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 f3bc5997..e6b07e6f 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 30d2cf81..7d8d8c8c 100644 --- a/bin/windows/contrib/4.2/PACKAGES +++ b/bin/windows/contrib/4.2/PACKAGES @@ -1892,7 +1892,7 @@ License: GPL (>= 2) Archs: x64 Package: RcppArmadillo -Version: 0.12.6.6.1 +Version: 0.12.8.0.0 Depends: R (>= 3.3.0) Imports: Rcpp (>= 0.11.0), stats, utils, methods LinkingTo: Rcpp @@ -2144,12 +2144,12 @@ Suggests: testthat, knitr, rmarkdown, clipr, covr License: MIT + file LICENSE Package: rvest -Version: 1.0.3 -Depends: R (>= 3.2) -Imports: glue, cli, httr (>= 0.5), lifecycle (>= 1.0.0), magrittr, - rlang (>= 1.0.0), selectr, tibble, xml2 (>= 1.3), withr -Suggests: covr, knitr, readr, repurrrsive, rmarkdown, spelling, stringi - (>= 0.3.1), testthat (>= 3.0.2), webfakes +Version: 1.0.4 +Depends: R (>= 3.6) +Imports: cli, glue, httr (>= 0.5), lifecycle (>= 1.0.3), magrittr, + rlang (>= 1.1.0), selectr, tibble, xml2 (>= 1.3) +Suggests: chromote, covr, knitr, R6, readr, repurrrsive, rmarkdown, + spelling, stringi (>= 0.3.1), testthat (>= 3.0.2), webfakes License: MIT + file LICENSE Package: S4Vectors @@ -2573,8 +2573,8 @@ License: GPL (>= 2) + file LICENSE Archs: x64 Package: xfun -Version: 0.41 -Imports: stats, tools +Version: 0.42 +Imports: grDevices, stats, tools Suggests: testit, parallel, codetools, rstudioapi, tinytex (>= 0.30), mime, markdown (>= 1.5), knitr (>= 1.42), htmltools, remotes, pak, rhub, renv, curl, jsonlite, magick, yaml, rmarkdown diff --git a/bin/windows/contrib/4.2/PACKAGES.gz b/bin/windows/contrib/4.2/PACKAGES.gz index 14797d1e..e7ae7f83 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 d7500529..13505d0a 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/RcppArmadillo_0.12.6.6.1.zip b/bin/windows/contrib/4.2/RcppArmadillo_0.12.8.0.0.zip similarity index 61% rename from bin/windows/contrib/4.2/RcppArmadillo_0.12.6.6.1.zip rename to bin/windows/contrib/4.2/RcppArmadillo_0.12.8.0.0.zip index e3533b24..0c1e2504 100644 Binary files a/bin/windows/contrib/4.2/RcppArmadillo_0.12.6.6.1.zip and b/bin/windows/contrib/4.2/RcppArmadillo_0.12.8.0.0.zip 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 24e17a7b..c9418eca 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 diff --git a/bin/windows/contrib/4.2/patRoon_2.3.1.zip b/bin/windows/contrib/4.2/patRoon_2.3.1.zip index 4e657f6d..2b81e4e7 100644 Binary files a/bin/windows/contrib/4.2/patRoon_2.3.1.zip and b/bin/windows/contrib/4.2/patRoon_2.3.1.zip differ diff --git a/bin/windows/contrib/4.2/rvest_1.0.3.zip b/bin/windows/contrib/4.2/rvest_1.0.3.zip deleted file mode 100644 index aafdc9ad..00000000 Binary files a/bin/windows/contrib/4.2/rvest_1.0.3.zip and /dev/null differ diff --git a/bin/windows/contrib/4.2/rvest_1.0.4.zip b/bin/windows/contrib/4.2/rvest_1.0.4.zip new file mode 100644 index 00000000..c93fd59e Binary files /dev/null and b/bin/windows/contrib/4.2/rvest_1.0.4.zip differ diff --git a/bin/windows/contrib/4.2/xfun_0.41.zip b/bin/windows/contrib/4.2/xfun_0.41.zip deleted file mode 100644 index 31411686..00000000 Binary files a/bin/windows/contrib/4.2/xfun_0.41.zip and /dev/null differ diff --git a/bin/windows/contrib/4.2/xfun_0.42.zip b/bin/windows/contrib/4.2/xfun_0.42.zip new file mode 100644 index 00000000..9c70cab4 Binary files /dev/null and b/bin/windows/contrib/4.2/xfun_0.42.zip differ diff --git a/bin/windows/contrib/4.3/GenomeInfoDb_1.38.5.zip b/bin/windows/contrib/4.3/GenomeInfoDb_1.38.6.zip similarity index 81% rename from bin/windows/contrib/4.3/GenomeInfoDb_1.38.5.zip