lattice, methods, rlang, rmarkdown (>= 2.12), RSQLite, testthat (>= 3.0.0) License: MIT + file LICENSE Package: xcms -Version: 4.0.1 +Version: 4.0.2 Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0), MSnbase (>= 2.23.1) Imports: mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.29.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet @@ -2689,7 +2689,7 @@ License: Apache License (== 2.0) | file LICENSE Archs: x64 Package: XML -Version: 3.99-0.16 +Version: 3.99-0.16.1 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 9ab886d8..8fec3564 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 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b/bin/windows/contrib/4.3/withr_3.0.0.zip differ diff --git a/bin/windows/contrib/4.3/xcms_4.0.1.zip b/bin/windows/contrib/4.3/xcms_4.0.2.zip similarity index 58% rename from bin/windows/contrib/4.3/xcms_4.0.1.zip rename to bin/windows/contrib/4.3/xcms_4.0.2.zip index 7dc43989..155395bc 100644 Binary files a/bin/windows/contrib/4.3/xcms_4.0.1.zip and b/bin/windows/contrib/4.3/xcms_4.0.2.zip differ diff --git a/patRoonDeps-4.2.tsv b/patRoonDeps-4.2.tsv index e614099d..0e238701 100644 --- a/patRoonDeps-4.2.tsv +++ b/patRoonDeps-4.2.tsv @@ -5,7 +5,7 @@ askpass 1.2.0 assertthat 0.2.1 backports 1.4.1 base64enc 0.1-3 -BH 1.81.0-1 +BH 1.84.0-0 Biobase 2.58.0 BiocBaseUtils 1.0.0 BiocGenerics 0.44.0 @@ -56,7 +56,7 @@ DelayedArray 0.23.2 dendextend 1.17.1 DEoptimR 1.1-3 diagram 1.6.5 -digest 0.6.33 +digest 0.6.34 docopt 0.7.1 doParallel 1.0.17 dplyr 1.1.4 @@ -73,9 +73,9 @@ evaluate 0.23 fansi 1.0.6 farver 2.1.1 fastAdaboost 1.0.0 f331ff8ccfe2e7f318448a29bc72af646dfaf2c1 -fastcluster 1.2.3 +fastcluster 1.2.6 fastmap 1.1.1 -ff 4.0.9 +ff 4.0.12 fingerprint 3.5.7 flexdashboard 0.6.2 fontawesome 0.5.2 @@ -100,10 +100,10 @@ GenomeInfoDbData 1.2.11 f3111730888a3d83e9465ffa2552003de153bbf2 GenomicRanges 1.50.2 getPass 0.2-4 ggplot2 3.4.4 -ggrepel 0.9.4 +ggrepel 0.9.5 GlobalOptions 0.1.2 globals 0.16.2 -glue 1.6.2 +glue 1.7.0 googledrive 2.1.1 googlesheets4 1.1.1 gower 1.0.1 @@ -155,9 +155,9 @@ lubridate 1.9.3 magick 2.8.2 magrittr 2.0.3 MALDIquant 1.22.1 -MASS 7.3-60 +MASS 7.3-60.0.1 MassSpecWavelet 1.64.1 -Matrix 1.6-4 +Matrix 1.6-5 MatrixGenerics 1.10.0 matrixStats 1.2.0 memoise 2.0.1 @@ -186,13 +186,13 @@ nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4 numDeriv 2016.8-1.1 openssl 2.1.1 parallelly 1.36.0 -patRoon 2.3.1 44da5141fd5bdb3565ad42720514f158ed96d939 +patRoon 2.3.1 5c43464b096a9632f6d6ec3b00b464e1509be349 pcaMethods 1.90.0 permute 0.9-7 pillar 1.9.0 pkgconfig 2.0.3 plogr 0.2.0 -plotly 4.10.3 +plotly 4.10.4 plotrix 3.8-4 plyr 1.8.9 png 0.1-8 @@ -206,7 +206,7 @@ progressr 0.14.0 promises 1.2.1 ProtGenerics 1.30.0 proxy 0.4-27 -ps 1.7.5 +ps 1.7.6 purrr 1.0.2 qap 0.1-2 qlcMatrix 0.9.7 d919872f69b07b6cf892f725ed3d6e4569319206 @@ -228,28 +228,28 @@ rbibutils 2.2.16 rcdk 3.8.1 rcdklibs 2.8 RColorBrewer 1.1-3 -Rcpp 1.0.11 +Rcpp 1.0.12 RcppArmadillo 0.12.6.6.1 -RCurl 1.98-1.13 +RCurl 1.98-1.14 RDCOMClient 0.95-1 1554833f8659461427a93732119756ae1c25bc32 Rdisop 1.58.0 Rdpack 2.6 reactable 0.4.4 reactR 0.5.0 readMzXmlData 2.8.3 -readr 2.1.4 +readr 2.1.5 readxl 1.4.3 recipes 1.0.9 registry 0.5-1 rematch 2.0.0 rematch2 2.1.2 -reprex 2.0.2 +reprex 2.1.0 reshape2 1.4.4 Rgraphviz 2.42.0 rhandsontable 0.3.8 Rhdf5lib 1.20.0 rJava 1.0-10 -rlang 1.1.2 +rlang 1.1.3 rlist 0.4.6.2 rmarkdown 2.25 robustbase 0.99-1 @@ -258,7 +258,7 @@ ropls 1.30.0 rpart 4.1.23 rprojroot 2.0.4 rsm 2.10.4 -RSQLite 2.3.4 +RSQLite 2.3.5 rstudioapi 0.15.0 rvest 1.0.3 S4Vectors 0.36.2 @@ -288,14 +288,14 @@ tibble 3.2.1 tidyr 1.3.0 tidyselect 1.2.0 tidyverse 2.0.0 -timechange 0.2.0 +timechange 0.3.0 timeDate 4032.109 tinytex 0.49 TSP 1.2-4 tzdb 0.4.0 UpSetR 1.4.0 utf8 1.2.4 -uuid 1.1-1 +uuid 1.2-0 vctrs 0.6.5 vegan 2.6-4 VennDiagram 1.7.3 @@ -306,7 +306,7 @@ vroom 1.6.5 vsn 3.66.0 webchem 1.3.0 webshot 0.5.5 -withr 2.5.2 +withr 3.0.0 xcms 3.20.0 xfun 0.41 xgboost 1.7.6.1 diff --git a/patRoonDeps-4.3.tsv b/patRoonDeps-4.3.tsv index f5cc66ab..258017b1 100644 --- a/patRoonDeps-4.3.tsv +++ b/patRoonDeps-4.3.tsv @@ -7,7 +7,7 @@ askpass 1.2.0 assertthat 0.2.1 backports 1.4.1 base64enc 0.1-3 -BH 1.81.0-1 +BH 1.84.0-0 Biobase 2.62.0 BiocBaseUtils 1.4.0 BiocGenerics 0.48.1 @@ -58,7 +58,7 @@ DelayedArray 0.28.0 dendextend 1.17.1 DEoptimR 1.1-3 diagram 1.6.5 -digest 0.6.33 +digest 0.6.34 docopt 0.7.1 doParallel 1.0.17 dplyr 1.1.4 @@ -75,9 +75,9 @@ evaluate 0.23 fansi 1.0.6 farver 2.1.1 fastAdaboost 1.0.0 f331ff8ccfe2e7f318448a29bc72af646dfaf2c1 -fastcluster 1.2.3 +fastcluster 1.2.6 fastmap 1.1.1 -ff 4.0.9 +ff 4.0.12 fingerprint 