Merge in v3.4.4 to main (#5480)

* Cherry-pick from #5327

* Add a NEWS item

* Hotfix 3.4.4 (#5449)

* is.atomic() --> is.atomic() || is.null()

* Polish news

* Put is.null() first

* Cherrypick rgeos removal from description (#5453)

* Remove rgeos from the dependency (#5242)

---------

Co-authored-by: Hiroaki Yutani <yutani.ini@gmail.com>

* run revdepcheck

* Update CRAN comments

* Increment version number to 3.4.4

* Fix Version 3.4.4 NEWS Typo (#5479)

Change "the upcoming retirement of rproj, rgeos, and maptools"
to "the upcoming retirement of rgdal, rgeos, and maptools"

* Increment version number to 3.4.4.9000

---------

Co-authored-by: Hiroaki Yutani <yutani.ini@gmail.com>
Co-authored-by: Thomas Lin Pedersen <thomasp85@gmail.com>
Co-authored-by: Matt Nield <64328730+matthewjnield@users.noreply.github.com>
This commit is contained in:
Teun van den Brand 2023-10-13 09:00:42 +02:00 committed by GitHub
parent 6dd9bb6611
commit bf0c64faab
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
12 changed files with 2509 additions and 1117 deletions

View File

@ -1,5 +1,5 @@
Package: ggplot2
Version: 3.4.3.9000
Version: 3.4.4.9000
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Authors@R: c(
person("Hadley", "Wickham", , "hadley@posit.co", role = "aut",
@ -54,7 +54,6 @@ Suggests:
knitr,
mapproj,
maps,
maptools,
multcomp,
munsell,
nlme,

11
NEWS.md
View File

@ -155,6 +155,17 @@
duplicated coordinates (@teunbrand, #5215).
* Improve performance of layers without positional scales (@zeehio, #4990)
# ggplot2 3.4.4
This hotfix release adapts to a change in r-devel's `base::is.atomic()` and
the upcoming retirement of maptools.
* `fortify()` for sp objects (e.g., `SpatialPolygonsDataFrame`) is now deprecated
and will be removed soon in support of [the upcoming retirement of rgdal, rgeos,
and maptools](https://r-spatial.org/r/2023/05/15/evolution4.html). In advance
of the whole removal, `fortify(<SpatialPolygonsDataFrame>, region = ...)`
no longer works as of this version (@yutannihilation, #5244).
# ggplot2 3.4.3
This hotfix release addresses a version comparison change in r-devel. There are
no user-facing or breaking changes.

View File

@ -226,7 +226,7 @@ is_calculated <- function(x, warn = FALSE) {
return(TRUE)
}
# Support of old recursive behaviour
if (is.atomic(x)) {
if (is.null(x) || is.atomic(x)) {
FALSE
} else if (is.symbol(x)) {
res <- is_dotted_var(as.character(x))
@ -266,7 +266,7 @@ is_staged <- function(x) {
# Strip dots from expressions
strip_dots <- function(expr, env, strip_pronoun = FALSE) {
if (is.atomic(expr)) {
if (is.null(expr) || is.atomic(expr)) {
expr
} else if (is.name(expr)) {
expr_ch <- as.character(expr)
@ -324,7 +324,7 @@ strip_stage <- function(expr) {
make_labels <- function(mapping) {
default_label <- function(aesthetic, mapping) {
# e.g., geom_smooth(aes(colour = "loess")) or aes(y = NULL)
if (is.atomic(mapping)) {
if (is.null(mapping) || is.atomic(mapping)) {
return(aesthetic)
}
mapping <- strip_stage(mapping)

View File

@ -285,7 +285,7 @@ aes_ <- function(x, y, ...) {
as_quosure_aes <- function(x) {
if (is.formula(x) && length(x) == 2) {
as_quosure(x)
} else if (is.call(x) || is.name(x) || is.atomic(x)) {
} else if (is.null(x) || is.call(x) || is.name(x) || is.atomic(x)) {
new_aesthetic(x, caller_env)
} else {
cli::cli_abort("Aesthetic must be a one-sided formula, call, name, or constant.")

