diff --git a/DESCRIPTION b/DESCRIPTION index 82dd2cc032..3b82c7e7dc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: ggplot2 -Version: 3.3.4.9000 +Version: 3.3.5.9000 Title: Create Elegant Data Visualisations Using the Grammar of Graphics Description: A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' diff --git a/NEWS.md b/NEWS.md index 163601b054..67e41b9427 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,19 @@ # ggplot2 (development version) +# ggplot2 3.3.5 +This is a very small release focusing on fixing a couple of untenable issues +that surfaced with the 3.3.4 release + +* Revert changes made in #4434 (apply transform to intercept in `geom_abline()`) + as it introduced undesirable issues far worse than the bug it fixed + (@thomasp85, #4514) +* Fixes an issue in `ggsave()` when producing emf/wmf files (@yutannihilation, + #4521) +* Warn when grDevices specific arguments are passed to ragg devices (@thomasp85, + #4524) +* Fix an issue where `coord_sf()` was reporting that it is non-linear + even when data is provided in projected coordinates (@clauswilke, #4527) + # ggplot2 3.3.4 This is a larger patch release fixing a huge number of bugs and introduces a small selection of feature refinements. diff --git a/R/coord-sf.R b/R/coord-sf.R index 8994d1323a..8f8b79f3c8 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -22,7 +22,7 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, params <- list( crs = crs, - default_crs = self$default_crs %||% crs + default_crs = self$default_crs ) self$params <- params diff --git a/R/ggplot-global.R b/R/ggplot-global.R index 7c347ef8ee..cd650e3e18 100644 --- a/R/ggplot-global.R +++ b/R/ggplot-global.R @@ -20,8 +20,7 @@ ggplot_global$element_tree <- list() "colour", "fg", "fill", "group", "hjust", "label", "linetype", "lower", "lty", "lwd", "max", "middle", "min", "pch", "radius", "sample", "shape", "size", "srt", "upper", "vjust", "weight", "width", "x", "xend", "xmax", - "xmin", "xintercept", "y", "yend", "ymax", "ymin", "yintercept", "z", - "intercept" + "xmin", "xintercept", "y", "yend", "ymax", "ymin", "yintercept", "z" ) ggplot_global$all_aesthetics <- .all_aesthetics @@ -49,7 +48,7 @@ ggplot_global$base_to_ggplot <- .base_to_ggplot # These two vectors must match in length and position of symmetrical aesthetics # xintercept2 is a filler to match to the intercept aesthetic in geom_abline ggplot_global$x_aes <- c("x", "xmin", "xmax", "xend", "xintercept", - "xmin_final", "xmax_final", "xlower", "xmiddle", "xupper", "x0", "xintercept2") + "xmin_final", "xmax_final", "xlower", "xmiddle", "xupper", "x0") ggplot_global$y_aes <- c("y", "ymin", "ymax", "yend", "yintercept", - "ymin_final", "ymax_final", "lower", "middle", "upper", "y0", "intercept") + "ymin_final", "ymax_final", "lower", "middle", "upper", "y0") diff --git a/R/save.r b/R/save.r index b71579ece9..8238f893c6 100644 --- a/R/save.r +++ b/R/save.r @@ -178,9 +178,9 @@ plot_dev <- function(device, filename = NULL, dpi = 300) { paper = "special") } if (requireNamespace('ragg', quietly = TRUE)) { - png_dev <- ragg::agg_png - jpeg_dev <- ragg::agg_jpeg - tiff_dev <- ragg::agg_tiff + png_dev <- absorb_grdevice_args(ragg::agg_png) + jpeg_dev <- absorb_grdevice_args(ragg::agg_jpeg) + tiff_dev <- absorb_grdevice_args(ragg::agg_tiff) } else { png_dev <- grDevices::png jpeg_dev <- grDevices::jpeg @@ -192,8 +192,9 @@ plot_dev <- function(device, filename = NULL, dpi = 300) { tex = function(filename, ...) grDevices::pictex(file = filename, ...), pdf = function(filename, ..., version = "1.4") grDevices::pdf(file = filename, ..., version = version), svg = function(filename, ...) svglite::svglite(file = filename, ...), - emf = function(...) grDevices::win.metafile(...), - wmf = function(...) grDevices::win.metafile(...), + # win.metafile() doesn't have `bg` arg so we need to absorb it before passing `...` + emf = function(..., bg = NULL) grDevices::win.metafile(...), + wmf = function(..., bg = NULL) grDevices::win.metafile(...), png = function(...) png_dev(..., res = dpi, units = "in"), jpg = function(...) jpeg_dev(..., res = dpi, units = "in"), jpeg = function(...) jpeg_dev(..., res = dpi, units = "in"), @@ -220,3 +221,12 @@ plot_dev <- function(device, filename = NULL, dpi = 300) { grid.draw.ggplot <- function(x, recording = TRUE) { print(x) } + +absorb_grdevice_args <- function(f) { + function(..., type, antialias) { + if (!missing(type) || !missing(antialias)) { + warn("Using ragg device as default. Ignoring `type` and `antialias` arguments") + } + f(...) + } +} diff --git a/README.md b/README.md index 5f443a0f6f..da3a046e0c 100644 --- a/README.md +++ b/README.md @@ -84,10 +84,15 @@ documentation pages. Currently, there are three good places to start: get you up to speed with the essentials of ggplot2 as quickly as possible. -2. If you’d like to follow a webinar, try [Plotting Anything with +2. If you’d like to take an online course, try [Data Visualization in R + With + ggplot2](https://learning.oreilly.com/videos/data-visualization-in/9781491963661/) + by Kara Woo. + +3. If you’d like to follow a webinar, try [Plotting Anything with ggplot2](https://youtu.be/h29g21z0a68) by Thomas Lin Pedersen. -3. If you want to dive into making common graphics as quickly as +4. If you want to dive into making common graphics as quickly as possible, I recommend [The R Graphics Cookbook](https://r-graphics.org) by Winston Chang. It provides a set of recipes to solve common graphics problems. diff --git a/cran-comments.md b/cran-comments.md index 437a718026..c205ecc5c0 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,98 +1,7 @@ -This is mainly a patch release, though we have folded in a couple of new -features. The release contains a couple of internal breaking changes which can -affect packages that inspects the internals of ggplot objects. All failing -reverse dependencies have been notified 3 weeks ago with information about what -needs to be fixed and how. Most of these have already published a fix or is in -the