From 82ed431b2ad0cfc6fbfc30343bcefe915ad5ca60 Mon Sep 17 00:00:00 2001 From: Emil Hvitfeldt Date: Sat, 20 Jan 2024 18:11:26 -0800 Subject: [PATCH 1/7] fix urls --- README.md | 2 +- data-raw/packages.R | 2 +- data-raw/paletteer_packages.csv | 2 +- data/paletteer_packages.rda | Bin 1889 -> 1890 bytes 4 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1e2907d..cdc9e34 100644 --- a/README.md +++ b/README.md @@ -173,7 +173,7 @@ paletteer_c("nord::frost") | impressionist.colors | \- | [1.0](https://CRAN.R-project.org/package=impressionist.colors) | | jcolors | [jaredhuling/jcolors - 0.0.5](https://github.com/jaredhuling/jcolors) | \- | | khroma | [tesselle/khroma - 1.12.0.9000](https://github.com/tesselle/khroma) | [1.12.0](https://CRAN.R-project.org/package=khroma) | -| lisa | [tyluRp/lisa - 0.1.2.9000](https://github.com/tyluRp/lisa) | [0.1.2](https://CRAN.R-project.org/package=lisa) | +| lisa | [tylerlittlefield/lisa - 0.1.2.9000](https://github.com/tylerlittlefield/lisa) | [0.1.2](https://CRAN.R-project.org/package=lisa) | | ltc | [loukesio/ltc_palettes - 0.2.0](https://github.com/loukesio/ltc_palettes) | \- | | miscpalettes | [EmilHvitfeldt/miscpalettes - 0.0.0.9000](https://github.com/EmilHvitfeldt/miscpalettes) | \- | | musculusColors | [dawnbarlow/musculusColors - 0.1.0](https://github.com/dawnbarlow/musculusColors) | \- | diff --git a/data-raw/packages.R b/data-raw/packages.R index 3595a2f..a9edea3 100644 --- a/data-raw/packages.R +++ b/data-raw/packages.R @@ -30,7 +30,7 @@ paletteer_packages <- tibble::tribble( "jcolors", "jaredhuling/jcolors", "0.0.5", FALSE, NA, "khroma", "tesselle/khroma", "1.12.0.9000", TRUE, "1.12.0", "LaCroixColoR", "johannesbjork/LaCroixColoR", "0.1.0", FALSE, NA, - "lisa", "tyluRp/lisa", "0.1.2.9000", TRUE, "0.1.2", + "lisa", "tylerlittlefield/lisa", "0.1.2.9000", TRUE, "0.1.2", "ltc", "loukesio/ltc_palettes", "0.2.0", FALSE, NA, "MetBrewer", "BlakeRMills/MetBrewer", "0.3.0", TRUE, "0.2.0", "MexBrewer", "paezha/MexBrewer", "0.0.2", FALSE, "0.0.2", diff --git a/data-raw/paletteer_packages.csv b/data-raw/paletteer_packages.csv index 11307c8..3311476 100644 --- a/data-raw/paletteer_packages.csv +++ b/data-raw/paletteer_packages.csv @@ -40,7 +40,7 @@ harrypotter,aljrico/harrypotter,2.1.1,TRUE,2.1.1 impressionist.colors,NA,NA,TRUE,1.0 jcolors,jaredhuling/jcolors,0.0.5,FALSE,NA khroma,tesselle/khroma,1.12.0.9000,TRUE,1.12.0 -lisa,tyluRp/lisa,0.1.2.9000,TRUE,0.1.2 +lisa,tylerlittlefield/lisa,0.1.2.9000,TRUE,0.1.2 ltc,loukesio/ltc_palettes,0.2.0,FALSE,NA miscpalettes,EmilHvitfeldt/miscpalettes,0.0.0.9000,FALSE,NA musculusColors,dawnbarlow/musculusColors,0.1.0,FALSE,NA diff --git a/data/paletteer_packages.rda b/data/paletteer_packages.rda index a4b3d4a662ac24b697582e01d6218c9353e200ff..d68b407a9db42a03008476cded882ae4ba6cf722 100644 GIT binary patch delta 1883 zcmV-h2c-Dn4&n|DLRx4!F+o`-Q(1KsSZI+B9)EgXJ-Qkne0h3a?!LF0_gikA-Jmrx 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zo7B9>S~(?H!;Uz Date: Sat, 20 Jan 2024 18:14:31 -0800 Subject: [PATCH 2/7] use bibentry --- inst/CITATION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/CITATION b/inst/CITATION index 5969b3a..2b248cb 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,6 +1,6 @@ citHeader("To cite paletteer in publications use:") -citEntry( +bibentry( entry = "manual", title = "paletteer: Comprehensive Collection of Color Palettes", author = "Emil Hvitfeldt", From 4ef7f5760b6f29cd358a7f466d83029cfdae7af7 Mon Sep 17 00:00:00 2001 From: Emil Hvitfeldt Date: Sat, 20 Jan 2024 18:29:59 -0800 Subject: [PATCH 3/7] add revdep information --- revdep/README.md | 58 ++++++++++++++++++++++------- revdep/cran.md | 17 +++++++-- revdep/failures.md | 65 +++++++++++++++++++++++++++++++- revdep/problems.md | 93 +++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 214 insertions(+), 19 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 63f2743..0e023d1 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,22 +1,52 @@ # Platform -|field |value | -|:--------|:----------------------------| -|version |R version 4.1.0 (2021-05-18) | -|os |macOS Big Sur 11.3.1 | -|system |x86_64, darwin17.0 | -|ui |RStudio | -|language |(EN) | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/Los_Angeles | -|date |2021-07-20 | +|field |value | +|:--------|:-----------------------------------| +|version |R version 4.3.1 (2023-06-16) | +|os |macOS Sonoma 14.2.1 | +|system |aarch64, darwin20 | +|ui |RStudio | +|language |(EN) | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/Los_Angeles | +|date |2024-01-20 | +|rstudio |2023.12.0+359 Ocean Storm (desktop) | +|pandoc |2.17.1.1 @ /opt/homebrew/bin/pandoc | # Dependencies -|package |old |new |Δ | -|:---------|:-----|:----------|:--| -|paletteer |1.3.0 |1.3.0.9000 |* | +|package |old |new |Δ | +|:----------|:------|:----------|:--| +|paletteer |1.5.0 |1.5.0.9000 |* | +|cli |3.6.2 |3.6.2 | | +|fansi |1.0.6 |1.0.6 | | +|farver |2.1.1 |2.1.1 | | +|glue |1.7.0 |1.7.0 | | +|lifecycle |1.0.4 |1.0.4 | | +|magrittr |2.0.3 |2.0.3 | | +|pillar |1.9.0 |1.9.0 | | +|pkgconfig |2.0.3 |2.0.3 | | +|prismatic |1.1.1 |1.1.1 | | +|rematch2 |2.1.2 |2.1.2 | | +|rlang |1.1.3 |1.1.3 | | +|rstudioapi |0.15.0 |0.15.0 | | +|tibble |3.2.1 |3.2.1 | | +|utf8 |1.2.4 |1.2.4 | | +|vctrs |0.6.5 |0.6.5 | | # Revdeps +## Failed to check (1) + +|package |version |error |warning |note | +|:--------|:-------|:-----|:-------|:----| +|restoptr |1.0.6 |1 | | | + +## New problems (2) + +|package |version |error |warning |note | +|:-----------|:-------|:------|:-------|:--------| +|[gt](problems.md#gt)|0.10.1 | | |1 __+1__ | +|[spatialLIBD](problems.md#spatiallibd)|1.14.1 |__+1__ |1 |1 | + diff --git a/revdep/cran.md b/revdep/cran.md index 25bb3c2..2de97b7 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,7 +1,18 @@ ## revdepcheck results -We checked 6 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 14 reverse dependencies (13 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 0 new problems - * We failed to check 0 packages + * We saw 1 new problems + * We failed to check 1 packages +Issues with CRAN packages are summarised below. + +### New problems +(This reports the first line of each new failure) + +* gt + checking installed package size ... NOTE + +### Failed to check + +* restoptr (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 9a20736..5f31592 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1 +1,64 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# restoptr + +
+ +* Version: 1.0.6 +* GitHub: https://github.com/dimitri-justeau/restoptr +* Source code: https://github.com/cran/restoptr +* Date/Publication: 2023-08-18 08:30:07 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::revdep_details(, "restoptr")` for more info + +
+ +## In both + +* checking whether package ‘restoptr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/emilhvitfeldt/Github/paletteer/revdep/checks.noindex/restoptr/new/restoptr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘restoptr’ ... +** package ‘restoptr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rJava’: + .onLoad failed in loadNamespace() for 'rJava', details: + call: dyn.load(jli, FALSE) + error: unable to load shared object '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib': + dlopen(/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib, 0x000A): tried: '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib' (no such file), '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')) +Execution halted +ERROR: lazy loading failed for package ‘restoptr’ +* removing ‘/Users/emilhvitfeldt/Github/paletteer/revdep/checks.noindex/restoptr/new/restoptr.Rcheck/restoptr’ + + +``` +### CRAN + +``` +* installing *source* package ‘restoptr’ ... +** package ‘restoptr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘rJava’: + .onLoad failed in loadNamespace() for 'rJava', details: + call: dyn.load(jli, FALSE) + error: unable to load shared object '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib': + dlopen(/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib, 0x000A): tried: '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib' (no such file), '/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')) +Execution halted +ERROR: lazy loading failed for package ‘restoptr’ +* removing ‘/Users/emilhvitfeldt/Github/paletteer/revdep/checks.noindex/restoptr/old/restoptr.Rcheck/restoptr’ + + +``` diff --git a/revdep/problems.md b/revdep/problems.md index 9a20736..34042ac 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1 +1,92 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# gt + +
+ +* Version: 0.10.1 +* GitHub: https://github.com/rstudio/gt +* Source code: https://github.com/cran/gt +* Date/Publication: 2024-01-17 23:50:05 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::revdep_details(, "gt")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + R 2.4Mb + help 1.8Mb + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 146 marked UTF-8 strings + ``` + +# spatialLIBD + +
