From b7e133dbfc4b306b61e5cd762f4e52be7554208b Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Sat, 1 Nov 2025 12:06:53 -0700 Subject: [PATCH 1/2] CLEANUP: Removed defunct progress() --- DESCRIPTION | 2 +- NAMESPACE | 1 - NEWS.md | 7 ++++++- R/progress.R | 36 ------------------------------------ man/progress.Rd | 24 ------------------------ 5 files changed, 7 insertions(+), 63 deletions(-) delete mode 100644 R/progress.R delete mode 100644 man/progress.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 009364ce..835456e6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: progressr -Version: 0.17.0-9005 +Version: 0.17.0-9006 Title: An Inclusive, Unifying API for Progress Updates Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will also work with parallel processing via the 'future' framework, e.g. future.apply::future_lapply(), furrr::future_map(), and 'foreach' with 'doFuture'. The package is compatible with Shiny applications. Authors@R: c(person("Henrik", "Bengtsson", diff --git a/NAMESPACE b/NAMESPACE index 410d39cf..a032e737 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -26,7 +26,6 @@ export(handler_void) export(handler_winprogressbar) export(handlers) export(make_progression_handler) -export(progress) export(progress_aggregator) export(progress_progressr) export(progression) diff --git a/NEWS.md b/NEWS.md index 64952be1..d50e7927 100644 --- a/NEWS.md +++ b/NEWS.md @@ -21,7 +21,12 @@ ignored. Also, warnings on "with_progress() received a progression 'initiate' request" were produced with **progressr** 0.17.0 (2025-10-15). - + +## Deprecated and Defunct + + * Removed `progress()`, which has been defunct since version 0.10.0 + (2021-12-18). + # Version 0.17.0 [2025-10-15] diff --git a/R/progress.R b/R/progress.R deleted file mode 100644 index 30fd9916..00000000 --- a/R/progress.R +++ /dev/null @@ -1,36 +0,0 @@ -#' Creates and Signals a Progression Condition -#' -#' _WARNING:_ `progress()` is defunct - don't use. -#' -#' @param \ldots Arguments pass to [progression()]. -#' -#' @param call (expression) A call expression. -#' -#' @return A [base::condition] of class `progression`. -#' -#' @seealso -#' To create a progression condition, use [progression()]. -#' To signal a progression condition, use [base::signalCondition()]. -#' -#' @keywords internal -#' @export -progress <- function(..., call = sys.call()) { - action <- getOption("progressr.lifecycle.progress", "defunct") - signal <- switch(action, deprecated = .Deprecated, defunct = .Defunct) - signal(msg = sprintf("progress() is %s", action), package = .packageName) - - args <- list(...) - if (length(args) == 1L && inherits(args[[1L]], "condition")) { - cond <- args[[1L]] - stop_if_not(inherits(cond, "progression")) - } else { - cond <- progression(..., call = call) - } - - withRestarts( - signalCondition(cond), - muffleProgression = function(p) NULL - ) - - invisible(cond) -} diff --git a/man/progress.Rd b/man/progress.Rd deleted file mode 100644 index 06afa917..00000000 --- a/man/progress.Rd +++ /dev/null @@ -1,24 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/progress.R -\name{progress} -\alias{progress} -\title{Creates and Signals a Progression Condition} -\usage{ -progress(..., call = sys.call()) -} -\arguments{ -\item{call}{(expression) A call expression.} - -\item{\ldots}{Arguments pass to \code{\link[=progression]{progression()}}.