View File

@ -9,32 +9,31 @@
#' @param ... not used by this method
#' @keywords internal
#' @name fortify.sp
#' @examples
#' if (require("maptools")) {
#' sids <- system.file("shapes/sids.shp", package="maptools")
#' nc1 <- readShapePoly(sids,
#' proj4string = CRS("+proj=longlat +datum=NAD27"))
#' nc1_df <- fortify(nc1)
#' }
NULL
#' @rdname fortify.sp
#' @export
#' @method fortify SpatialPolygonsDataFrame
fortify.SpatialPolygonsDataFrame <- function(model, data, region = NULL, ...) {
deprecate_warn0("3.4.4",
I("`fortify(<SpatialPolygonsDataFrame>)`"),
details = "Please migrate to sf."
)
attr <- as.data.frame(model)
# If not specified, split into regions based on polygons
if (is.null(region)) {
coords <- lapply(model@polygons,fortify)
# Suppress duplicated warnings
withr::with_options(list(lifecycle_verbosity = "quiet"), {
coords <- lapply(model@polygons,fortify)
})
coords <- vec_rbind0(!!!coords)
cli::cli_inform("Regions defined for each Polygons")
} else {
cp <- sp::polygons(model)
# Union together all polygons that make up a region
unioned <- maptools::unionSpatialPolygons(cp, attr[, region])
coords <- fortify(unioned)
coords$order <- 1:nrow(coords)
lifecycle::deprecate_stop("3.4.4",
I("`fortify(<SpatialPolygonsDataFrame>, region = ...)` is defunct'"),
details = "Please migrate to sf."
)
}
coords
}
@ -43,7 +42,15 @@ fortify.SpatialPolygonsDataFrame <- function(model, data, region = NULL, ...) {
#' @export
#' @method fortify SpatialPolygons
fortify.SpatialPolygons <- function(model, data, ...) {
polys <- lapply(model@polygons, fortify)
deprecate_warn0("3.4.4",
I("`fortify(<SpatialPolygons>)`"),
details = "Please migrate to sf."
)
# Suppress duplicated warnings
withr::with_options(list(lifecycle_verbosity = "quiet"), {
polys <- lapply(model@polygons, fortify)
})
vec_rbind0(!!!polys)
}
@ -51,6 +58,11 @@ fortify.SpatialPolygons <- function(model, data, ...) {
#' @export
#' @method fortify Polygons
fortify.Polygons <- function(model, data, ...) {
deprecate_warn0("3.4.4",
I("`fortify(<Polygons>)`"),
details = "Please migrate to sf."
)
subpolys <- model@Polygons
pieces <- lapply(seq_along(subpolys), function(i) {
df <- fortify(subpolys[[model@plotOrder[i]]])
@ -70,6 +82,11 @@ fortify.Polygons <- function(model, data, ...) {
#' @export
#' @method fortify Polygon
fortify.Polygon <- function(model, data, ...) {
deprecate_warn0("3.4.4",
I("`fortify(<Polygon>)`"),
details = "Please migrate to sf."
)
df <- as.data.frame(model@coords)
names(df) <- c("long", "lat")
df$order <- 1:nrow(df)
@ -81,6 +98,11 @@ fortify.Polygon <- function(model, data, ...) {
#' @export
#' @method fortify SpatialLinesDataFrame
fortify.SpatialLinesDataFrame <- function(model, data, ...) {
deprecate_warn0("3.4.4",
I("`fortify(<SpatialLinesDataFrame>)`"),
details = "Please migrate to sf."
)
lines <- lapply(model@lines, fortify)
vec_rbind0(!!!lines)
}
@ -89,6 +111,11 @@ fortify.SpatialLinesDataFrame <- function(model, data, ...) {
#' @export
#' @method fortify Lines
fortify.Lines <- function(model, data, ...) {
deprecate_warn0("3.4.4",
I("`fortify(<Lines>)`"),
details = "Please migrate to sf."
)
lines <- model@Lines
pieces <- lapply(seq_along(lines), function(i) {
df <- fortify(lines[[i]])
@ -108,6 +135,11 @@ fortify.Lines <- function(model, data, ...) {
#' @export
#' @method fortify Line
fortify.Line <- function(model, data, ...) {
deprecate_warn0("3.4.4",
I("`fortify(<Line>)`"),
details = "Please migrate to sf."
)
df <- as.data.frame(model@coords)
names(df) <- c("long", "lat")
df$order <- 1:nrow(df)