process of doing so. +This is a very quick patch release addressing some unforeseen issues with the +latest release. It does not contain any breaking changes and no changes to worse +in the reverse dependencies was detected. ## R CMD check results 0 errors | 0 warnings | 0 note - -## revdepcheck results - -We checked 3149 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 11 new problems - * We failed to check 39 packages - -Issues with CRAN packages are summarised below. - -### New problems -(This reports the first line of each new failure) - -* bayesAB - checking tests ... ERROR - -* BayesianReasoning - checking tests ... ERROR - -* cvms - checking tests ... ERROR - -* ezEDA - checking tests ... ERROR - -* ggseg - checking examples ... ERROR - checking tests ... ERROR - -* HRM - checking dependencies in R code ... NOTE - -* plotly - checking tests ... ERROR - -* ratPASTA - checking tests ... ERROR - -* rBiasCorrection - checking tests ... ERROR - -* tricolore - checking examples ... ERROR - -* xpose - checking tests ... ERROR - -### Failed to check - -* ActivePathways (NA) -* apc (NA) -* apisensr (NA) -* backShift (NA) -* bayesdfa (NA) -* bayesGAM (NA) -* bayesZIB (NA) -* bmgarch (NA) -* CausalImpact (NA) -* CB2 (NA) -* cbar (NA) -* dfpk (NA) -* diceR (NA) -* GenHMM1d (NA) -* ggmsa (NA) -* ggtern (NA) -* glmmfields (NA) -* MarketMatching (NA) -* mcmcabn (NA) -* metagam (NA) -* mlr3pipelines (NA) -* OncoBayes2 (NA) -* osmplotr (NA) -* pcalg (NA) -* penaltyLearning (NA) -* phylopath (NA) -* rabhit (NA) -* raw (NA) -* rstap (NA) -* scoper (NA) -* spectralAnalysis (NA) -* StroupGLMM (NA) -* SynthETIC (NA) -* tigger (NA) -* trackr (NA) -* valse (NA) -* vivid (NA) -* wrswoR (NA) -* zenplots (NA) diff --git a/revdep/README.md b/revdep/README.md index 9eade158bd..8f74a75cd0 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,62 +1,58 @@ # Revdeps -## Failed to check (39) +## Failed to check (45) -|package |version |error |warning |note | -|:------------------------------------|:-------|:------|:-------|:----| -|ActivePathways |? | | | | -|apc |? | | | | -|apisensr |? | | | | -|backShift |? | | | | -|bayesdfa |1.1.0 |1 | | | -|bayesGAM |0.0.1 |1 | | | -|bayesZIB |0.0.2 |1 | | | -|bmgarch |1.0.0 |1 | | | -|CausalImpact |? | | | | -|CB2 |? | | | | -|cbar |? | | | | -|dfpk |3.5.1 |1 | | | -|diceR |? | | | | -|GenHMM1d |? | | | | -|ggmsa |? | | | | -|[ggtern](failures.md#ggtern) |3.3.0 |__+1__ | |1 -2 | -|glmmfields |0.1.4 |1 | | | -|MarketMatching |? | | | | -|mcmcabn |? | | | | -|metagam |? | | | | -|mlr3pipelines |? | | | | -|[OncoBayes2](failures.md#oncobayes2) |0.7-0 |__+1__ | |-2 | -|osmplotr |? | | | | -|pcalg |? | | | | -|penaltyLearning |? | | | | -|phylopath |? | | | | -|rabhit |? | | | | -|raw |? | | | | -|rstap |1.0.3 |1 | | | -|scoper |? | | | | -|spectralAnalysis |? | | | | -|StroupGLMM |? | | | | -|SynthETIC |? | | | | -|tigger |? | | | | -|trackr |? | | | | -|valse |0.1-0 |1 | | | -|vivid |? | | | | -|wrswoR |? | | | | -|zenplots |? | | | | +|package |version |error |warning |note | +|:----------------|:-------|:-----|:-------|:----| +|ActivePathways |? | | | | +|apc |? | | | | +|apisensr |? | | | | +|backShift |? | | | | +|bayesdfa |1.1.0 |1 | | | +|bayesZIB |0.0.2 |1 | | | +|NA |? | | | | +|NA |? | | | | +|btergm |1.9.13 |1 | | | +|CausalImpact |? | | | | +|CB2 |? | | | | +|cbar |? | | | | +|NA |? | | | | +|dfpk |3.5.1 |1 | | | +|diceR |? | | | | +|GenHMM1d |? | | | | +|ggmsa |? | | | | +|ggtern |3.3.0 |1 | |1 | +|glmmfields |0.1.4 |1 | | | +|NA |? | | | | +|mcmcabn |? | | | | +|NA |? | | | | +|metagam |? | | | | +|MoMPCA |? | | | | +|osmplotr |? | | | | +|pcalg |? | | | | +|penaltyLearning |? | | | | +|phylopath |? | | | | +|NA |? | | | | +|rabhit |? | | | | +|raw |? | | | | +|rstap |1.0.3 |1 | | | +|scoper |? | | | | +|spectralAnalysis |? | | | | +|NA |? | | | | +|StroupGLMM |? | | | | +|superb |? | | | | +|SynthETIC |? | | | | +|NA |? | | | | +|tigger |? | | | | +|trackr |? | | | | +|valse |0.1-0 |1 | | | +|vivid |? | | | | +|wrswoR |? | | | | +|zenplots |? | | | | -## New problems (11) +## New problems (1) -|package |version |error |warning |note | -|:--------------------------------------------------|:-------|:------|:-------|:------| -|[bayesAB](problems.md#bayesab) |1.1.2 |__+1__ | | | -|[BayesianReasoning](problems.md#bayesianreasoning) |0.3.2 |__+1__ | | | -|[cvms](problems.md#cvms) |1.3.0 |__+1__ | | | -|[ezEDA](problems.md#ezeda) |0.1.0 |__+1__ | | | -|[ggseg](problems.md#ggseg) |1.6.3 |__+2__ | | | -|[HRM](problems.md#hrm) |1.2.1 | | |__+1__ | -|[plotly](problems.md#plotly) |4.9.4 |__+1__ | |1 | -|[ratPASTA](problems.md#ratpasta) |0.2.1 |__+1__ | |1 | -|[rBiasCorrection](problems.md#rbiascorrection) |0.3.0 |__+1__ | | | -|[tricolore](problems.md#tricolore) |1.2.2 |__+1__ | | | -|[xpose](problems.md#xpose) |0.4.12 |__+1__ | | | +|package |version |error |warning |note | +|:----------------------------------------|:---------|:-----|:-------|:------| +|[rvinecopulib](problems.md#rvinecopulib) |0.5.5.1.1 |-1 | |__+1__ | diff --git a/revdep/cran.md b/revdep/cran.md index c5fc2fffdf..5b78fa18c9 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,48 +1,17 @@ ## revdepcheck results -We checked 3149 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 3197 reverse dependencies (3189 from CRAN + 8 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 11 new problems - * We failed to check 39 packages + * We saw 1 new problems + * We failed to check 37 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* bayesAB - checking tests ... ERROR - -* BayesianReasoning - checking tests ... ERROR - -* cvms - checking tests ... ERROR - -* ezEDA - checking tests ... ERROR - -* ggseg - checking examples ... ERROR - checking tests ... ERROR - -* HRM - checking dependencies in R code ... NOTE - -* plotly - checking tests ... ERROR - -* ratPASTA - checking tests ... ERROR - -* rBiasCorrection - checking tests ... ERROR - -* tricolore - checking examples ... ERROR - -* xpose - checking tests ... ERROR +* rvinecopulib + checking installed package size ... NOTE ### Failed to check @@ -51,9 +20,8 @@ Issues with CRAN packages are summarised below. * apisensr (NA) * backShift (NA) * bayesdfa (NA) -* bayesGAM (NA) * bayesZIB (NA) -* bmgarch (NA) +* btergm (NA) * CausalImpact (NA) * CB2 (NA) * cbar (NA) @@ -63,11 +31,9 @@ Issues with CRAN packages are summarised below. * ggmsa (NA) * ggtern (NA) * glmmfields (NA) -* MarketMatching (NA) * mcmcabn (NA) * metagam (NA) -* mlr3pipelines (NA) -* OncoBayes2 (NA) +* MoMPCA (NA) * osmplotr (NA) * pcalg (NA) * penaltyLearning (NA) @@ -78,6 +44,7 @@ Issues with CRAN packages are summarised below. * scoper (NA) * spectralAnalysis (NA) * StroupGLMM (NA) +* superb (NA) * SynthETIC (NA) * tigger (NA) * trackr (NA) diff --git a/revdep/failures.md b/revdep/failures.md index bcf48468d5..8757d9517a 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -82,7 +82,7 @@ Status: 1 ERROR, 1 NOTE * GitHub: NA * Source code: https://github.com/cran/apc * Date/Publication: 2020-10-01 23:20:06 UTC -* Number of recursive dependencies: 112 +* Number of recursive dependencies: 113 Run `cloud_details(, "apc")` for more info @@ -148,7 +148,7 @@ Status: 1 ERROR * GitHub: https://github.com/dhaine/apisensr * Source code: https://github.com/cran/apisensr * Date/Publication: 2021-03-15 11:20:09 UTC -* Number of recursive dependencies: 127 +* Number of recursive dependencies: 128 Run `cloud_details(, "apisensr")` for more info @@ -360,26 +360,26 @@ ERROR: compilation failed for package ‘bayesdfa’ ``` -# bayesGAM +# bayesZIB
-* Version: 0.0.1 +* Version: 0.0.2 * GitHub: NA -* Source code: https://github.com/cran/bayesGAM -* Date/Publication: 2020-11-18 10:20:06 UTC -* Number of recursive dependencies: 84 +* Source code: https://github.com/cran/bayesZIB +* Date/Publication: 2021-05-26 09:50:02 UTC +* Number of recursive dependencies: 53 -Run `cloud_details(, "bayesGAM")` for more info +Run `cloud_details(, "bayesZIB")` for more info
## In both -* checking whether package ‘bayesGAM’ can be installed ... ERROR +* checking whether package ‘bayesZIB’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bayesGAM/new/bayesGAM.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/bayesZIB/new/bayesZIB.Rcheck/00install.out’ for details. ``` ## Installation @@ -387,129 +387,121 @@ Run `cloud_details(, "bayesGAM")` for more info ### Devel ``` -* installing *source* package ‘bayesGAM’ ... -** package ‘bayesGAM’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bayesZIB’ ... +** package ‘bayesZIB’ successfully unpacked and MD5 sums checked ** using staged installation -** libs +Error in loadNamespace(name) : there is no package called ‘rstantools’ +Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: configuration failed for package ‘bayesZIB’ +* removing ‘/tmp/workdir/bayesZIB/new/bayesZIB.Rcheck/bayesZIB’ + + +``` +### CRAN + +``` +* installing *source* package ‘bayesZIB’ ... +** package ‘bayesZIB’ successfully unpacked and MD5 sums checked +** using staged installation +Error in loadNamespace(name) : there is no package called ‘rstantools’ +Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: configuration failed for package ‘bayesZIB’ +* removing ‘/tmp/workdir/bayesZIB/old/bayesZIB.Rcheck/bayesZIB’ + + +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + -g++ -std=gnu++14 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/opt/R/4.0.3/lib/R/site-library/BH/include' -I'/opt/R/4.0.3/lib/R/site-library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.0.3/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.0.3/lib/R/site-library/rstan/include' -I'/opt/R/4.0.3/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.0.3/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/Core:397, - from /opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/Dense:1, - from /opt/R/4.0.3/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30, -... -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_glmm_continuous_namespace::model_glmm_continuous; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10: required from here -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] -stanExports_glmm_continuous.cc:32:1: fatal error: error writing to /tmp/ccgpCpsc.s: Cannot allocate memory - 32 | } - | ^ -compilation terminated. -make: *** [/opt/R/4.0.3/lib/R/etc/Makeconf:179: stanExports_glmm_continuous.o] Error 1 -ERROR: compilation failed for package ‘bayesGAM’ -* removing ‘/tmp/workdir/bayesGAM/new/bayesGAM.Rcheck/bayesGAM’ ``` ### CRAN ``` -* installing *source* package ‘bayesGAM’ ... -** package ‘bayesGAM’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -g++ -std=gnu++14 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/opt/R/4.0.3/lib/R/site-library/BH/include' -I'/opt/R/4.0.3/lib/R/site-library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.0.3/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.0.3/lib/R/site-library/rstan/include' -I'/opt/R/4.0.3/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.0.3/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/Core:397, - from /opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/Dense:1, - from /opt/R/4.0.3/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30, -... -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’ -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_glmm_discrete_namespace::model_glmm_discrete; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10: required from here -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.0.3/lib/R/etc/Makeconf:179: stanExports_glmm_discrete.o] Error 1 -ERROR: compilation failed for package ‘bayesGAM’ -* removing ‘/tmp/workdir/bayesGAM/old/bayesGAM.Rcheck/bayesGAM’ + + ``` -# bayesZIB +# NA
-* Version: 0.0.2 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/bayesZIB -* Date/Publication: 2021-05-26 09:50:02 UTC -* Number of recursive dependencies: 53 +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 -Run `cloud_details(, "bayesZIB")` for more info +Run `cloud_details(, "NA")` for more info