} -} -\value{ -A \link[base:conditions]{base::condition} of class \code{progression}. -} -\description{ -\emph{WARNING:} \code{progress()} is defunct - don't use. -} -\seealso{ -To create a progression condition, use \code{\link[=progression]{progression()}}. -To signal a progression condition, use \code{\link[base:conditions]{base::signalCondition()}}. -} -\keyword{internal} From dc5e7656740bb5b0745ca53a1ede68a0f62962e1 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Wed, 5 Nov 2025 12:19:53 -0800 Subject: [PATCH 2/2] REVDEP: with progress() removed => 3 pkgs fail [#189] [ci skip] --- revdep/README.md | 328 ++++++++++++++++++++++++--------------------- revdep/cran.md | 15 ++- revdep/failures.md | 64 ++++++++- revdep/problems.md | 318 +++++++++++++++++++------------------------ 4 files changed, 384 insertions(+), 341 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 23d3fd07..4971d49f 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,169 +1,185 @@ # Platform -|field |value | -|:--------|:-----------------------------------------------------------| -|version |R version 4.5.0 (2025-04-11) | -|os |Rocky Linux 8.10 (Green Obsidian) | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |en | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/Los_Angeles | -|date |2025-10-14 | -|pandoc |3.6.3 @ /software/c4/cbi/software/pandoc-3.6.3/bin/pandoc | -|quarto |1.6.42 @ /software/c4/cbi/software/quarto-1.6.42/bin/quarto | +|field |value | +|:--------|:-------------------------------------------------------------| +|version |R version 4.5.2 (2025-10-31) | +|os |Rocky Linux 8.10 (Green Obsidian) | +|system |x86_64, linux-gnu | +|ui |X11 | +|language |en | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/Los_Angeles | +|date |2025-11-05 | +|pandoc |3.8.2.1 @ /software/c4/cbi/software/pandoc-3.8.2.1/bin/pandoc | +|quarto |1.8.25 @ /software/c4/cbi/software/quarto-1.8.25/bin/quarto | # Dependencies |package |old |new |Δ | |:---------|:------|:-----------|:--| -|progressr |0.16.0 |0.16.0-9015 |* | +|progressr |0.17.0 |0.17.0-9006 |* | |digest |0.6.37 |0.6.37 | | # Revdeps -## All (139) +## Failed to check (1) -|package |version |error |warning |note | -|:----------------------|:----------|:-----|:-------|:----| -|[adestr](problems.md#adestr)|1.0.0 | | |1 | -|AIPW |0.6.9.2 | | | | -|ale |0.5.3 | | | | -|[AlpsNMR](problems.md#alpsnmr)|4.10.1 |1 | | | -|antaresEditObject |0.9.2 | | | | -|ao |1.2.1 | | | | -|[baseballr](problems.md#baseballr)|1.6.0 | | |1 | -|[baskexact](problems.md#baskexact)|1.0.1 | | |1 | -|basksim |1.0.0 | | | | -|[bayesmove](problems.md#bayesmove)|0.2.1 | | |1 | -|BayesRegDTR |1.0.1 | | | | -|bbotk |1.7.0 | | | | -|beer |1.12.0 | | | | -|binaryRL |0.9.7 | | | | -|bolasso |0.4.0 | | | | -|calmr |0.8.1 | | | | -|campsis |1.7.0 | | | | -|canaper |1.0.1 | | | | -|[caretSDM](problems.md#caretsdm)|1.1.4 |2 | | | -|cccrm |3.0.5 | | | | -|cfbfastR |2.0.0 | | | | -|[collinear](problems.md#collinear)|2.0.0 | | |1 | -|ConFluxPro |1.3.1 | | | | -|[crumble](problems.md#crumble)|0.1.2 |1 | | | -|[cSEM](problems.md#csem)|0.6.1 | | |1 | -|cyclestreets |1.0.3 | | | | -|dapper |1.0.1 | | | | -|dbmss |2.11-0 | | | | -|deseats |1.1.1 | | | | -|[dipsaus](problems.md#dipsaus)|0.3.1 | | |1 | -|distantia |2.0.2 | | | | -|drugdevelopR |1.0.2 | | | | -|easyalluvial |0.4.0 | | | | -|ecic |0.0.4 | | | | -|EconCausal |1.0.2 | | | | -|[econet](problems.md#econet)|1.0.0.1 | |1 | | -|[EFAtools](problems.md#efatools)|0.6.1 | | |1 | -|EGAnet |2.3.0 | | | | -|elevatr |0.99.1 | | | | -|EpiForsk |0.2.0 | | | | -|EpiModel |2.5.0 | | | | -|EpiNow2 |1.7.1 | | | | -|fabletools |0.5.1 | | | | -|fastbioclim |0.2.1 | | | | -|[fastRhockey](problems.md#fastrhockey)|0.4.0 | | |1 | -|[fdacluster](problems.md#fdacluster)|0.4.1 | |1 |1 | -|FDOTT |0.1.0 | | | | -|flexFitR |1.2.0 | | | | -|funGp |1.0.0 | | | | -|futureverse |0.1.0 | | | | -|fxTWAPLS |0.1.3 | | | | -|geocausal |0.3.4 | | | | -|[geocmeans](problems.md#geocmeans)|0.3.4 |1 | | | -|GeoModels |2.2.0 | | | | -|gtfs2emis |0.1.1 | | | | -|[gtfs2gps](problems.md#gtfs2gps)|2.1-3 |1 | | | -|hbamr |2.4.4 | | | | -|hgwrr |0.6-2 | | | | -|hmer |1.6.0 | | | | -|hoopR |2.1.0 | | | | -|iccTraj |1.1.0 | | | | -|ino |1.1.0 | | | | -|[ISAnalytics](problems.md#isanalytics)|1.18.0 | | |1 | -|JANE |2.0.0 | | | | -|kmeRtone |1.0 | | | | -|[lava](problems.md#lava)|1.8.1 | | |1 | -|lightr |1.9.0 | | | | -|LLMR |0.6.3 | | | | -|lmtp |1.5.3 | | | | -|LWFBrook90R |0.6.2 | | | | -|[mapme.biodiversity](problems.md#mapmebiodiversity)|0.9.5 |1 |1 |1 | -|mcmcensemble |3.2.0 | | | | -|metasnf |2.1.2 | | | | -|MIC |1.2.0 | | | | -|mikropml |1.6.2 | | | | -|mlr3 |1.2.0 | | | | -|modeltime.resample |0.3.0 | | | | -|MOODE |1.1.0 | | | | -|[mpathsenser](problems.md#mpathsenser)|1.2.3 | | |1 | -|nflfastR |5.1.0 | | | | -|nflreadr |1.5.0 | | | | -|nflseedR |2.0.1 | | | | -|nlrx |0.4.5 | | | | -|oddsapiR |0.0.3 | | | | -|oeli |0.7.5 | | | | -|opentripplanner |0.5.2 | | | | -|parseRPDR |1.1.2 | | | | -|[pavo](problems.md#pavo)|2.9.0 | |1 | | -|pcpr |1.0.0 | | | | -|plnr |2022.11.23 | | | | -|polle |1.5 | | | | -|polykde |1.1.7 | | | | -|poppr |2.9.8 | | | | -|[powRICLPM](problems.md#powriclpm)|0.2.1 | | |1 | -|projpred |2.9.0 | | | | -|[PWIR](problems.md#pwir)|0.0.3.1 | | |1 | -|R4GoodPersonalFinances |1.1.0 | | | | -|RAINBOWR |0.1.38 | | | | -|rainette |0.3.1.1 | | | | -|rangeMapper |2.0.3 | | | | -|readsdr |0.3.0 | | | | -|readyomics |0.1.2 | | | | -|[receptiviti](problems.md#receptiviti)|0.2.0 |1 | | | -|rechaRge |1.0.0 | | | | -|remiod |1.0.2 | | | | -|restriktor |0.6-10 | | | | -|[rsi](problems.md#rsi) |0.3.2 | | |1 | -|saeczi |0.2.0 | | | | -|SCGLR |3.1.0 | | | | -|semPower |2.1.3 | | | | -|sentopics |0.7.5 | | | | -|seqHMM |2.1.0 | | | | -|Seurat |5.3.0 | | | | -|SeuratObject |5.2.0 | | | | -|shapr |1.0.5 | | | | -|simaerep |0.7.0 | | | | -|SimDesign |2.21 | | | | -|sims |0.0.4 | | | | -|skpr |1.9.2 | | | | -|smoots |1.1.4 | | | | -|sphunif |1.4.2 | | | | -|spNetwork |0.4.4.7 | | | | -|squat |0.4.0 | | | | -|[stppSim](problems.md#stppsim)|1.3.4 | |1 | | -|survex |1.2.0 | | | | -|[targeted](problems.md#targeted)|0.5 | | |1 | -|terrainr |0.7.6 | | | | -|tidyfit |0.7.4 | | | | -|tidySEM |0.2.9 | | | | -|[tsdistributions](problems.md#tsdistributions)|1.0.3 |1 | | | -|[tsgarch](problems.md#tsgarch)|1.0.3 | | |1 | -|tsissm |1.0.2 | | | | -|vecmatch |1.2.0 | | | | -|vital |2.0.1 | | | | -|[vmeasur](problems.md#vmeasur)|0.1.4 | |1 | | -|WARDEN |2.0.0 | | | | -|wehoop |2.1.0 | | | | -|[WeightedCluster](problems.md#weightedcluster)|1.8-1 | |1 | | -|ycevo |0.3.0 | | | | +|package |version |error |warning |note | +|:-------|:-------|:------|:-------|:----| +|[beer](failures.md#beer)|1.14.0 |__+1__ | | | + +## New problems (2) + +|package |version |error |warning |note | +|:-----------|:-------|:-----|:-------|:----| +|[futureverse](problems.md#futureverse)|0.1.0 | |__+1__ | | +|[mpathsenser](problems.md#mpathsenser)|1.2.3 | |__+1__ |1 | + +## All (142) + +|package |version |error |warning |note | +|:----------------------|:----------|:------|:-------|:----| +|[adestr](problems.md#adestr)|1.0.0 | | |1 | +|AIPW |0.6.9.2 | | | | +|ale |0.5.3 | | | | +|[AlpsNMR](problems.md#alpsnmr)|4.12.0 |1 | | | +|antaresEditObject |0.9.2 | | | | +|ao |1.2.1 | | | | +|[baseballr](problems.md#baseballr)|1.6.0 | | |1 | +|[baskexact](problems.md#baskexact)|1.0.1 | | |1 | +|basksim |1.0.0 | | | | +|bayesmove |0.2.3 | | | | +|BayesRegDTR |1.1.1 | | | | +|bbotk |1.7.1 | | | | +|[beer](failures.md#beer)|1.14.0 |__+1__ | | | +|binaryRL |0.9.8 | | | | +|bolasso |0.4.0 | | | | +|calmr |0.8.1 | | | | +|campsis |1.7.0 | | | | +|canaper |1.0.1 | | | | +|[caretSDM](problems.md#caretsdm)|1.1.4 |2 | | | +|cccrm |3.0.5 | | | | +|cfbfastR |2.0.0 | | | | +|[collinear](problems.md#collinear)|2.0.0 | | |1 | +|ConFluxPro |1.3.1 | | | | +|[crumble](problems.md#crumble)|0.1.2 |1 | | | +|[cSEM](problems.md#csem)|0.6.1 | | |1 | +|cyclestreets |1.0.3 | | | | +|dapper |1.0.1 | | | | +|dbmss |2.11-0 | | | | +|deseats |1.1.1 | | | | +|[dipsaus](problems.md#dipsaus)|0.3.1 | | |1 | +|distantia |2.0.2 | | | | +|drugdevelopR |1.0.2 | | | | +|easyalluvial |0.4.0 | | | | +|ecic |0.0.4 | | | | +|EconCausal |1.0.2 | | | | +|[econet](problems.md#econet)|1.0.0.1 | |1 | | +|[EFAtools](problems.md#efatools)|0.6.1 | | |1 | +|EGAnet |2.3.0 | | | | +|elevatr |0.99.1 | | | | +|EpiForsk |0.2.0 | | | | +|EpiModel |2.5.0 | | | | +|EpiNow2 |1.7.1 | | | | +|fabletools |0.5.1 | | | | +|fastbioclim |0.2.1 | | | | +|[fastRhockey](problems.md#fastrhockey)|0.4.0 | | |1 | +|[fdacluster](problems.md#fdacluster)|0.4.1 | |1 |1 | +|FDOTT |0.1.0 | | | | +|flexFitR |1.2.0 | | | | +|funGp |1.0.0 | | | | +|[futureverse](problems.md#futureverse)|0.1.0 | |__+1__ | | +|fxTWAPLS |0.1.3 | | | | +|geocausal |0.3.4 | | | | +|geocmeans |0.3.4 | | | | +|geomeTriD |1.4.0 | | | | +|GeoModels |2.2.0 | | | | +|gtfs2emis |0.1.1 | | | | +|gtfs2gps |2.1-3 | | | | +|hbamr |2.4.4 | | | | +|hgwrr |0.6-2 | | | | +|hmer |1.6.0 | | | | +|hoopR |2.1.0 | | | | +|iccTraj |1.1.0 | | | | +|ino |1.2.0 | | | | +|[ISAnalytics](problems.md#isanalytics)|1.20.0 | | |1 | +|JANE |2.0.0 | | | | +|kmeRtone |1.0 | | | | +|lava |1.8.2 | | | | +|lightr |1.9.0 | | | | +|LLMR |0.6.3 | | | | +|lmtp |1.5.3 | | | | +|LWFBrook90R |0.6.2 | | | | +|[mapme.biodiversity](problems.md#mapmebiodiversity)|0.9.5 |1 | | | +|mcmcensemble |3.2.0 | | | | +|metasnf |2.1.2 | | | | +|MIC |1.2.0 | | | | +|[mikropml](problems.md#mikropml)|1.7.0 | | |1 | +|mlr3 |1.2.0 | | | | +|modeltime.resample |0.3.0 | | | | +|modeltuning |0.1.2 | | | | +|MOODE |1.1.0 | | | | +|[mpathsenser](problems.md#mpathsenser)|1.2.3 | |__+1__ |1 | +|nflfastR |5.1.0 | | | | +|nflreadr |1.5.0 | | | | +|nflseedR |2.0.1 | | | | +|nlrx |0.4.5 | | | | +|oddsapiR |0.0.3 | | | | +|oeli |0.7.5 | | | | +|opentripplanner |0.5.2 | | | | +|parseRPDR |1.1.2 | | | | +|[pavo](problems.md#pavo)|2.9.0 | |1 | | +|pcpr |1.0.0 | | | | +|plnr |2022.11.23 | | | | +|polle |1.6.0 | | | | +|polykde |1.1.7 | | | | +|poppr |2.9.8 | | | | +|[powRICLPM](problems.md#powriclpm)|0.2.1 | | |1 | +|projpred |2.9.1 | | | | +|[PWIR](problems.md#pwir)|0.0.3.1 | | |1 | +|R4GoodPersonalFinances |1.1.0 | | | | +|RAINBOWR |0.1.38 | | | | +|rainette |0.3.1.1 | | | | +|rangeMapper |2.0.3 | | | | +|readsdr |0.3.0 | | | | +|readyomics |0.2.0 | | | | +|[receptiviti](problems.md#receptiviti)|0.2.0 |1 | | | +|rechaRge |1.0.0 | | | | +|remiod |1.0.2 | | | | +|restriktor |0.6-10 | | | | +|Rfuzzycoco |0.1.0 | | | | +|[rsi](problems.md#rsi) |0.3.2 | | |1 | +|saeczi |0.2.0 | | | | +|SCGLR |3.1.0 | | | | +|semPower |2.1.3 | | | | +|sentopics |0.7.6 | | | | +|seqHMM |2.1.0 | | | | +|Seurat |5.3.1 | | | | +|SeuratObject |5.2.0 | | | | +|shapr |1.0.5 | | | | +|simaerep |1.0.0 | | | | +|SimDesign |2.21 | | | | +|sims |0.0.4 | | | | +|skpr |1.9.2 | | | | +|smoots |1.1.4 | | | | +|sphunif |1.4.2 | | | | +|spNetwork |0.4.4.7 | | | | +|squat |0.4.0 | | | | +|[stppSim](problems.md#stppsim)|1.3.4 | |1 | | +|survex |1.2.0 | | | | +|targeted |0.6 | | | | +|terrainr |0.7.6 | | | | +|tidyfit |0.7.4 | | | | +|tidySEM |0.2.9 | | | | +|[tsdistributions](problems.md#tsdistributions)|1.0.3 |1 | | | +|[tsgarch](problems.md#tsgarch)|1.0.3 | | |1 | +|tsissm |1.0.2 | | | | +|vecmatch |1.2.0 | | | | +|vital |2.0.1 | | | | +|[vmeasur](problems.md#vmeasur)|0.1.4 | |1 | | +|WARDEN |2.0.0 | | | | +|wehoop |2.1.0 | | | | +|[WeightedCluster](problems.md#weightedcluster)|1.8-1 | |1 | | +|ycevo |0.3.0 | | | | diff --git a/revdep/cran.md b/revdep/cran.md index 6bb06475..98ce9c73 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,7 +1,18 @@ ## revdepcheck results -We checked 139 reverse dependencies (136 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 142 reverse dependencies (138 from CRAN + 4 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 0 new problems + * We saw 2 new problems * We failed to check 0 packages +Issues with CRAN packages are summarised below. + +### New problems +(This reports the first line of each new failure) + +* futureverse + checking dependencies in R code ... WARNING + +* mpathsenser + checking Rd cross-references ... WARNING + diff --git a/revdep/failures.md b/revdep/failures.md index 9a207363..a182e4bc 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1 +1,63 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# beer + +