View File

@ -1,5 +1,66 @@
This is a patch release responding to a request from CRAN about numeric
version comparisons in R-devel. It also includes a workaround for changes
in the `stats::density()` function in R-devel that affected visual tests.
There are no user facing changes, so no reverse dependencies are expected to
be affected.
This is a patch release responding to changes in R-devel concerning the behavior
of `is.atomic()`. Further, it contains the removal of maptools and rgeos which
is set for archival soon
## revdepcheck results
We checked 4771 reverse dependencies (4716 from CRAN + 55 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
* We saw 2 new problems
* We failed to check 42 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
* jfa
checking re-building of vignette outputs ... WARNING
* SCORPIUS
checking tests ... ERROR
### Failed to check
* ale (NA)
* aPEAR (NA)
* bayesdfa (NA)
* BrailleR (NA)
* CausalImpact (NA)
* CensMFM (NA)
* cinaR (NA)
* fdacluster (NA)
* genekitr (NA)
* ggPMX (NA)
* grandR (NA)
* HeckmanEM (NA)
* immcp (NA)
* loon.ggplot (NA)
* MACP (NA)
* MarketMatching (NA)
* MARVEL (NA)
* MSclassifR (NA)
* nlmixr2 (NA)
* nlmixr2extra (NA)
* nlmixr2plot (NA)
* nlmixr2rpt (NA)
* numbat (NA)
* oHMMed (NA)
* OlinkAnalyze (NA)
* OpenMx (NA)
* phylosem (NA)
* PsychWordVec (NA)
* RcppCensSpatial (NA)
* rmsb (NA)
* rstanarm (NA)
* RVA (NA)
* SCpubr (NA)
* SSVS (NA)
* streamDAG (NA)
* TestAnaAPP (NA)
* tidySEM (NA)
* tinyarray (NA)
* TOmicsVis (NA)
* valse (NA)
* vivid (NA)
* xpose.nlmixr2 (NA)

View File

@ -38,12 +38,4 @@
To figure out the correct variable name for region, inspect
\code{as.data.frame(model)}.
}
\examples{
if (require("maptools")) {
sids <- system.file("shapes/sids.shp", package="maptools")
nc1 <- readShapePoly(sids,
proj4string = CRS("+proj=longlat +datum=NAD27"))
nc1_df <- fortify(nc1)
}
}
\keyword{internal}

View File

@ -1,84 +1,111 @@
# Revdeps
## Failed to check (64)
## Failed to check (97)
|package |version |error |warning |note |
|:--------------------------|:-------|:------|:-------|:----|
|NA |? | | | |
|beadplexr |? | | | |
|CausalImpact |? | | | |
|CensMFM |? | | | |
|cinaR |? | | | |
|NA |? | | | |
|NA |? | | | |
|ctsem |3.7.6 |1 | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|genekitr |? | | | |
|[ggh4x](failures.md#ggh4x) |0.2.3 |__+1__ | | |
|NA |? | | | |
|glmmPen |1.5.3.0 |1 | | |
|grandR |? | | | |
|immcp |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|loon.ggplot |? | | | |
|MACP |? | | | |
|NA |? | | | |
|MarketMatching |? | | | |
|MARVEL |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|nlmixr2rpt |? | | | |
|numbat |? | | | |
|NA |? | | | |
|OlinkAnalyze |? | | | |
|OpenMx |? | | | |
|Platypus |? | | | |
|PsychWordVec |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|RcppCensSpatial |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|rstan |2.21.8 |1 | | |
|RVA |? | | | |
|rxode2 |2.0.11 |1 | |1 |
|NA |? | | | |
|SCpubr |? | | | |
|tidySEM |? | | | |
|NA |? | | | |
|tinyarray |? | | | |
|valse |0.1-0 |1 | | |
|NA |? | | | |
|NA |? | | | |
|vivid |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|package |version |error |warning |note |
|:---------------|:-------|:-----|:-------|:----|
|NA |? | | | |
|NA |? | | | |
|ale |0.1.0 |1 | | |
|aPEAR |? | | | |
|NA |? | | | |
|bayesdfa |1.2.0 |1 | | |
|NA |? | | | |
|BrailleR |1.0.2 |1 | | |
|NA |? | | | |
|CausalImpact |? | | | |
|CensMFM |? | | | |
|cinaR |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|fdacluster |0.3.0 |1 | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|genekitr |? | | | |
|NA |? | | | |
|ggPMX |? | | | |
|NA |? | | | |
|grandR |? | | | |
|HeckmanEM |? | | | |
|immcp |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|loon.ggplot |? | | | |
|MACP |? | | | |
|NA |? | | | |
|MarketMatching |? | | | |
|MARVEL |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|MSclassifR |? | | | |
|nlmixr2 |? | | | |
|nlmixr2extra |? | | | |
|nlmixr2plot |? | | | |
|nlmixr2rpt |? | | | |
|NA |? | | | |
|numbat |? | | | |
|NA |? | | | |
|oHMMed |? | | | |
|OlinkAnalyze |? | | | |
|OpenMx |? | | | |
|phylosem |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|PsychWordVec |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|RcppCensSpatial |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|rmsb |1.0-0 |1 | | |
|rstanarm |2.26.1 |1 | | |
|NA |? | | | |
|RVA |? | | | |
|NA |? | | | |
|SCpubr |? | | | |
|NA |? | | | |
|NA |? | | | |
|SSVS |? | | | |
|streamDAG |? | | | |
|TestAnaAPP |? | | | |
|tidySEM |? | | | |
|NA |? | | | |
|tinyarray |? | | | |
|TOmicsVis |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|NA |? | | | |
|valse |0.1-0 |1 | | |
|NA |? | | | |
|NA |? | | | |
|vivid |? | | | |
|NA |? | | | |
|NA |? | | | |
|xpose.nlmixr2 |? | | | |
|NA |? | | | |
## New problems (8)
## New problems (2)
|package |version |error |warning |note |
|:--------------------------------------|:-------|:------|:-------|:----|
|[afex](problems.md#afex) |1.2-1 | |__+1__ | |
|[dalmatian](problems.md#dalmatian) |1.0.0 | |__+1__ | |
|[DriveML](problems.md#driveml) |0.1.5 | |__+1__ |1 |
|[EcoEnsemble](problems.md#ecoensemble) |1.0.2 | |__+1__ |3 |
|[ggtern](problems.md#ggtern) |3.4.1 | |__+1__ |2 |
|[siland](problems.md#siland) |2.0.5 | |__+1__ | |
|[TCIU](problems.md#tciu) |1.2.2 | |__+1__ |1 |
|[xpose](problems.md#xpose) |0.4.15 |__+1__ | | |
|package |version |error |warning |note |
|:--------------------------------|:-------|:------|:-------|:----|
|[jfa](problems.md#jfa) |0.7.0 | |__+1__ |3 |
|[SCORPIUS](problems.md#scorpius) |1.0.9 |__+1__ | | |