-## In both - -* checking whether package ‘bayesZIB’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/bayesZIB/new/bayesZIB.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘bayesZIB’ ... -** package ‘bayesZIB’ successfully unpacked and MD5 sums checked -** using staged installation -Error in loadNamespace(name) : there is no package called ‘rstantools’ -Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: configuration failed for package ‘bayesZIB’ -* removing ‘/tmp/workdir/bayesZIB/new/bayesZIB.Rcheck/bayesZIB’ + + + + ``` ### CRAN ``` -* installing *source* package ‘bayesZIB’ ... -** package ‘bayesZIB’ successfully unpacked and MD5 sums checked -** using staged installation -Error in loadNamespace(name) : there is no package called ‘rstantools’ -Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: configuration failed for package ‘bayesZIB’ -* removing ‘/tmp/workdir/bayesZIB/old/bayesZIB.Rcheck/bayesZIB’ + + + + ``` -# bmgarch +# btergm
-* Version: 1.0.0 -* GitHub: https://github.com/ph-rast/bmgarch -* Source code: https://github.com/cran/bmgarch -* Date/Publication: 2020-09-17 13:00:03 UTC -* Number of recursive dependencies: 0 +* Version: 1.9.13 +* GitHub: https://github.com/leifeld/btergm +* Source code: https://github.com/cran/btergm +* Date/Publication: 2020-10-26 14:30:02 UTC +* Number of recursive dependencies: 75 -Run `cloud_details(, "bmgarch")` for more info +Run `cloud_details(, "btergm")` for more info
## In both -* checking whether package ‘bmgarch’ can be installed ... ERROR +* checking whether package ‘btergm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bmgarch/new/bmgarch.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/btergm/new/btergm.Rcheck/00install.out’ for details. ``` ## Installation @@ -517,54 +509,32 @@ Run `cloud_details(, "bmgarch")` for more info ### Devel ``` -* installing *source* package ‘bmgarch’ ... -** package ‘bmgarch’ successfully unpacked and MD5 sums checked +* installing *source* package ‘btergm’ ... +** package ‘btergm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -"/opt/R/4.0.3/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/pdBEKKMGARCH.stan -DIAGNOSTIC(S) FROM PARSER: -Info: integer division implicitly rounds to integer. Found int division: nt * nt - nt / 2 - Positive values rounded down, negative values rounded up or down in platform-dependent way. - -Wrote C++ file "stan_files/pdBEKKMGARCH.cc" -... -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_pdBEKKMGARCH_namespace::model_pdBEKKMGARCH; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10: required from here -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.0.3/lib/R/etc/Makeconf:179: stan_files/pdBEKKMGARCH.o] Error 1 -rm stan_files/pdBEKKMGARCH.cc -ERROR: compilation failed for package ‘bmgarch’ -* removing ‘/tmp/workdir/bmgarch/new/bmgarch.Rcheck/bmgarch’ +** R +** inst +** byte-compile and prepare package for lazy loading +Error: object ‘ergm.Cprepare’ is not exported by 'namespace:ergm' +Execution halted +ERROR: lazy loading failed for package ‘btergm’ +* removing ‘/tmp/workdir/btergm/new/btergm.Rcheck/btergm’ ``` ### CRAN ``` -* installing *source* package ‘bmgarch’ ... -** package ‘bmgarch’ successfully unpacked and MD5 sums checked +* installing *source* package ‘btergm’ ... +** package ‘btergm’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -"/opt/R/4.0.3/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/pdBEKKMGARCH.stan -DIAGNOSTIC(S) FROM PARSER: -Info: integer division implicitly rounds to integer. Found int division: nt * nt - nt / 2 - Positive values rounded down, negative values rounded up or down in platform-dependent way. - -Wrote C++ file "stan_files/pdBEKKMGARCH.cc" -... -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_pdBEKKMGARCH_namespace::model_pdBEKKMGARCH; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10: required from here -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.0.3/lib/R/etc/Makeconf:179: stan_files/pdBEKKMGARCH.o] Error 1 -rm stan_files/pdBEKKMGARCH.cc -ERROR: compilation failed for package ‘bmgarch’ -* removing ‘/tmp/workdir/bmgarch/old/bmgarch.Rcheck/bmgarch’ +** R +** inst +** byte-compile and prepare package for lazy loading +Error: object ‘ergm.Cprepare’ is not exported by 'namespace:ergm' +Execution halted +ERROR: lazy loading failed for package ‘btergm’ +* removing ‘/tmp/workdir/btergm/old/btergm.Rcheck/btergm’ ``` @@ -765,6 +735,41 @@ Status: 1 ERROR +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # dfpk @@ -920,7 +925,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/GenHMM1d * Date/Publication: 2021-01-21 08:20:03 UTC -* Number of recursive dependencies: 77 +* Number of recursive dependencies: 78 Run `cloud_details(, "GenHMM1d")` for more info @@ -988,7 +993,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/ggmsa * Date/Publication: 2021-02-02 10:10:07 UTC -* Number of recursive dependencies: 70 +* Number of recursive dependencies: 74 Run `cloud_details(, "ggmsa")` for more info @@ -1064,7 +1069,7 @@ Run `cloud_details(, "ggtern")` for more info -## Newly broken +## In both * checking whether package ‘ggtern’ can be installed ... ERROR ``` @@ -1072,21 +1077,6 @@ Run `cloud_details(, "ggtern")` for more info See ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/00install.out’ for details. ``` -## Newly fixed - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘hexbin’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘chemometrics’ - ``` - -## In both - * checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘sp’ @@ -1125,13 +1115,12 @@ ERROR: lazy loading failed for package ‘ggtern’ ** demo ** inst ** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (ggtern) +Error in get(x, envir = ns, inherits = FALSE) : + object 'try_require' not found +Error: unable to load R code in package ‘ggtern’ +Execution halted +ERROR: lazy loading failed for package ‘ggtern’ +* removing ‘/tmp/workdir/ggtern/old/ggtern.Rcheck/ggtern’ ``` @@ -1213,17 +1202,16 @@ ERROR: compilation failed for package ‘glmmfields’ ``` -# MarketMatching +# NA
-* Version: 1.2.0 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/MarketMatching -* Date/Publication: 2021-01-08 20:10:02 UTC -* Number of recursive dependencies: 67 +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 -Run `cloud_details(, "MarketMatching")` for more info +Run `cloud_details(, "NA")` for more info