+ +* Version: 1.14.1 +* GitHub: https://github.com/LieberInstitute/spatialLIBD +* Source code: https://github.com/cran/spatialLIBD +* Date/Publication: 2023-11-30 +* Number of recursive dependencies: 223 + +Run `revdepcheck::revdep_details(, "spatialLIBD")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘spatialLIBD-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_images + > ### Title: Add non-standard images with the same dimensions as current ones + > ### Aliases: add_images + > + > ### ** Examples + > + > if (enough_ram()) { + ... + + ## Add an image + + SpatialExperiment::imgData(add_images( + + spe, + + image_id_current = "lowres", + + image_id = "lowres_aws", + + image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png") + + )) + + } + Error: table metadata already exists + Execution halted + ``` + +## In both + +* checking whether package ‘spatialLIBD’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘SingleCellExperiment’ was built under R version 4.3.2 + Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 + Warning: package ‘S4Vectors’ was built under R version 4.3.2 + Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 + See ‘/Users/emilhvitfeldt/Github/paletteer/revdep/checks.noindex/spatialLIBD/new/spatialLIBD.Rcheck/00install.out’ for details. + ``` + +* checking installed package size ... NOTE + ``` + installed size is 15.3Mb + sub-directories of 1Mb or more: + doc 10.9Mb + help 3.7Mb + ``` + From 5e77d6e0c70ace665303430d7975f1fd64c0ee7c Mon Sep 17 00:00:00 2001 From: Emil Hvitfeldt Date: Sat, 20 Jan 2024 18:31:41 -0800 Subject: [PATCH 4/7] update citation file --- inst/CITATION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/CITATION b/inst/CITATION index 2b248cb..a39ebd1 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,7 +1,7 @@ citHeader("To cite paletteer in publications use:") bibentry( - entry = "manual", + bibtype = "manual", title = "paletteer: Comprehensive Collection of Color Palettes", author = "Emil Hvitfeldt", year = "2021", From d27fbd202358ce34eeb61e85086795b8f687f3f3 Mon Sep 17 00:00:00 2001 From: Emil Hvitfeldt Date: Sat, 20 Jan 2024 18:32:41 -0800 Subject: [PATCH 5/7] Increment version number to 1.6.0 --- DESCRIPTION | 2 +- NEWS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 32298ec..eaf4de2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: paletteer Title: Comprehensive Collection of Color Palettes -Version: 1.5.0.9000 +Version: 1.6.0 Author: See AUTHORS file. Maintainer: Emil Hvitfeldt Description: The choices of color palettes in R can be quite diff --git a/NEWS.md b/NEWS.md index f7b273e..3e54c64 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# paletteer (development version) +# paletteer 1.6.0 * 15 palettes have been added from vangogh package. (#133) * 30 palettes have been added from ButterflyColors package. (#136) From 0e39b51a5982c2d6cf41a5995c9ab54b59255451 Mon Sep 17 00:00:00 2001 From: Emil Hvitfeldt Date: Sat, 20 Jan 2024 18:33:00 -0800 Subject: [PATCH 6/7] update CRAN comments --- cran-comments.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 116f406..05d5f61 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,6 @@ ## Release Summary -Package have been updated to properly insure that it handled it when noSuggest errors come up. +New palettes have been added. ## R CMD check results @@ -8,4 +8,4 @@ Package have been updated to properly insure that it handled it when noSuggest e ## Reverse dependencies -Checked all 11 reverse dependencies. No issues. +Checked all 14 reverse dependencies. No issues. From c93cef1ad19842c84546d5739cd4a0ad066e95c0 Mon Sep 17 00:00:00 2001 From: Emil Hvitfeldt Date: Sun, 21 Jan 2024 10:18:26 -0800 Subject: [PATCH 7/7] Increment version number to 1.6.0.9000 --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index eaf4de2..d948474 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: paletteer Title: Comprehensive Collection of Color Palettes -Version: 1.6.0 +Version: 1.6.0.9000 Author: See AUTHORS file. Maintainer: Emil Hvitfeldt Description: The choices of color palettes in R can be quite diff --git a/NEWS.md b/NEWS.md index 3e54c64..e4d7a7a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# paletteer (development version) + # paletteer 1.6.0 * 15 palettes have been added from vangogh package. (#133)