View File

@ -1,67 +1,62 @@
## revdepcheck results
We checked 4503 reverse dependencies (4468 from CRAN + 35 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
We checked 4771 reverse dependencies (4716 from CRAN + 55 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
* We saw 8 new problems
* We failed to check 29 packages
* We saw 2 new problems
* We failed to check 42 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
* afex
* jfa
checking re-building of vignette outputs ... WARNING
* dalmatian
checking re-building of vignette outputs ... WARNING
* DriveML
checking re-building of vignette outputs ... WARNING
* EcoEnsemble
checking re-building of vignette outputs ... WARNING
* ggtern
checking Rd files ... WARNING
* siland
checking re-building of vignette outputs ... WARNING
* TCIU
checking re-building of vignette outputs ... WARNING
* xpose
* SCORPIUS
checking tests ... ERROR
### Failed to check
* beadplexr (NA)
* ale (NA)
* aPEAR (NA)
* bayesdfa (NA)
* BrailleR (NA)
* CausalImpact (NA)
* CensMFM (NA)
* cinaR (NA)
* ctsem (NA)
* fdacluster (NA)
* genekitr (NA)
* ggh4x (NA)
* glmmPen (NA)
* ggPMX (NA)
* grandR (NA)
* HeckmanEM (NA)
* immcp (NA)
* loon.ggplot (NA)
* MACP (NA)
* MarketMatching (NA)
* MARVEL (NA)
* MSclassifR (NA)
* nlmixr2 (NA)
* nlmixr2extra (NA)
* nlmixr2plot (NA)
* nlmixr2rpt (NA)
* numbat (NA)
* oHMMed (NA)
* OlinkAnalyze (NA)
* OpenMx (NA)
* Platypus (NA)
* phylosem (NA)
* PsychWordVec (NA)
* RcppCensSpatial (NA)
* rstan (NA)
* rmsb (NA)
* rstanarm (NA)
* RVA (NA)
* rxode2 (NA)
* SCpubr (NA)
* SSVS (NA)
* streamDAG (NA)
* TestAnaAPP (NA)
* tidySEM (NA)
* tinyarray (NA)
* TOmicsVis (NA)
* valse (NA)
* vivid (NA)
* xpose.nlmixr2 (NA)