+ +* Version: 1.14.0 +* GitHub: https://github.com/athchen/beer +* Source code: https://github.com/cran/beer +* Date/Publication: 2025-10-29 +* Number of recursive dependencies: 121 + +Run `revdepcheck::revdep_details(, "beer")` for more info + +
+ +## Newly broken + +* checking whether package ‘beer’ can be installed ... ERROR + ``` + Installation failed. + See ‘/scratch/henrik/revdep/progressr/checks/beer/new/beer.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘beer’ ... +** this is package ‘beer’ version ‘1.14.0’ +** package ‘beer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: object ‘progress’ is not exported by 'namespace:progressr' +Execution halted +ERROR: lazy loading failed for package ‘beer’ +* removing ‘/scratch/henrik/revdep/progressr/checks/beer/new/beer.Rcheck/beer’ + + +``` +### CRAN + +``` +* installing *source* package ‘beer’ ... +** this is package ‘beer’ version ‘1.14.0’ +** package ‘beer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +*** copying figures +** building package indices +** installing vignettes +** 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 (beer) + + +``` diff --git a/revdep/problems.md b/revdep/problems.md index ff7a935c..dea8a424 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -30,11 +30,11 @@ Run `revdepcheck::revdep_details(, "adestr")` for more info
-* Version: 4.10.1 +* Version: 4.12.0 * GitHub: https://github.com/sipss/AlpsNMR * Source code: https://github.com/cran/AlpsNMR -* Date/Publication: 2025-09-28 -* Number of recursive dependencies: 180 +* Date/Publication: 2025-10-29 +* Number of recursive dependencies: 182 Run `revdepcheck::revdep_details(, "AlpsNMR")` for more info @@ -46,14 +46,14 @@ Run `revdepcheck::revdep_details(, "AlpsNMR")` for more info ``` Error(s) in re-building vignettes: --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown + [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. + Error: processing vignette 'Vig01-introduction-to-alpsnmr.Rmd' failed with diagnostics: + LaTeX failed to compile /scratch/henrik/revdep/progressr/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01-introduction-to-alpsnmr.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. + --- failed re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ - Quitting from Vig01-introduction-to-alpsnmr.Rmd:94-99 [load-samples] - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Error in `socketConnection()`: - ! cannot open the connection - --- - Backtrace: + --- re-building ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using rmarkdown + [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. + Error: processing vignette 'Vig01b-introduction-to-alpsnmr-old-api.Rmd' failed with diagnostics: ... LaTeX failed to compile /scratch/henrik/revdep/progressr/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’ @@ -113,29 +113,69 @@ Run `revdepcheck::revdep_details(, "baskexact")` for more info All declared Imports should be used. ``` -# bayesmove +# beer
-* Version: 0.2.1 -* GitHub: https://github.com/joshcullen/bayesmove -* Source code: https://github.com/cran/bayesmove -* Date/Publication: 2021-10-22 08:50:09 UTC -* Number of recursive dependencies: 160 +* Version: 1.14.0 +* GitHub: https://github.com/athchen/beer +* Source code: https://github.com/cran/beer +* Date/Publication: 2025-10-29 +* Number of recursive dependencies: 121 -Run `revdepcheck::revdep_details(, "bayesmove")` for more info +Run `revdepcheck::revdep_details(, "beer")` for more info