rename to bin/windows/contrib/4.3/GenomeInfoDb_1.38.6.zip index 3094d815..37107ab8 100644 Binary files a/bin/windows/contrib/4.3/GenomeInfoDb_1.38.5.zip and b/bin/windows/contrib/4.3/GenomeInfoDb_1.38.6.zip differ 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 809bbfa2..1e5c66bf 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 5d882201..512ed4e1 100644 --- a/bin/windows/contrib/4.3/PACKAGES +++ b/bin/windows/contrib/4.3/PACKAGES @@ -789,7 +789,7 @@ Suggests: covr, pkgload, testthat (>= 3.0.0), tibble, withr License: MIT + file LICENSE Package: GenomeInfoDb -Version: 1.38.5 +Version: 1.38.6 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData @@ -1945,7 +1945,7 @@ License: GPL (>= 2) Archs: x64 Package: RcppArmadillo -Version: 0.12.6.6.1 +Version: 0.12.8.0.0 Depends: R (>= 3.3.0) Imports: Rcpp (>= 0.11.0), stats, utils, methods LinkingTo: Rcpp @@ -2090,7 +2090,7 @@ Suggests: knitr, rmarkdown, shiny (>= 0.13), miniUI (>= 0.1.1), License: MIT + file LICENSE Package: Rhdf5lib -Version: 1.24.1 +Version: 1.24.2 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 @@ -2197,12 +2197,12 @@ Suggests: testthat, knitr, rmarkdown, clipr, covr License: MIT + file LICENSE Package: rvest -Version: 1.0.3 -Depends: R (>= 3.2) -Imports: glue, cli, httr (>= 0.5), lifecycle (>= 1.0.0), magrittr, - rlang (>= 1.0.0), selectr, tibble, xml2 (>= 1.3), withr -Suggests: covr, knitr, readr, repurrrsive, rmarkdown, spelling, stringi - (>= 0.3.1), testthat (>= 3.0.2), webfakes +Version: 1.0.4 +Depends: R (>= 3.6) +Imports: cli, glue, httr (>= 0.5), lifecycle (>= 1.0.3), magrittr, + rlang (>= 1.1.0), selectr, tibble, xml2 (>= 1.3) +Suggests: chromote, covr, knitr, R6, readr, repurrrsive, rmarkdown, + spelling, stringi (>= 0.3.1), testthat (>= 3.0.2), webfakes License: MIT + file LICENSE Package: S4Arrays @@ -2311,7 +2311,7 @@ License: MIT + file LICENSE Archs: x64 Package: SparseArray -Version: 1.2.3 +Version: 1.2.4 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 @@ -2668,8 +2668,8 @@ License: GPL (>= 2) + file LICENSE Archs: x64 Package: xfun -Version: 0.41 -Imports: stats, tools +Version: 0.42 +Imports: grDevices, stats, tools Suggests: testit, parallel, codetools, rstudioapi, tinytex (>= 0.30), mime, markdown (>= 1.5), knitr (>= 1.42), htmltools, remotes, pak, rhub, renv, curl, jsonlite, magick, yaml, rmarkdown diff --git a/bin/windows/contrib/4.3/PACKAGES.gz b/bin/windows/contrib/4.3/PACKAGES.gz index aedee772..ebd231d4 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 b58aa1d8..7feb8f51 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/RcppArmadillo_0.12.6.6.1.zip b/bin/windows/contrib/4.3/RcppArmadillo_0.12.8.0.0.zip similarity index 61% rename from bin/windows/contrib/4.3/RcppArmadillo_0.12.6.6.1.zip rename to bin/windows/contrib/4.3/RcppArmadillo_0.12.8.0.0.zip index cf82cca3..4980fc99 100644 Binary files a/bin/windows/contrib/4.3/RcppArmadillo_0.12.6.6.1.zip and b/bin/windows/contrib/4.3/RcppArmadillo_0.12.8.0.0.zip differ diff --git a/bin/windows/contrib/4.3/Rhdf5lib_1.24.1.zip b/bin/windows/contrib/4.3/Rhdf5lib_1.24.2.zip similarity index 93% rename from bin/windows/contrib/4.3/Rhdf5lib_1.24.1.zip rename to bin/windows/contrib/4.3/Rhdf5lib_1.24.2.zip index e6c08576..8debed11 100644 Binary files a/bin/windows/contrib/4.3/Rhdf5lib_1.24.1.zip and b/bin/windows/contrib/4.3/Rhdf5lib_1.24.2.zip differ diff --git a/bin/windows/contrib/4.3/SparseArray_1.2.3.zip b/bin/windows/contrib/4.3/SparseArray_1.2.3.zip deleted file mode 100644 index 638a4ac8..00000000 Binary files a/bin/windows/contrib/4.3/SparseArray_1.2.3.zip and /dev/null differ diff --git a/bin/windows/contrib/4.3/SparseArray_1.2.4.zip b/bin/windows/contrib/4.3/SparseArray_1.2.4.zip new file mode 100644 index 00000000..37928a36 Binary files /dev/null and b/bin/windows/contrib/4.3/SparseArray_1.2.4.