From 0d1e234ae56e3e78b174f6a72d830a002693b9cf Mon Sep 17 00:00:00 2001 From: Kdreval Date: Tue, 18 Jun 2024 11:45:59 -0700 Subject: [PATCH 01/10] bug fix: handling of custom colors for numeric annotations --- R/prettyOncoplot.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R index 6c08681..63520e7 100644 --- a/R/prettyOncoplot.R +++ b/R/prettyOncoplot.R @@ -700,8 +700,10 @@ prettyOncoplot = function(maf_df, replace(is.na(.), "NA") # Only keep the annotation colors for the remaining patients for(column in colnames(metadata_df)){ - remaining <- unique(metadata_df[column]) %>% pull() - colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining] + if((!missing(numericMetadataColumns)) & (!column %in% numericMetadataColumns)){ + remaining <- unique(metadata_df[column]) %>% pull() + colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining] + } } ch = ComplexHeatmap::oncoPrint(mat[intersect(genes, genes_kept),patients_kept], From 67c8784a0863a696bb6e1651a4d820e88d7a9988 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Tue, 18 Jun 2024 12:08:03 -0700 Subject: [PATCH 02/10] bug fix: allow missing numeric metadata annotations in new implementation --- R/prettyOncoplot.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R index 63520e7..c927d8e 100644 --- a/R/prettyOncoplot.R +++ b/R/prettyOncoplot.R @@ -700,7 +700,10 @@ prettyOncoplot = function(maf_df, replace(is.na(.), "NA") # Only keep the annotation colors for the remaining patients for(column in colnames(metadata_df)){ - if((!missing(numericMetadataColumns)) & (!column %in% numericMetadataColumns)){ + if(missing(numericMetadataColumns)){ + remaining <- unique(metadata_df[column]) %>% pull() + colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining] + }else if(!column %in% numericMetadataColumns){ remaining <- unique(metadata_df[column]) %>% pull() colours[[column]] <- (colours[column] %>% unname %>% unlist)[remaining] } From 0802b52194dee245412ead7e98fcc4e682f9d9e3 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Tue, 18 Jun 2024 12:53:15 -0700 Subject: [PATCH 03/10] cleanup: update env to allow installation of ggplot --- envs/r.yaml | 168 ++++++++++++++++++++++++---------------------------- 1 file changed, 79 insertions(+), 89 deletions(-) diff --git a/envs/r.yaml b/envs/r.yaml index fdceb73..3ef73b3 100644 --- a/envs/r.yaml +++ b/envs/r.yaml @@ -5,121 +5,113 @@ channels: dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - - _r-mutex=1.0.1 - - _sysroot_linux-64_curr_repodata_hack=3 - - binutils_impl_linux-64=2.40 - - bwidget=1.9.14 + - _r-mutex=1.0.0 + - binutils_impl_linux-64=2.38 + - bwidget=1.9.16 - bzip2=1.0.8 - - c-ares=1.27.0 - - ca-certificates=2024.2.2 + - c-ares=1.19.1 + - ca-certificates=2023.12.12 - cairo=1.18.0 - curl=8.5.0 - - expat=2.6.2 + - expat=2.5.0 - font-ttf-dejavu-sans-mono=2.37 - - font-ttf-inconsolata=3.000 - - font-ttf-source-code-pro=2.038 + - font-ttf-inconsolata=2.001 + - font-ttf-source-code-pro=2.030 - font-ttf-ubuntu=0.83 - fontconfig=2.14.2 - fonts-anaconda=1 - fonts-conda-ecosystem=1 - - fonts-conda-forge=1 - freetype=2.12.1 - fribidi=1.0.10 - - gcc_impl_linux-64=13.2.0 - - gettext=0.21.1 - - gfortran_impl_linux-64=13.2.0 - - graphite2=1.3.13 - - gxx_impl_linux-64=13.2.0 + - gcc_impl_linux-64=11.2.0 + - gettext=0.21.0 + - gfortran_impl_linux-64=11.2.0 + - graphite2=1.3.14 + - gxx_impl_linux-64=11.2.0 - harfbuzz=8.3.0 - icu=73.2 - - kernel-headers_linux-64=4.18.0 - - keyutils=1.6.1 - - krb5=1.21.2 - - ld_impl_linux-64=2.40 + - kernel-headers_linux-64=2.6.32 + - krb5=1.20.1 + - ld_impl_linux-64=2.38 - lerc=4.0.0 - libblas=3.9.0 - libcurl=8.5.0 - libdeflate=1.19 - - libedit=3.1.20191231 + - libedit=3.1.20230828 - libev=4.33 - - libexpat=2.6.2 - - libffi=3.4.2 - - libgcc-devel_linux-64=13.2.0 + - libffi=3.4.4 + - libgcc-devel_linux-64=11.2.0 - libgcc-ng=13.2.0 - - libgfortran-ng=13.2.0 - - libgfortran5=13.2.0 - - libgit2=1.7.2 - - libglib=2.80.0 + - libgfortran-ng=11.2.0 + - libgfortran5=11.2.0 + - libgit2=1.6.4 + - libglib=2.78.4 - libgomp=13.2.0 - libiconv=1.17 - libjpeg-turbo=3.0.0 - liblapack=3.9.0 - - libnghttp2=1.58.0 - - libopenblas=0.3.26 + - libnghttp2=1.57.0 + - libopenblas=0.3.21 - libpng=1.6.43 - - libsanitizer=13.2.0 - - libssh2=1.11.0 - - libstdcxx-devel_linux-64=13.2.0 + - libssh2=1.10.0 + - libstdcxx-devel_linux-64=11.2.0 - libstdcxx-ng=13.2.0 - libtiff=4.6.0 - libuuid=2.38.1 - libwebp-base=1.3.2 - libxcb=1.15 - - libxml2=2.12.5 + - libxml2=2.10.4 - libzlib=1.2.13 - lz4-c=1.9.4 - - make=4.3 + - make=4.2.1 - ncurses=6.4 - - openssl=3.2.1 - - pandoc=3.1.12.2 - - pango=1.52.1 - - pcre2=10.43 + - openssl=3.0.13 + - pandoc=2.12 + - pango=1.52.0 + - pcre2=10.42 - pixman=0.43.2 - - pthread-stubs=0.4 - r-askpass=1.2.0 - - r-assertthat=0.2.1 - - r-base=4.2.3 + - r-base=4.3.3 - r-base64enc=0.1_3 - - r-biocmanager=1.30.22 - - r-brew=1.0_10 - - r-brio=1.1.4 - - r-bslib=0.6.1 + - r-brew=1.0_8 + - r-brio=1.1.3 + - r-bslib=0.5.1 - r-cachem=1.0.8 - - r-callr=3.7.5 - - r-cli=3.6.2 + - r-callr=3.7.3 + - r-cli=3.6.1 - r-clipr=0.8.0 - - r-commonmark=1.9.1 - - r-cpp11=0.4.7 + - r-commonmark=1.9.0 + - r-cpp11=0.4.6 - r-crayon=1.5.2 - r-credentials=2.0.1 - r-curl=5.1.0 - - r-desc=1.4.3 + - r-desc=1.4.2 - r-devtools=2.4.5 - r-diffobj=0.3.5 - - r-digest=0.6.35 + - r-digest=0.6.33 - r-downlit=0.4.3 - r-ellipsis=0.3.2 - - r-evaluate=0.23 - - r-fansi=1.0.6 + - r-evaluate=0.22 + - r-fansi=1.0.5 - r-fastmap=1.1.1 - r-fontawesome=0.5.2 - r-fs=1.6.3 - - r-gert=2.0.1 + - r-gert=2.0.0 - r-gh=1.4.0 - r-gitcreds=0.1.2 - - r-glue=1.7.0 + - r-glue=1.6.2 - r-highr=0.10 - - r-htmltools=0.5.7 - - r-htmlwidgets=1.6.4 - - r-httpuv=1.6.14 + - r-htmltools=0.5.6.1 + - r-htmlwidgets=1.6.2 + - r-httpuv=1.6.11 - r-httr=1.4.7 - - r-httr2=1.0.0 + - r-httr2=0.2.3 - r-ini=0.3.1 - r-jquerylib=0.1.4 - - r-jsonlite=1.8.8 - - r-knitr=1.45 - - r-later=1.3.2 - - r-lifecycle=1.0.4 + - r-jsonlite=1.8.7 + - r-knitr=1.44 + - r-later=1.3.1 + - r-lifecycle=1.0.3 - r-magrittr=2.0.3 - r-memoise=2.0.1 - r-mime=0.12 @@ -129,69 +121,67 @@ dependencies: - r-pkgbuild=1.4.2 - r-pkgconfig=2.0.3 - r-pkgdown=2.0.7 - - r-pkgload=1.3.4 + - r-pkgload=1.3.3 - r-praise=1.0.0 - r-prettyunits=1.2.0 - - r-processx=3.8.3 + - r-processx=3.8.2 - r-profvis=0.3.8 - r-promises=1.2.1 - - r-ps=1.7.6 + - r-ps=1.7.5 - r-purrr=1.0.2 - r-r6=2.5.1 - - r-ragg=1.3.0 + - r-ragg=1.2.6 - r-rappdirs=0.3.3 - r-rcmdcheck=1.4.0 - - r-rcpp=1.0.12 + - r-rcpp=1.0.11 - r-rematch2=2.1.2 - r-remotes=2.4.2.1 - - r-rlang=1.1.3 + - r-rlang=1.1.1 - r-rmarkdown=2.25 - - r-roxygen2=7.3.1 - - r-rprojroot=2.0.4 + - r-roxygen2=7.2.3 + - r-rprojroot=2.0.3 - r-rstudioapi=0.15.0 - r-rversions=2.1.2 - - r-sass=0.4.8 + - r-sass=0.4.7 - r-sessioninfo=1.2.2 - - r-shiny=1.8.0 + - r-shiny=1.7.5.1 - r-sourcetools=0.1.7_1 - - r-stringi=1.8.3 - - r-stringr=1.5.1 + - r-stringi=1.7.12 + - r-stringr=1.5.0 - r-sys=3.4.2 - r-systemfonts=1.0.5 - - r-testthat=3.2.1 + - r-testthat=3.2.0 - r-textshaping=0.3.7 - r-tibble=3.2.1 - - r-tinytex=0.49 + - r-tinytex=0.48 - r-urlchecker=1.0.1 - - r-usethis=2.2.3 + - r-usethis=2.2.2 - r-utf8=1.2.4 - - r-vctrs=0.6.5 - - r-waldo=0.5.2 + - r-vctrs=0.6.4 + - r-waldo=0.5.1 - r-whisker=0.4.1 - - r-withr=3.0.0 - - r-xfun=0.42 - - r-xml2=1.3.6 + - r-withr=2.5.1 + - r-xfun=0.40 + - r-xml2=1.3.5 - r-xopen=1.0.0 - r-xtable=1.8_4 - - r-yaml=2.3.8 - - r-zip=2.3.1 + - r-yaml=2.3.7 + - r-zip=2.3.0 - readline=8.2 - sed=4.8 - - sysroot_linux-64=2.28 + - sysroot_linux-64=2.12 - tk=8.6.13 - tktable=2.10 - xorg-kbproto=1.0.7 - xorg-libice=1.1.1 - xorg-libsm=1.2.4 - xorg-libx11=1.8.7 - - xorg-libxau=1.0.11 - - xorg-libxdmcp=1.1.3 - xorg-libxext=1.3.4 - xorg-libxrender=0.9.11 - xorg-libxt=1.3.0 - xorg-renderproto=0.11.1 - xorg-xextproto=7.3.0 - xorg-xproto=7.0.31 - - xz=5.2.6 + - xz=5.4.6 - zlib=1.2.13 - zstd=1.5.5 From b1f1715ae19f40ad3bed385441d503c2f767c70c Mon Sep 17 00:00:00 2001 From: Kdreval Date: Tue, 18 Jun 2024 13:35:24 -0700 Subject: [PATCH 04/10] bug fix: oups forgot biocmanager --- envs/r.yaml | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/envs/r.yaml b/envs/r.yaml index 3ef73b3..4c9f2e8 100644 --- a/envs/r.yaml +++ b/envs/r.yaml @@ -10,7 +10,7 @@ dependencies: - bwidget=1.9.16 - bzip2=1.0.8 - c-ares=1.19.1 - - ca-certificates=2023.12.12 + - ca-certificates=2024.3.11 - cairo=1.18.0 - curl=8.5.0 - expat=2.5.0 @@ -21,6 +21,7 @@ dependencies: - fontconfig=2.14.2 - fonts-anaconda=1 - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 - freetype=2.12.1 - fribidi=1.0.10 - gcc_impl_linux-64=11.2.0 @@ -31,6 +32,7 @@ dependencies: - harfbuzz=8.3.0 - icu=73.2 - kernel-headers_linux-64=2.6.32 + - keyutils=1.6.1 - krb5=1.20.1 - ld_impl_linux-64=2.38 - lerc=4.0.0 @@ -39,6 +41,7 @@ dependencies: - libdeflate=1.19 - libedit=3.1.20230828 - libev=4.33 + - libexpat=2.5.0 - libffi=3.4.4 - libgcc-devel_linux-64=11.2.0 - libgcc-ng=13.2.0 @@ -64,15 +67,18 @@ dependencies: - libzlib=1.2.13 - lz4-c=1.9.4 - make=4.2.1 - - ncurses=6.4 - - openssl=3.0.13 + - ncurses=6.4.20240210 + - openssl=3.0.14 - pandoc=2.12 - pango=1.52.0 - pcre2=10.42 - pixman=0.43.2 + - pthread-stubs=0.4 - r-askpass=1.2.0 + - r-assertthat=0.2.1 - r-base=4.3.3 - r-base64enc=0.1_3 + - r-biocmanager=1.30.22 - r-brew=1.0_8 - r-brio=1.1.3 - r-bslib=0.5.1 @@ -176,6 +182,8 @@ dependencies: - xorg-libice=1.1.1 - xorg-libsm=1.2.4 - xorg-libx11=1.8.7 + - xorg-libxau=1.0.11 + - xorg-libxdmcp=1.1.3 - xorg-libxext=1.3.4 - xorg-libxrender=0.9.11 - xorg-libxt=1.3.0 From b30e2e9ff16999c4b1c406a5d98076c6d346633f Mon Sep 17 00:00:00 2001 From: Kdreval Date: Tue, 18 Jun 2024 14:12:13 -0700 Subject: [PATCH 05/10] bug fix: try this env --- envs/r.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/envs/r.yaml b/envs/r.yaml index 4c9f2e8..91f9d2e 100644 --- a/envs/r.yaml +++ b/envs/r.yaml @@ -1,5 +1,6 @@ name: r channels: + - r - conda-forge - defaults dependencies: @@ -117,8 +118,11 @@ dependencies: - r-jsonlite=1.8.7 - r-knitr=1.44 - r-later=1.3.1 + - r-lattice=0.22_5 - r-lifecycle=1.0.3 - r-magrittr=2.0.3 + - r-mass=7.3_60 + - r-matrix=1.6_1.1 - r-memoise=2.0.1 - r-mime=0.12 - r-miniui=0.1.1.1 From 174793b0e5419d88e8213d3638948cf769808c63 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Tue, 2 Jul 2024 20:52:20 -0700 Subject: [PATCH 06/10] bug fix: handling of noncoding variants --- R/prettyOncoplot.R | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R index c927d8e..a382a52 100644 --- a/R/prettyOncoplot.R +++ b/R/prettyOncoplot.R @@ -249,6 +249,24 @@ prettyOncoplot = function(maf_df, colnames(tsb.include) = tsbs[!tsbs %in% colnames(mat_origin)] rownames(tsb.include) = rownames(mat_origin) mat_origin = cbind(mat_origin, tsb.include) + }else if(length(include_noncoding) > 0){ + print( + "You requested to include noncoding mutations and remove non-mutated patients ..." + ) + these_have_noncoding <- maf_df %>% + filter( + Tumor_Sample_Barcode %in% patients, + Hugo_Symbol %in% names(include_noncoding), + Variant_Classification %in% unname(include_noncoding) + ) %>% + distinct( + Tumor_Sample_Barcode, Hugo_Symbol, Variant_Classification, Start_Position, End_Position + ) %>% + pull(Tumor_Sample_Barcode) + tsb.include = matrix(data = 0, nrow = nrow(mat_origin), ncol = length(these_have_noncoding[!these_have_noncoding %in% colnames(mat_origin)])) + colnames(tsb.include) = these_have_noncoding[!these_have_noncoding %in% colnames(mat_origin)] + rownames(tsb.include) = rownames(mat_origin) + mat_origin = cbind(mat_origin, tsb.include) } write.table(mat_origin, file = onco_matrix_path, quote = F, sep = "\t") } From d6de5110a1ecd6969b6504370f57a11124650d6d Mon Sep 17 00:00:00 2001 From: Kdreval Date: Fri, 5 Jul 2024 22:55:27 -0700 Subject: [PATCH 07/10] bug fix: handle list in include noncoding --- R/prettyOncoplot.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R index a382a52..4e711c6 100644 --- a/R/prettyOncoplot.R +++ b/R/prettyOncoplot.R @@ -257,7 +257,7 @@ prettyOncoplot = function(maf_df, filter( Tumor_Sample_Barcode %in% patients, Hugo_Symbol %in% names(include_noncoding), - Variant_Classification %in% unname(include_noncoding) + Variant_Classification %in% unlist(unname(include_noncoding)) ) %>% distinct( Tumor_Sample_Barcode, Hugo_Symbol, Variant_Classification, Start_Position, End_Position From eebe6a77d8156fa9bf58688197527b694ff2b23b Mon Sep 17 00:00:00 2001 From: Kdreval Date: Wed, 10 Jul 2024 12:52:08 -0700 Subject: [PATCH 08/10] bug fix: update to working env recipe --- envs/r.yaml | 225 +++++++++++++++++++++++++++++----------------------- 1 file changed, 125 insertions(+), 100 deletions(-) diff --git a/envs/r.yaml b/envs/r.yaml index 91f9d2e..9eb1874 100644 --- a/envs/r.yaml +++ b/envs/r.yaml @@ -1,191 +1,216 @@ -name: r +name: deps channels: - - r - conda-forge - defaults dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - - _r-mutex=1.0.0 - - binutils_impl_linux-64=2.38 - - bwidget=1.9.16 + - _r-mutex=1.0.1 + - binutils_impl_linux-64=2.40 + - binutils_linux-64=2.40 + - bwidget=1.9.14 - bzip2=1.0.8 - - c-ares=1.19.1 - - ca-certificates=2024.3.11 - - cairo=1.18.0 - - curl=8.5.0 - - expat=2.5.0 + - c-ares=1.28.1 + - ca-certificates=2024.7.4 + - cairo=1.16.0 + - cmake=3.30.0 + - curl=8.8.0 + - expat=2.6.2 - font-ttf-dejavu-sans-mono=2.37 - - font-ttf-inconsolata=2.001 - - font-ttf-source-code-pro=2.030 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 - font-ttf-ubuntu=0.83 - fontconfig=2.14.2 - - fonts-anaconda=1 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 - freetype=2.12.1 - fribidi=1.0.10 - - gcc_impl_linux-64=11.2.0 - - gettext=0.21.0 - - gfortran_impl_linux-64=11.2.0 - - graphite2=1.3.14 - - gxx_impl_linux-64=11.2.0 - - harfbuzz=8.3.0 - - icu=73.2 + - gcc_impl_linux-64=13.2.0 + - gcc_linux-64=13.2.0 + - gettext=0.22.5 + - gettext-tools=0.22.5 + - gfortran_impl_linux-64=13.2.0 + - graphite2=1.3.13 + - gsl=2.7 + - gxx_impl_linux-64=13.2.0 + - harfbuzz=7.3.0 + - icu=72.1 - kernel-headers_linux-64=2.6.32 - keyutils=1.6.1 - - krb5=1.20.1 - - ld_impl_linux-64=2.38 + - krb5=1.21.3 + - ld_impl_linux-64=2.40 - lerc=4.0.0 + - libasprintf=0.22.5 + - libasprintf-devel=0.22.5 - libblas=3.9.0 - - libcurl=8.5.0 - - libdeflate=1.19 - - libedit=3.1.20230828 + - libcblas=3.9.0 + - libcurl=8.8.0 + - libdeflate=1.18 + - libedit=3.1.20191231 - libev=4.33 - - libexpat=2.5.0 - - libffi=3.4.4 - - libgcc-devel_linux-64=11.2.0 - - libgcc-ng=13.2.0 - - libgfortran-ng=11.2.0 - - libgfortran5=11.2.0 - - libgit2=1.6.4 - - libglib=2.78.4 - - libgomp=13.2.0 + - libexpat=2.6.2 + - libffi=3.4.2 + - libgcc-devel_linux-64=13.2.0 + - libgcc-ng=14.1.0 + - libgettextpo=0.22.5 + - libgettextpo-devel=0.22.5 + - libgfortran-ng=14.1.0 + - libgfortran5=14.1.0 + - libgit2=1.5.1 + - libglib=2.78.1 + - libgomp=14.1.0 - libiconv=1.17 - - libjpeg-turbo=3.0.0 + - libjpeg-turbo=2.1.5.1 - liblapack=3.9.0 - - libnghttp2=1.57.0 - - libopenblas=0.3.21 + - libnghttp2=1.58.0 + - libnsl=2.0.1 + - libopenblas=0.3.27 - libpng=1.6.43 - - libssh2=1.10.0 - - libstdcxx-devel_linux-64=11.2.0 - - libstdcxx-ng=13.2.0 - - libtiff=4.6.0 + - libsanitizer=13.2.0 + - libsqlite=3.46.0 + - libssh2=1.11.0 + - libstdcxx-devel_linux-64=13.2.0 + - libstdcxx-ng=14.1.0 + - libtiff=4.5.1 - libuuid=2.38.1 - - libwebp-base=1.3.2 + - libuv=1.48.0 + - libwebp-base=1.4.0 - libxcb=1.15 - - libxml2=2.10.4 - - libzlib=1.2.13 - - lz4-c=1.9.4 - - make=4.2.1 - - ncurses=6.4.20240210 - - openssl=3.0.14 - - pandoc=2.12 - - pango=1.52.0 - - pcre2=10.42 + - libxcrypt=4.4.36 + - libxml2=2.11.5 + - libzlib=1.3.1 + - make=4.3 + - mysql-common=8.3.0 + - mysql-connector-c=6.1.11 + - mysql-libs=8.3.0 + - mysqlclient=2.2.4 + - ncurses=6.5 + - openssl=3.3.1 + - pandoc=2.19.2 + - pango=1.50.14 + - pcre2=10.40 + - pip=24.0 - pixman=0.43.2 - pthread-stubs=0.4 - - r-askpass=1.2.0 + - r-askpass=1.1 - r-assertthat=0.2.1 - - r-base=4.3.3 + - r-backports=1.4.1 + - r-base=4.1.3 - r-base64enc=0.1_3 - - r-biocmanager=1.30.22 + - r-biocmanager=1.30.21 - r-brew=1.0_8 - r-brio=1.1.3 - - r-bslib=0.5.1 + - r-bslib=0.5.0 - r-cachem=1.0.8 - r-callr=3.7.3 - r-cli=3.6.1 - r-clipr=0.8.0 - r-commonmark=1.9.0 - - r-cpp11=0.4.6 + - r-cpp11=0.4.7 - r-crayon=1.5.2 - - r-credentials=2.0.1 - - r-curl=5.1.0 + - r-credentials=1.3.2 + - r-curl=4.3.3 + - r-dbi=1.1.3 - r-desc=1.4.2 - r-devtools=2.4.5 - r-diffobj=0.3.5 - - r-digest=0.6.33 - - r-downlit=0.4.3 + - r-digest=0.6.31 + - r-downlit=0.4.2 - r-ellipsis=0.3.2 - - r-evaluate=0.22 - - r-fansi=1.0.5 + - r-evaluate=0.21 + - r-fansi=1.0.4 - r-fastmap=1.1.1 - - r-fontawesome=0.5.2 - - r-fs=1.6.3 - - r-gert=2.0.0 + - r-fontawesome=0.5.1 + - r-fs=1.6.2 + - r-gert=1.9.2 - r-gh=1.4.0 + - r-git2r=0.31.0 - r-gitcreds=0.1.2 - r-glue=1.6.2 - r-highr=0.10 - - r-htmltools=0.5.6.1 + - r-htmltools=0.5.5 - r-htmlwidgets=1.6.2 - r-httpuv=1.6.11 - - r-httr=1.4.7 + - r-httr=1.4.6 - r-httr2=0.2.3 - r-ini=0.3.1 - r-jquerylib=0.1.4 - - r-jsonlite=1.8.7 - - r-knitr=1.44 + - r-jsonlite=1.8.5 + - r-knitr=1.43 - r-later=1.3.1 - - r-lattice=0.22_5 + - r-lattice=0.21_8 - r-lifecycle=1.0.3 - r-magrittr=2.0.3 - - r-mass=7.3_60 - - r-matrix=1.6_1.1 + - r-mass=7.3_58.3 + - r-matrix=1.5_4.1 - r-memoise=2.0.1 - r-mime=0.12 - r-miniui=0.1.1.1 - - r-openssl=2.1.1 + - r-openssl=2.0.6 - r-pillar=1.9.0 - - r-pkgbuild=1.4.2 + - r-pkgbuild=1.4.0 - r-pkgconfig=2.0.3 - r-pkgdown=2.0.7 - - r-pkgload=1.3.3 + - r-pkgload=1.3.2 - r-praise=1.0.0 - - r-prettyunits=1.2.0 - - r-processx=3.8.2 + - r-prettyunits=1.1.1 + - r-processx=3.8.1 - r-profvis=0.3.8 - - r-promises=1.2.1 + - r-promises=1.2.0.1 - r-ps=1.7.5 - - r-purrr=1.0.2 + - r-purrr=1.0.1 - r-r6=2.5.1 - - r-ragg=1.2.6 + - r-ragg=1.2.5 - r-rappdirs=0.3.3 - r-rcmdcheck=1.4.0 - - r-rcpp=1.0.11 + - r-rcpp=1.0.10 - r-rematch2=2.1.2 - - r-remotes=2.4.2.1 + - r-remotes=2.4.2 - r-rlang=1.1.1 - - r-rmarkdown=2.25 + - r-rmarkdown=2.22 + - r-rmysql=0.10.25 - r-roxygen2=7.2.3 - r-rprojroot=2.0.3 - - r-rstudioapi=0.15.0 + - r-rstudioapi=0.14 - r-rversions=2.1.2 - - r-sass=0.4.7 + - r-sass=0.4.6 - r-sessioninfo=1.2.2 - - r-shiny=1.7.5.1 + - r-shiny=1.7.4 - r-sourcetools=0.1.7_1 - r-stringi=1.7.12 - r-stringr=1.5.0 - r-sys=3.4.2 - - r-systemfonts=1.0.5 - - r-testthat=3.2.0 - - r-textshaping=0.3.7 + - r-systemfonts=1.0.4 + - r-testthat=3.1.8 + - r-textshaping=0.3.6 - r-tibble=3.2.1 - - r-tinytex=0.48 + - r-tinytex=0.45 - r-urlchecker=1.0.1 - - r-usethis=2.2.2 - - r-utf8=1.2.4 - - r-vctrs=0.6.4 + - r-usethis=2.2.0 + - r-utf8=1.2.3 + - r-vctrs=0.6.2 - r-waldo=0.5.1 - r-whisker=0.4.1 - - r-withr=2.5.1 - - r-xfun=0.40 - - r-xml2=1.3.5 + - r-withr=2.5.0 + - r-xfun=0.39 + - r-xml2=1.3.4 - r-xopen=1.0.0 - r-xtable=1.8_4 - r-yaml=2.3.7 - r-zip=2.3.0 - readline=8.2 + - rhash=1.4.4 - sed=4.8 + - setuptools=70.1.1 - sysroot_linux-64=2.12 - tk=8.6.13 - tktable=2.10 + - tzdata=2024a + - wheel=0.43.0 - xorg-kbproto=1.0.7 - xorg-libice=1.1.1 - xorg-libsm=1.2.4 - - xorg-libx11=1.8.7 + - xorg-libx11=1.8.9 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - xorg-libxext=1.3.4 @@ -194,6 +219,6 @@ dependencies: - xorg-renderproto=0.11.1 - xorg-xextproto=7.3.0 - xorg-xproto=7.0.31 - - xz=5.4.6 - - zlib=1.2.13 - - zstd=1.5.5 + - xz=5.2.6 + - zlib=1.3.1 + - zstd=1.5.6 From 66cfdf9cb6202685a99d9334a2ade0214744b382 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Wed, 10 Jul 2024 12:53:06 -0700 Subject: [PATCH 09/10] bug fix: update actions run command --- .github/workflows/build_check.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_check.yaml b/.github/workflows/build_check.yaml index d87ef24..0da669e 100644 --- a/.github/workflows/build_check.yaml +++ b/.github/workflows/build_check.yaml @@ -35,11 +35,11 @@ jobs: - name: Build package run: - Rscript -e "devtools::install(repos = BiocManager::repositories())" + Rscript --vanilla -e "devtools::install(repos = BiocManager::repositories(), upgrade = FALSE)" - name: Check package run: - Rscript -e "devtools::check(vignettes = FALSE, args = '--no-examples')" + Rscript --vanilla -e "devtools::check(vignettes = FALSE, args = '--no-examples')" - name: Upload check results if: failure() From 4e2d594e11dcf739481f458b189f307df1e075f1 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Fri, 12 Jul 2024 08:46:13 -0700 Subject: [PATCH 10/10] bug fix: adding tested env --- envs/r.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/envs/r.yaml b/envs/r.yaml index 9eb1874..ed6ea57 100644 --- a/envs/r.yaml +++ b/envs/r.yaml @@ -143,11 +143,13 @@ dependencies: - r-magrittr=2.0.3 - r-mass=7.3_58.3 - r-matrix=1.5_4.1 + - r-matrixmodels=0.5_0 - r-memoise=2.0.1 - r-mime=0.12 - r-miniui=0.1.1.1 - r-openssl=2.0.6 - r-pillar=1.9.0 + - r-pbkrtest=0.5.2 - r-pkgbuild=1.4.0 - r-pkgconfig=2.0.3 - r-pkgdown=2.0.7