@@ -1232,22 +1220,7 @@ Run `cloud_details(, "MarketMatching")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/MarketMatching/new/MarketMatching.Rcheck’ -* using R version 4.0.3 (2020-10-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using options ‘--no-manual --no-build-vignettes’ -* checking for file ‘MarketMatching/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘MarketMatching’ version ‘1.2.0’ -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'CausalImpact', 'bsts', 'Boom' -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR @@ -1257,22 +1230,7 @@ Status: 1 ERROR ### CRAN ``` -* using log directory ‘/tmp/workdir/MarketMatching/old/MarketMatching.Rcheck’ -* using R version 4.0.3 (2020-10-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using options ‘--no-manual --no-build-vignettes’ -* checking for file ‘MarketMatching/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘MarketMatching’ version ‘1.2.0’ -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'CausalImpact', 'bsts', 'Boom' -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR @@ -1344,6 +1302,41 @@ Status: 1 ERROR +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # metagam @@ -1417,17 +1410,17 @@ Status: 1 ERROR ``` -# mlr3pipelines +# MoMPCA
-* Version: 0.3.4 -* GitHub: https://github.com/mlr-org/mlr3pipelines -* Source code: https://github.com/cran/mlr3pipelines -* Date/Publication: 2021-03-05 22:10:08 UTC -* Number of recursive dependencies: 166 +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/MoMPCA +* Date/Publication: 2021-01-21 13:10:03 UTC +* Number of recursive dependencies: 82 -Run `cloud_details(, "mlr3pipelines")` for more info +Run `cloud_details(, "MoMPCA")` for more info
@@ -1436,27 +1429,7 @@ Run `cloud_details(, "mlr3pipelines")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/mlr3pipelines/new/mlr3pipelines.Rcheck’ -* using R version 4.0.3 (2020-10-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using options ‘--no-manual --no-build-vignettes’ -* checking for file ‘mlr3pipelines/DESCRIPTION’ ... OK -* this is package ‘mlr3pipelines’ version ‘0.3.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... NOTE -... -149: virginica 5.4 2.3 6.2 3.4 -150: virginica 5.1 1.8 5.9 3.0 -> pop$train(list(task))[[1]]$data() -Error: The following packages could not be loaded: NMF -Execution halted -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 1 ERROR, 2 NOTEs + @@ -1466,122 +1439,30 @@ Status: 1 ERROR, 2 NOTEs ### CRAN ``` -* using log directory ‘/tmp/workdir/mlr3pipelines/old/mlr3pipelines.Rcheck’ +* using log directory ‘/tmp/workdir/MoMPCA/old/MoMPCA.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-manual --no-build-vignettes’ -* checking for file ‘mlr3pipelines/DESCRIPTION’ ... OK -* this is package ‘mlr3pipelines’ version ‘0.3.4’ +* checking for file ‘MoMPCA/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘MoMPCA’ version ‘1.0.1’ * package encoding: UTF-8 * checking package namespace information ... OK -* checking package dependencies ... NOTE ... -149: virginica 5.4 2.3 6.2 3.4 -150: virginica 5.1 1.8 5.9 3.0 -> pop$train(list(task))[[1]]$data() -Error: The following packages could not be loaded: NMF -Execution halted -* checking for unstated dependencies in ‘tests’ ... OK -* checking tests ... OK - Running ‘testthat.R’ -* DONE -Status: 1 ERROR, 2 NOTEs - - - - - -``` -# OncoBayes2 - -
- -* Version: 0.7-0 -* GitHub: NA -* Source code: https://github.com/cran/OncoBayes2 -* Date/Publication: 2021-05-07 19:30:02 UTC -* Number of recursive dependencies: 89 - -Run `cloud_details(, "OncoBayes2")` for more info - -
- -## Newly broken - -* checking whether package ‘OncoBayes2’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/OncoBayes2/new/OncoBayes2.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - -* checking installed package size ... NOTE - ``` - installed size is 59.6Mb - sub-directories of 1Mb or more: - libs 58.4Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘OncoBayes2’ ... -** package ‘OncoBayes2’ successfully unpacked and MD5 sums checked -** using staged installation -DIAGNOSTIC(S) FROM PARSER: -Info: integer division implicitly rounds to integer. Found int division: current / base - Positive values rounded down, negative values rounded up or down in platform-dependent way. -Info: integer division implicitly rounds to integer. Found int division: left_ind + right_ind / 2 - Positive values rounded down, negative values rounded up or down in platform-dependent way. - -** libs -... -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’ -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_blrm_exnex_namespace::model_blrm_exnex; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10: required from here -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.0.3/lib/R/etc/Makeconf:179: stanExports_blrm_exnex.o] Error 1 -ERROR: compilation failed for package ‘OncoBayes2’ -* removing ‘/tmp/workdir/OncoBayes2/new/OncoBayes2.Rcheck/OncoBayes2’ - - -``` -### CRAN + Error: package or namespace load failed for ‘utils’: + .onLoad failed in loadNamespace() for 'utils', details: + call: system("uname -a", intern = TRUE) + error: cannot popen 'uname -a', probable reason 'Cannot allocate memory' + internal error -3 in R_decompress1 + 3: package ‘stats’ in options("defaultPackages") was not found + Killed +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... -``` -* installing *source* package ‘OncoBayes2’ ... -** package ‘OncoBayes2’ successfully unpacked and MD5 sums checked -** using staged installation -DIAGNOSTIC(S) FROM PARSER: -Info: integer division implicitly rounds to