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 74042b0a..3925bc20 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/patRoon_2.3.1.zip b/bin/windows/contrib/4.3/patRoon_2.3.1.zip index acf1e5c4..9a29d109 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/rvest_1.0.3.zip b/bin/windows/contrib/4.3/rvest_1.0.3.zip deleted file mode 100644 index 3b8522a2..00000000 Binary files a/bin/windows/contrib/4.3/rvest_1.0.3.zip and /dev/null differ diff --git a/bin/windows/contrib/4.3/rvest_1.0.4.zip b/bin/windows/contrib/4.3/rvest_1.0.4.zip new file mode 100644 index 00000000..cbeddd85 Binary files /dev/null and b/bin/windows/contrib/4.3/rvest_1.0.4.zip differ diff --git a/bin/windows/contrib/4.3/xfun_0.41.zip b/bin/windows/contrib/4.3/xfun_0.41.zip deleted file mode 100644 index 5061dd9c..00000000 Binary files a/bin/windows/contrib/4.3/xfun_0.41.zip and /dev/null differ diff --git a/bin/windows/contrib/4.3/xfun_0.42.zip b/bin/windows/contrib/4.3/xfun_0.42.zip new file mode 100644 index 00000000..a9b34495 Binary files /dev/null and b/bin/windows/contrib/4.3/xfun_0.42.zip differ diff --git a/patRoonDeps-4.2.tsv b/patRoonDeps-4.2.tsv index 8e011331..c7a6b773 100644 --- a/patRoonDeps-4.2.tsv +++ b/patRoonDeps-4.2.tsv @@ -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 9f186020ee9ef8cb538ce7de32d8c1b456928d65 +patRoon 2.3.1 31f6f6a15df48cda66d1a9abcf2ecb3ec1e06c13 pcaMethods 1.90.0 permute 0.9-7 pillar 1.9.0 @@ -229,7 +229,7 @@ rcdk 3.8.1 rcdklibs 2.8 RColorBrewer 1.1-3 Rcpp 1.0.12 -RcppArmadillo 0.12.6.6.1 +RcppArmadillo 0.12.8.0.0 RCurl 1.98-1.14 RDCOMClient 0.95-1 1554833f8659461427a93732119756ae1c25bc32 Rdisop 1.58.0 @@ -260,7 +260,7 @@ rprojroot 2.0.4 rsm 2.10.4 RSQLite 2.3.5 rstudioapi 0.15.0 -rvest 1.0.3 +rvest 1.0.4 S4Vectors 0.36.2 sass 0.4.8 scales 1.3.0 @@ -308,7 +308,7 @@ webchem 1.3.0 webshot 0.5.5 withr 3.0.0 xcms 3.20.0 -xfun 0.41 +xfun 0.42 xgboost 1.7.7.1 XML 3.99-0.16.1 xml2 1.3.6 diff --git a/patRoonDeps-4.3.tsv b/patRoonDeps-4.3.tsv index f343782b..72736c95 100644 --- a/patRoonDeps-4.3.tsv +++ b/patRoonDeps-4.3.tsv @@ -97,7 +97,7 @@ GA 3.2.4 gargle 1.5.2 gclus 1.3.2 generics 0.1.3 -GenomeInfoDb 1.38.5 +GenomeInfoDb 1.38.6 GenomeInfoDbData 1.2.11 f3111730888a3d83e9465ffa2552003de153bbf2 GenomicRanges 1.54.1 getPass 0.2-4 @@ -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 9f186020ee9ef8cb538ce7de32d8c1b456928d65 +patRoon 2.3.1 31f6f6a15df48cda66d1a9abcf2ecb3ec1e06c13 pcaMethods 1.94.0 permute 0.9-7 pillar 1.9.0 @@ -235,7 +235,7 @@ rcdk 3.8.1 rcdklibs 2.8 RColorBrewer 1.1-3 Rcpp 1.0.12 -RcppArmadillo 0.12.6.6.1 +RcppArmadillo 0.12.8.0.0 RCurl 1.98-1.14 RDCOMClient 0.95-1 1554833f8659461427a93732119756ae1c25bc32 Rdisop 1.62.0 @@ -253,7 +253,7 @@ reprex 2.1.0 reshape2 1.4.4 Rgraphviz 2.46.0 rhandsontable 0.3.8 -Rhdf5lib 1.24.1 +Rhdf5lib 1.24.2 rJava 1.0-11 rlang 1.1.3 rlist 0.4.6.2 @@ -266,7 +266,7 @@ rprojroot 2.0.4 rsm 2.10.4 RSQLite 2.3.5 rstudioapi 0.15.0 -rvest 1.0.3 +rvest 1.0.4 S4Arrays 1.2.0 S4Vectors 0.40.2 sass 0.4.8 @@ -279,7 +279,7 @@ shinyjs 2.1.0 slam 0.1-50 snow 0.4-4 sourcetools 0.1.7-1 -SparseArray 1.2.3 +SparseArray 1.2.4 sparsesvd 0.2-2 Spectra 1.12.0 splashR 0.0.4 174fbf289a0357535f9bacda282b9a2dbb7807cc @@ -318,7 +318,7 @@ webchem 1.3.0 webshot 0.5.5 withr 3.0.0 xcms 4.0.2 -xfun 0.41 +xfun 0.42 xgboost 1.7.7.1 XML 3.99-0.16.1 xml2 1.3.6