-## In both +## Newly broken -* checking Rd files ... NOTE +* checking whether package ‘beer’ can be installed ... ERROR ``` - checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup? - 22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed. - | ^ + Installation failed. + See ‘/scratch/henrik/revdep/progressr/checks/beer/new/beer.Rcheck/00install.out’ for details. ``` +## Installation + +### Devel + +``` +* installing *source* package ‘beer’ ... +** this is package ‘beer’ version ‘1.14.0’ +** package ‘beer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error: object ‘progress’ is not exported by 'namespace:progressr' +Execution halted +ERROR: lazy loading failed for package ‘beer’ +* removing ‘/scratch/henrik/revdep/progressr/checks/beer/new/beer.Rcheck/beer’ + + +``` +### CRAN + +``` +* installing *source* package ‘beer’ ... +** this is package ‘beer’ version ‘1.14.0’ +** package ‘beer’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +*** copying figures +** building package indices +** installing vignettes +** 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 (beer) + + +``` # caretSDM
@@ -144,7 +184,7 @@ Run `revdepcheck::revdep_details(, "bayesmove")` for more info * GitHub: https://github.com/luizesser/caretSDM * Source code: https://github.com/cran/caretSDM * Date/Publication: 2025-08-29 13:50:02 UTC -* Number of recursive dependencies: 183 +* Number of recursive dependencies: 184 Run `revdepcheck::revdep_details(, "caretSDM")` for more info @@ -262,7 +302,7 @@ Run `revdepcheck::revdep_details(, "crumble")` for more info * GitHub: https://github.com/FloSchuberth/cSEM * Source code: https://github.com/cran/cSEM * Date/Publication: 2025-05-16 09:40:14 UTC -* Number of recursive dependencies: 143 +* Number of recursive dependencies: 144 Run `revdepcheck::revdep_details(, "cSEM")` for more info @@ -284,7 +324,7 @@ Run `revdepcheck::revdep_details(, "cSEM")` for more info * GitHub: https://github.com/dipterix/dipsaus * Source code: https://github.com/cran/dipsaus * Date/Publication: 2025-04-03 16:50:02 UTC -* Number of recursive dependencies: 62 +* Number of recursive dependencies: 63 Run `revdepcheck::revdep_details(, "dipsaus")` for more info @@ -399,7 +439,7 @@ Run `revdepcheck::revdep_details(, "fastRhockey")` for more info * GitHub: https://github.com/astamm/fdacluster * Source code: https://github.com/cran/fdacluster * Date/Publication: 2025-01-14 16:50:09 UTC -* Number of recursive dependencies: 125 +* Number of recursive dependencies: 126 Run `revdepcheck::revdep_details(, "fdacluster")` for more info @@ -429,97 +469,36 @@ Run `revdepcheck::revdep_details(, "fdacluster")` for more info ‘caps-plot.R’ ‘utils.R’ ``` -# geocmeans - -
- -* Version: 0.3.4 -* GitHub: https://github.com/JeremyGelb/geocmeans -* Source code: https://github.com/cran/geocmeans -* Date/Publication: 2023-09-12 03:10:02 UTC -* Number of recursive dependencies: 208 - -Run `revdepcheck::revdep_details(, "geocmeans")` for more info - -
- -## In both - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘introduction.Rmd’ using rmarkdown - - Quitting from introduction.Rmd:487-489 [unnamed-chunk-38] - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Error in `st_transform.bbox()`: - ! method not available for GDAL: 3.0.4 - --- - Backtrace: - ... - - Error: processing vignette 'introduction.Rmd' failed with diagnostics: - method not available for GDAL: 3.0.4 - --- failed re-building ‘introduction.Rmd’ - - SUMMARY: processing the following file failed: - ‘introduction.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# gtfs2gps +# futureverse