integer. Found int division: current / base - Positive values rounded down, negative values rounded up or down in platform-dependent way. -Info: integer division implicitly rounds to integer. Found int division: left_ind + right_ind / 2 - Positive values rounded down, negative values rounded up or down in platform-dependent way. -** libs -... -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** checking absolute paths in shared objects and dynamic libraries -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (OncoBayes2) ``` @@ -1862,6 +1743,41 @@ Status: 1 ERROR +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # rabhit @@ -1939,7 +1855,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/raw * Date/Publication: 2021-02-05 15:40:03 UTC -* Number of recursive dependencies: 159 +* Number of recursive dependencies: 160 Run `cloud_details(, "raw")` for more info @@ -2218,6 +2134,41 @@ Status: 1 ERROR +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # StroupGLMM @@ -2284,6 +2235,74 @@ Status: 1 ERROR +``` +# superb + +
+ +* Version: 0.9.7.5 +* GitHub: https://github.com/dcousin3/superb +* Source code: https://github.com/cran/superb +* Date/Publication: 2021-06-23 04:10:02 UTC +* Number of recursive dependencies: 159 + +Run `cloud_details(, "superb")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/superb/new/superb.Rcheck’ +* using R version 4.0.3 (2020-10-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using options ‘--no-manual --no-build-vignettes’ +* checking for file ‘superb/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘superb’ version ‘0.9.7.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘referenceIntervals’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/superb/old/superb.Rcheck’ +* using R version 4.0.3 (2020-10-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using options ‘--no-manual --no-build-vignettes’ +* checking for file ‘superb/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘superb’ version ‘0.9.7.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘referenceIntervals’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # SynthETIC @@ -2293,7 +2312,7 @@ Status: 1 ERROR * GitHub: https://github.com/agi-lab/SynthETIC * Source code: https://github.com/cran/SynthETIC * Date/Publication: 2021-04-02 12:10:02 UTC -* Number of recursive dependencies: 105 +* Number of recursive dependencies: 106 Run `cloud_details(, "SynthETIC")` for more info @@ -2360,6 +2379,41 @@ Status: 1 NOTE +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # tigger diff --git a/revdep/problems.md b/revdep/problems.md index 95141aeefa..87d39ccc89 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,626 +1,32 @@ -# bayesAB +# rvinecopulib
-* Version: 1.1.2 -* GitHub: https://github.com/FrankPortman/bayesAB -* Source code: https://github.com/cran/bayesAB -* Date/Publication: 2019-07-02 23:11:08 UTC -* Number of recursive dependencies: 67 - -Run `cloud_details(, "bayesAB")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("bayesAB") - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure (test-generics.R:41:3): Success ───────────────────────────────────── - `plot(x)` produced warnings. - ── Failure (test-generics.R:42:3): Success ───────────────────────────────────── - `plot(x, rep(0.5, 4))` produced warnings. - ── Failure (test-generics.R:46:3): Success ───────────────────────────────────── - `print(plot(x))` produced warnings. - ── Failure (test-generics.R:47:3): Success ───────────────────────────────────── - `print(plot(x, rep(0.5, 4)))` produced warnings. - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 137 ] - Error: Test failures - Execution halted - ``` - -# BayesianReasoning - -
- -* Version: 0.3.2 -* GitHub: https://github.com/gorkang/BayesianReasoning -* Source code: https://github.com/cran/BayesianReasoning -* Date/Publication: 2020-07-03 16:40:16 UTC -* Number of recursive dependencies: 80 - -Run `cloud_details(, "BayesianReasoning")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > library(testthat) - > library(BayesianReasoning) - > - > test_check("BayesianReasoning") - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure (test-PPV_heatmap.R:117:3): PPV calculation with area overlay, low uncertainty, and decimals in y axis ── - p$layers[[3]]$geom_params$description not identical to "40 y.o.\n2 out of 8\nFP = 4.8%\nPPV = 85%". - target is NULL, current is character - ── Failure (test-PPV_heatmap.R:146:3): NPV calculation with area overlay and low uncertainty ── - p$layers[[3]]$geom_params$description not identical to "40 y.o.\n67 out of 68\nFN = 1%\nNPV = 59%". - target is NULL, current is character - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 27 ] - Error: Test failures - Execution halted - ``` - -# cvms - -
- -* Version: 1.3.0 -* GitHub: https://github.com/ludvigolsen/cvms -* Source code: https://github.com/cran/cvms -* Date/Publication: 2021-06-07 14:40:02 UTC -* Number of recursive dependencies: 124 - -Run `cloud_details(, "cvms")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - █ - 1. └─testthat::expect_true(!p1$guides$fill[[1]]) test_plotting_functions.R:183:2 - 2. └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. └─rlang::eval_bare(expr, quo_get_env(quo)) - ── Error (test_plotting_functions.R:340:3): plot_confusion_matrix() with sum tiles, class order, and intensity_by percentage ── - Error: invalid argument type - Backtrace: - █ - 1. └─testthat::expect_true(!p1$guides$fill[[1]]) test_plotting_functions.R:340:2 - 2. └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. └─rlang::eval_bare(expr, quo_get_env(quo)) - - [ FAIL 3 | WARN 6 | SKIP 68 | PASS 3743 ] - Error: Test failures - Execution halted - ``` - -# ezEDA - -