3.5.7 flexdashboard 0.6.2 fontawesome 0.5.2 @@ -102,10 +102,10 @@ GenomeInfoDbData 1.2.11 f3111730888a3d83e9465ffa2552003de153bbf2 GenomicRanges 1.54.1 getPass 0.2-4 ggplot2 3.4.4 -ggrepel 0.9.4 +ggrepel 0.9.5 GlobalOptions 0.1.2 globals 0.16.2 -glue 1.6.2 +glue 1.7.0 googledrive 2.1.1 googlesheets4 1.1.1 gower 1.0.1 @@ -156,10 +156,10 @@ listenv 0.9.0 lubridate 1.9.3 magick 2.8.2 magrittr 2.0.3 -MALDIquant 1.22.1 -MASS 7.3-60 +MALDIquant 1.22.2 +MASS 7.3-60.0.1 MassSpecWavelet 1.68.0 -Matrix 1.6-4 +Matrix 1.6-5 MatrixGenerics 1.14.0 matrixStats 1.2.0 memoise 2.0.1 @@ -191,13 +191,13 @@ nontargetData 1.1 75b2a92cd549f72cc71dfe7b86bd42947d62f2c4 numDeriv 2016.8-1.1 openssl 2.1.1 parallelly 1.36.0 -patRoon 2.3.1 44da5141fd5bdb3565ad42720514f158ed96d939 +patRoon 2.3.1 5c43464b096a9632f6d6ec3b00b464e1509be349 pcaMethods 1.94.0 permute 0.9-7 pillar 1.9.0 pkgconfig 2.0.3 plogr 0.2.0 -plotly 4.10.3 +plotly 4.10.4 plotrix 3.8-4 plyr 1.8.9 png 0.1-8 @@ -211,7 +211,7 @@ progressr 0.14.0 promises 1.2.1 ProtGenerics 1.34.0 proxy 0.4-27 -ps 1.7.5 +ps 1.7.6 purrr 1.0.2 qap 0.1-2 QFeatures 1.12.0 @@ -234,28 +234,28 @@ rbibutils 2.2.16 rcdk 3.8.1 rcdklibs 2.8 RColorBrewer 1.1-3 -Rcpp 1.0.11 +Rcpp 1.0.12 RcppArmadillo 0.12.6.6.1 -RCurl 1.98-1.13 +RCurl 1.98-1.14 RDCOMClient 0.95-1 1554833f8659461427a93732119756ae1c25bc32 Rdisop 1.62.0 Rdpack 2.6 reactable 0.4.4 reactR 0.5.0 readMzXmlData 2.8.3 -readr 2.1.4 +readr 2.1.5 readxl 1.4.3 recipes 1.0.9 registry 0.5-1 rematch 2.0.0 rematch2 2.1.2 -reprex 2.0.2 +reprex 2.1.0 reshape2 1.4.4 Rgraphviz 2.46.0 rhandsontable 0.3.8 Rhdf5lib 1.24.1 rJava 1.0-10 -rlang 1.1.2 +rlang 1.1.3 rlist 0.4.6.2 rmarkdown 2.25 robustbase 0.99-1 @@ -264,7 +264,7 @@ ropls 1.34.0 rpart 4.1.23 rprojroot 2.0.4 rsm 2.10.4 -RSQLite 2.3.4 +RSQLite 2.3.5 rstudioapi 0.15.0 rvest 1.0.3 S4Arrays 1.2.0 @@ -298,14 +298,14 @@ tibble 3.2.1 tidyr 1.3.0 tidyselect 1.2.0 tidyverse 2.0.0 -timechange 0.2.0 +timechange 0.3.0 timeDate 4032.109 tinytex 0.49 TSP 1.2-4 tzdb 0.4.0 UpSetR 1.4.0 utf8 1.2.4 -uuid 1.1-1 +uuid 1.2-0 vctrs 0.6.5 vegan 2.6-4 VennDiagram 1.7.3 @@ -316,11 +316,11 @@ vroom 1.6.5 vsn 3.70.0 webchem 1.3.0 webshot 0.5.5 -withr 2.5.2 -xcms 4.0.1 +withr 3.0.0 +xcms 4.0.2 xfun 0.41 xgboost 1.7.6.1 -XML 3.99-0.16 +XML 3.99-0.16.1 xml2 1.3.6 xtable 1.8-4 XVector 0.42.0