-* Version: 2.1-3 -* GitHub: https://github.com/ipeaGIT/gtfs2gps -* Source code: https://github.com/cran/gtfs2gps -* Date/Publication: 2025-10-08 15:00:02 UTC -* Number of recursive dependencies: 86 +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/futureverse +* Date/Publication: 2024-06-07 14:10:22 UTC +* Number of recursive dependencies: 43 -Run `revdepcheck::revdep_details(, "gtfs2gps")` for more info +Run `revdepcheck::revdep_details(, "futureverse")` for more info
-## In both +## Newly broken -* checking tests ... +* checking dependencies in R code ... WARNING ``` - Running ‘testthat.R’ - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(gtfs2gps) - gtfs2gps version 2.1-3 is now loaded - - > - > test_check("gtfs2gps") - ... - 4. └─terra (local) .local(x, ...) - 5. ├─terra::makeValid(x) - 6. └─terra::makeValid(x) - 7. └─terra (local) .local(x, ...) - 8. └─terra:::messages(x) - 9. └─terra:::error(f, x@pntr$getError()) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ] - Error: Test failures - Execution halted + Missing or unexported object: ‘progressr::progress’ ``` # ISAnalytics
-* Version: 1.18.0 +* Version: 1.20.0 * GitHub: https://github.com/calabrialab/ISAnalytics * Source code: https://github.com/cran/ISAnalytics -* Date/Publication: 2025-04-15 -* Number of recursive dependencies: 176 +* Date/Publication: 2025-10-29 +* Number of recursive dependencies: 177 Run `revdepcheck::revdep_details(, "ISAnalytics")` for more info @@ -534,30 +513,6 @@ Run `revdepcheck::revdep_details(, "ISAnalytics")` for more info | ^ ``` -# lava - -
- -* Version: 1.8.1 -* GitHub: https://github.com/kkholst/lava -* Source code: https://github.com/cran/lava -* Date/Publication: 2025-01-12 11:40:02 UTC -* Number of recursive dependencies: 130 - -Run `revdepcheck::revdep_details(, "lava")` for more info - -
- -## In both - -* checking DESCRIPTION meta-information ... NOTE - ``` - Missing dependency on R >= 4.1.0 because package code uses the pipe - |> or function shorthand \(...) syntax added in R 4.1.0. - File(s) using such syntax: - ‘contr.Rd’ - ``` - # mapme.biodiversity
@@ -579,42 +534,46 @@ Run `revdepcheck::revdep_details(, "mapme.biodiversity")` for more info Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. - Last 50 lines of output: - 'test-calc_treecover_area_and_emissions.R:30:3', - 'test-calc_treecoverloss_emissions.R:27:3', 'test-calc_tri.R:33:3', - 'test-get_carbon.R:2:3', 'test-get_carbon.R:29:3', 'test-get_chelsa.R:2:3', - 'test-get_esalandcover.R:2:3', 'test-get_fritz_et_al.R:2:3', - 'test-get_gfw_emissions.R:2:3', 'test-get_gfw_lossyear.R:2:3', - 'test-get_gfw_treecover.R:7:3', 'test-get_gmw.R:2:3', 'test-get_gsw.R:2:3', + Complete output: + > library(testthat) + > library(mapme.biodiversity) + > + > options(pillar.advice = FALSE) + > mapme_options(verbose = FALSE) + > test_check("mapme.biodiversity") ... - 12. │ └─jsonlite:::parseJSON(txt, bigint_as_char) - 13. │ └─jsonlite:::parse_string(txt, bigint_as_char) - 14. └─base::.handleSimpleError(...) - 15. └─purrr (local) h(simpleError(msg, call)) - 16. └─cli::cli_abort(...) - 17. └─rlang::abort(...) + `x2 <- .split_dateline(x)` produced warnings. + ── Failure ('test-chunking.R:8:3'): .crosses_dateline and .split_dateline works ── + nrow(x2) (`actual`) not equal to 2 (`expected`). - [ FAIL 2 | WARN 0 | SKIP 44 | PASS 515 ] + `actual`: 1.0 + `expected`: 2.0 + + [ FAIL 2 | WARN 0 | SKIP 43 | PASS 532 ] Error: Test failures Execution halted ``` -* checking whether package ‘mapme.biodiversity’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: GDAL system library version (3.0.4) < 3.7.0 - See ‘/scratch/henrik/revdep/progressr/checks/mapme.biodiversity/new/mapme.biodiversity.Rcheck/00install.out’ for details. - ``` +# mikropml + +