- -* Version: 0.1.0 -* GitHub: https://github.com/kviswana/ezEDA -* Source code: https://github.com/cran/ezEDA -* Date/Publication: 2020-06-25 09:20:06 UTC +* Version: 0.5.5.1.1 +* GitHub: https://github.com/vinecopulib/rvinecopulib +* Source code: https://github.com/cran/rvinecopulib +* Date/Publication: 2021-01-06 16:00:12 UTC * Number of recursive dependencies: 72 -Run `cloud_details(, "ezEDA")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - p$labels$y not identical to "count". - Attributes: < Modes: list, NULL > - Attributes: < Lengths: 1, 0 > - Attributes: < names for target but not for current > - Attributes: < current is not list-like > - ── Failure (test_two_category_tally.R:19:3): y axis is labeled 'count' ───────── - p$labels$y not identical to "count". - Attributes: < Modes: list, NULL > - Attributes: < Lengths: 1, 0 > - Attributes: < names for target but not for current > - Attributes: < current is not list-like > - - [ FAIL 8 | WARN 1 | SKIP 0 | PASS 79 ] - Error: Test failures - Execution halted - ``` - -# ggseg - -
- -* Version: 1.6.3 -* GitHub: https://github.com/LCBC-UiO/ggseg -* Source code: https://github.com/cran/ggseg -* Date/Publication: 2021-05-19 11:00:05 UTC -* Number of recursive dependencies: 125 - -Run `cloud_details(, "ggseg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggseg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geom_brain - > ### Title: Brain geom - > ### Aliases: geom_brain GeomBrain - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 5. └─ggplot2:::by_layer(function(l, d) l$compute_statistic(d, layout)) - 6. └─ggplot2:::f(l = layers[[i]], d = data[[i]]) - 7. └─l$compute_statistic(d, layout) - 8. └─ggplot2:::f(..., self = self) - 9. └─self$stat$compute_layer(data, self$computed_stat_params, layout) - 10. └─ggplot2:::f(..., self = self) - 11. └─ggproto_parent(Stat, self)$compute_layer(data, params, layout) - 12. └─ggplot2:::f(..., self = self) - 13. └─ggplot2:::check_required_aesthetics(...) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 7. ├─ggplot2::ggplot_build(x) - 8. └─ggplot2:::ggplot_build.ggplot(x) - 9. └─ggplot2:::by_layer(function(l, d) l$compute_statistic(d, layout)) - 10. └─ggplot2:::f(l = layers[[i]], d = data[[i]]) - 11. └─l$compute_statistic(d, layout) - 12. └─ggplot2:::f(..., self = self) - 13. └─self$stat$compute_layer(data, self$computed_stat_params, layout) - 14. └─ggplot2:::f(..., self = self) - 15. └─ggproto_parent(Stat, self)$compute_layer(data, params, layout) - 16. └─ggplot2:::f(..., self = self) - 17. └─ggplot2:::check_required_aesthetics(...) - - [ FAIL 1 | WARN 0 | SKIP 7 | PASS 108 ] - Error: Test failures - Execution halted - ``` - -# ggtern - -
- -* Version: 3.3.0 -* GitHub: NA -* Source code: https://github.com/cran/ggtern -* Date/Publication: 2020-04-11 14:50:05 UTC -* Number of recursive dependencies: 45 - -Run `cloud_details(, "ggtern")` for more info - -
- -## Newly broken - -* checking whether package ‘ggtern’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘hexbin’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘chemometrics’ - ``` - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘sp’ - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘ggtern’ ... -** package ‘ggtern’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** demo -** inst -** byte-compile and prepare package for lazy loading -Error in get(x, envir = ns, inherits = FALSE) : - object 'try_require' not found -Error: unable to load R code in package ‘ggtern’ -Execution halted -ERROR: lazy loading failed for package ‘ggtern’ -* removing ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/ggtern’ - - -``` -### CRAN - -``` -* installing *source* package ‘ggtern’ ... -** package ‘ggtern’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** demo -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (ggtern) - - -``` -# HRM - -
- -* Version: 1.2.1 -* GitHub: https://github.com/happma/HRM -* Source code: https://github.com/cran/HRM -* Date/Publication: 2020-02-06 14:50:02 UTC -* Number of recursive dependencies: 83 - -Run `cloud_details(, "HRM")` for more info - -
- -## Newly broken - -* checking dependencies in R code ... NOTE - ``` - - (R:42550): Gtk-WARNING **: 09:01:27.551: gtk_disable_setlocale() must be called before gtk_init() - ``` - -# OncoBayes2 - -
- -* Version: 0.7-0 -* GitHub: NA -* Source code: https://github.com/cran/OncoBayes2 -* Date/Publication: 2021-05-07 19:30:02 UTC -* Number of recursive dependencies: 89 - -Run `cloud_details(, "OncoBayes2")` for more info +Run `cloud_details(, "rvinecopulib")` for more info
## Newly broken -* checking whether package ‘OncoBayes2’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/OncoBayes2/new/OncoBayes2.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - * checking installed package size ... NOTE ``` - installed size is 59.6Mb + installed size is 75.0Mb sub-directories of 1Mb or more: - libs 58.4Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. + include 4.0Mb + libs 70.6Mb ``` -## Installation - -### Devel - -``` -* installing *source* package ‘OncoBayes2’ ... -** package ‘OncoBayes2’ successfully unpacked and MD5 sums checked -** using staged installation -DIAGNOSTIC(S) FROM PARSER: -Info: integer division implicitly rounds to integer. Found int division: current / base - Positive values rounded down, negative values rounded up or down in platform-dependent way. -Info: integer division implicitly rounds to integer. Found int division: left_ind + right_ind / 2 - Positive values rounded down, negative values rounded up or down in platform-dependent way. - -** libs -... -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’ -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_blrm_exnex_namespace::model_blrm_exnex; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.0.3/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10: required from here -/opt/R/4.0.3/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.0.3/lib/R/etc/Makeconf:179: stanExports_blrm_exnex.o] Error 1 -ERROR: compilation failed for package ‘OncoBayes2’ -* removing ‘/tmp/workdir/OncoBayes2/new/OncoBayes2.Rcheck/OncoBayes2’ - - -``` -### CRAN - -``` -* installing *source* package ‘OncoBayes2’ ... -** package ‘OncoBayes2’ successfully unpacked and MD5 sums checked -** using staged installation -DIAGNOSTIC(S) FROM PARSER: -Info: integer division implicitly rounds to integer. Found int division: current / base - Positive values rounded down, negative values rounded up or down in platform-dependent way. -Info: integer division implicitly rounds to integer. Found int division: left_ind + right_ind / 2 - Positive values rounded down, negative values rounded up or down in platform-dependent way. - -** libs -... - -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** checking absolute paths in shared objects and dynamic libraries -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (OncoBayes2) - - -``` -# plotly - -
- -* Version: 4.9.4 -* GitHub: https://github.com/ropensci/plotly -* Source code: https://github.com/cran/plotly -* Date/Publication: 2021-06-08 17:40:02 UTC -* Number of recursive dependencies: 154 - -Run `cloud_details(, "plotly")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - `expected` is a logical vector (TRUE) - ── Failure (test-animate-highlight.R:119:7): When key is equivalent to group, produce simple keys ── - tr$key == tr$name is not TRUE - - `actual`: - `expected`: TRUE - ── Failure (test-animate-highlight.R:120:7): When key is equivalent to group, produce simple keys ── - tr$`_isSimpleKey` is not TRUE - - `actual` is NULL - `expected` is a logical vector (TRUE) - - [ FAIL 4 | WARN 36 | SKIP 56 | PASS 1404 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.1Mb - sub-directories of 1Mb or more: - examples 1.1Mb - htmlwidgets 3.8Mb - ``` - -# ratPASTA - -
- -* Version: 0.2.1 -* GitHub: https://github.com/ikodvanj/ratPASTA -* Source code: https://github.com/cran/ratPASTA -* Date/Publication: 2021-06-02 08:00:02 UTC -* Number of recursive dependencies: 127 - -Run `cloud_details(, "ratPASTA")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure (test-latency.R:20:3): Testing output of latency plot ─────────────── - `l` not equal to readRDS("lp.rds"). - Component "LatencyVsCycle": Component "y": Mean relative difference: 0.009602421 - Component "LatencyVsCycle": Component "x": Mean relative difference: 0.1132548 - Component "LatencyVsGroup": Component "y": Mean relative difference: 0.006664163 - Component "LatencyVsGroup": Component "x": Mean relative difference: 0.026796 - ── Failure (test-startleplot.r:26:3): Testing output of startle plot ─────────── - `pld` not equal to `plde`. - Component "x": Mean relative difference: 0.1892022 - Component "y": Mean relative difference: 7.335276e-05 - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 21 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘hms’ - All declared Imports should be used. - ``` - -# rBiasCorrection - -
- -* Version: 0.3.0 -* GitHub: https://github.com/kapsner/rBiasCorrection -* Source code: https://github.com/cran/rBiasCorrection -* Date/Publication: 2021-05-17 17:20:02 UTC -* Number of recursive dependencies: 132 - -Run `cloud_details(, "rBiasCorrection")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in (function (formula, data = parent.frame(), start, control = nls.control(), : - singular gradient - ══ Skipped tests ═══════════════════════════════════════════════════════════════ - • On CRAN (9) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure (test-plotting.R:236:5): create_exampleplot ───────────────────────── - `virtual_list` is not NULL - - `actual` is a character vector ('/tmp/RtmpcmmfYc/plotdir//exampleplot.png') - `expected` is NULL - - [ FAIL 1 | WARN 31 | SKIP 9 | PASS 50 ] - Error: Test failures - Execution halted - ``` - -# tricolore - -
- -* Version: 1.2.2 -* GitHub: NA -* Source code: https://github.com/cran/tricolore -* Date/Publication: 2020-04-28 13:10:02 UTC -* Number of recursive dependencies: 110 - -Run `cloud_details(, "tricolore")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘tricolore-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ColorKeySextant - > ### Title: Sextant Scheme Legend - > ### Aliases: ColorKeySextant - > ### Keywords: internal - > - > ### ** Examples - > - ... - 1. ├─(function (x, ...) ... - 2. └─ggtern:::print.ggplot(x) - 3. ├─ggtern::ggplot_build(x) - 4. └─ggtern:::ggplot_build.ggplot(x) - 5. └─ggtern:::by_layer(function(l, d) l$compute_geom_1(d)) - 6. └─ggtern:::f(l = layers[[i]], d = data[[i]]) - 7. └─l$compute_geom_1(d) - 8. └─ggplot2:::f(..., self = self) - 9. └─ggplot2:::check_required_aesthetics(...) - Execution halted - ``` - -# xpose - -
- -* Version: 0.4.12 -* GitHub: https://github.com/UUPharmacometrics/xpose -* Source code: https://github.com/cran/xpose -* Date/Publication: 2021-01-12 16:50:02 UTC -* Number of recursive dependencies: 96 - -Run `cloud_details(, "xpose")` for more info - -
- -## Newly broken +## Newly fixed -* checking tests ... ERROR +* checking whether package ‘rvinecopulib’ can be installed ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. └─ggplot2::ggsave(...) - 3. └─ggplot2:::plot_dim(...) - 4. └─base::match.arg(units) - ── Error (test-xpose_save.R:80:3): mutlitple pages are properly saved ────────── - Error: 'arg' must be of length 1 - Backtrace: - █ - 1. └─xpose::xpose_save(...) test-xpose_save.R:80:2 - 2. └─ggplot2::ggsave(...) - 3. └─ggplot2:::plot_dim(...) - 4. └─base::match.arg(units) - - [ FAIL 4 | WARN 0 | SKIP 7 | PASS 516 ] - Error: Test failures - Execution halted + Installation failed. + See ‘/tmp/workdir/rvinecopulib/old/rvinecopulib.Rcheck/00install.out’ for details. ``` diff --git a/tests/testthat/helper-vdiffr.R b/tests/testthat/helper-vdiffr.R index 9fa69eb1a6..20823ba45c 100644 --- a/tests/testthat/helper-vdiffr.R +++ b/tests/testthat/helper-vdiffr.R @@ -2,7 +2,7 @@ # VDIFFR_RUN_TESTS is explicitly set to "true", which should be the case only on # a GitHub Actions CI runner with stable version of R. -if (requireNamespace("vdiffr", quietly = TRUE)) { +if (requireNamespace("vdiffr", quietly = TRUE) && utils::packageVersion('testthat') >= '3.0.3') { expect_doppelganger <- vdiffr::expect_doppelganger } else { # If vdiffr is not available and visual tests are explicitly required, raise error.