+ +* Version: 1.7.0 +* GitHub: https://github.com/SchlossLab/mikropml +* Source code: https://github.com/cran/mikropml +* Date/Publication: 2025-10-29 03:30:02 UTC +* Number of recursive dependencies: 180 + +Run `revdepcheck::revdep_details(, "mikropml")` for more info + +
+ +## In both -* checking whether the namespace can be loaded with stated dependencies ... NOTE +* checking dependencies in R code ... NOTE ``` - Warning: GDAL system library version (3.0.4) < 3.7.0 - - A namespace must be able to be loaded with just the base namespace - loaded: otherwise if the namespace gets loaded by a saved object, the - session will be unable to start. - - Probably some imports need to be declared in the NAMESPACE file. + Namespace in Imports field not imported from: ‘methods’ + All declared Imports should be used. ``` # mpathsenser @@ -631,6 +590,25 @@ Run `revdepcheck::revdep_details(, "mpathsenser")` for more info
+## Newly broken + +* checking Rd cross-references ... WARNING + ``` + Missing link(s) in Rd file 'fix_jsons.Rd': + ‘[progressr:progress]{progressr::progress()}’ + + Missing link(s) in Rd file 'import.Rd': + ‘[progressr:progress]{progressr::progress()}’ + + Missing link(s) in Rd file 'test_jsons.Rd': + ‘[progressr:progress]{progressr::progress()}’ + + Missing link(s) in Rd file 'unzip_data.Rd': + ‘[progressr:progress]{progressr::progress()}’ + + See section 'Cross-references' in the 'Writing R Extensions' manual. + ``` + ## In both * checking DESCRIPTION meta-information ... NOTE @@ -698,7 +676,7 @@ Run `revdepcheck::revdep_details(, "powRICLPM")` for more info * GitHub: NA * Source code: https://github.com/cran/PWIR * Date/Publication: 2025-07-24 11:10:17 UTC -* Number of recursive dependencies: 107 +* Number of recursive dependencies: 108 Run `revdepcheck::revdep_details(, "PWIR")` for more info @@ -801,30 +779,6 @@ Run `revdepcheck::revdep_details(, "stppSim")` for more info See ‘/scratch/henrik/revdep/progressr/checks/stppSim/new/stppSim.Rcheck/00install.out’ for details. ``` -# targeted - -
- -* Version: 0.5 -* GitHub: https://github.com/kkholst/targeted -* Source code: https://github.com/cran/targeted -* Date/Publication: 2024-02-22 10:00:21 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::revdep_details(, "targeted")` for more info - -
- -## In both - -* checking DESCRIPTION meta-information ... NOTE - ``` - Missing dependency on R >= 4.1.0 because package code uses the pipe - |> or function shorthand \(...) syntax added in R 4.1.0. - File(s) using such syntax: - ‘alean.Rd’ ‘nondom.Rd’ - ``` - # tsdistributions
@@ -844,19 +798,19 @@ Run `revdepcheck::revdep_details(, "tsdistributions")` for more info * checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: - ... --- re-building ‘estimation_demo.Rmd’ using rmarkdown + [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘estimation_demo.Rmd’ --- re-building ‘location_scale_distributions.Rmd’ using rmarkdown + [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. ! Undefined control sequence. l.56 \NewDocumentCommand \citeproctext{}{} - ... - --- finished re-building ‘profile_demo.Rmd’ --- re-building ‘spd_demo.Rmd’ using rmarkdown + [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘spd_demo.Rmd’ SUMMARY: processing the following file failed: @@ -933,14 +887,14 @@ Run `revdepcheck::revdep_details(, "WeightedCluster")` for more info ``` Error(s) in re-building vignettes: --- re-building ‘BigDataSA.Rmd’ using rmarkdown + [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘BigDataSA.Rmd’ --- re-building ‘ClusterExternalValidSA.Rmd’ using rmarkdown + [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘ClusterExternalValidSA.Rmd’ --- re-building ‘ClusterValidSA.Rmd’ using rmarkdown - --- finished re-building ‘ClusterValidSA.Rmd’ - ... l.85 \usepackage {tikz}^^M