View File

@ -33,17 +33,16 @@ Run `cloud_details(, "NA")` for more info
```
# beadplexr
# NA
<details>
* Version: 0.4.1
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/beadplexr
* Date/Publication: 2022-03-05 13:50:02 UTC
* Number of recursive dependencies: 128
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "beadplexr")` for more info
Run `cloud_details(, "NA")` for more info
</details>
@ -52,27 +51,7 @@ Run `cloud_details(, "beadplexr")` for more info
### Devel
```
* using log directory /tmp/workdir/beadplexr/new/beadplexr.Rcheck
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option --no-manual
* checking for file beadplexr/DESCRIPTION ... OK
* checking extension type ... Package
* this is package beadplexr version 0.4.1
* package encoding: UTF-8
* checking package namespace information ... OK
...
Running testthat.R
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in inst/doc ... OK
* checking running R code from vignettes ... NONE
cba_macsplex_example.Rmd using UTF-8... OK
legendplex_analysis.Rmd using UTF-8... OK
preparing_flow_data.Rmd using UTF-8... OK
* checking re-building of vignette outputs ... OK
* DONE
Status: 1 NOTE
@ -82,27 +61,382 @@ Status: 1 NOTE
### CRAN
```
* using log directory /tmp/workdir/beadplexr/old/beadplexr.Rcheck
```
# ale
<details>
* Version: 0.1.0
* GitHub: https://github.com/Tripartio/ale
* Source code: https://github.com/cran/ale
* Date/Publication: 2023-08-29 16:30:15 UTC
* Number of recursive dependencies: 76
Run `cloud_details(, "ale")` for more info
</details>
## In both
* checking whether package ale can be installed ... ERROR
```
Installation failed.
See /tmp/workdir/ale/new/ale.Rcheck/00install.out for details.
```
## Installation
### Devel
```
* installing *source* package ale ...
** package ale successfully unpacked and MD5 sums checked
** using staged installation
** R
Error in parse(outFile) :
/tmp/workdir/ale/new/ale.Rcheck/00_pkg_src/ale/R/ale_core.R:720:22: unexpected input
719: }) |>
720: c(0, y = _
^
ERROR: unable to collate and parse R files for package ale
* removing /tmp/workdir/ale/new/ale.Rcheck/ale
```
### CRAN
```
* installing *source* package ale ...
** package ale successfully unpacked and MD5 sums checked
** using staged installation
** R
Error in parse(outFile) :
/tmp/workdir/ale/old/ale.Rcheck/00_pkg_src/ale/R/ale_core.R:720:22: unexpected input
719: }) |>
720: c(0, y = _
^
ERROR: unable to collate and parse R files for package ale
* removing /tmp/workdir/ale/old/ale.Rcheck/ale
```
# aPEAR
<details>
* Version: 1.0.0
* GitHub: NA
* Source code: https://github.com/cran/aPEAR
* Date/Publication: 2023-06-12 18:10:13 UTC
* Number of recursive dependencies: 169
Run `cloud_details(, "aPEAR")` for more info
</details>
## Error before installation
### Devel
```
* using log directory /tmp/workdir/aPEAR/new/aPEAR.Rcheck
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option --no-manual
* checking for file beadplexr/DESCRIPTION ... OK
* checking extension type ... Package
* this is package beadplexr version 0.4.1
* checking for file aPEAR/DESCRIPTION ... OK
* this is package aPEAR version 1.0.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
...
Running testthat.R
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in inst/doc ... OK
* checking running R code from vignettes ... NONE
cba_macsplex_example.Rmd using UTF-8... OK
legendplex_analysis.Rmd using UTF-8... OK
preparing_flow_data.Rmd using UTF-8... OK
* checking re-building of vignette outputs ... OK
--- failed re-building aPEAR-vignette.Rmd
SUMMARY: processing the following file failed:
aPEAR-vignette.Rmd
Error: Vignette re-building failed.
Execution halted
* DONE
Status: 1 NOTE
Status: 1 WARNING, 1 NOTE
```
### CRAN
```
* using log directory /tmp/workdir/aPEAR/old/aPEAR.Rcheck
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option --no-manual
* checking for file aPEAR/DESCRIPTION ... OK
* this is package aPEAR version 1.0.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
...
--- failed re-building aPEAR-vignette.Rmd
SUMMARY: processing the following file failed:
aPEAR-vignette.Rmd
Error: Vignette re-building failed.
Execution halted
* DONE
Status: 1 WARNING, 1 NOTE
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# bayesdfa
<details>
* Version: 1.2.0
* GitHub: https://github.com/fate-ewi/bayesdfa
* Source code: https://github.com/cran/bayesdfa
* Date/Publication: 2021-09-28 13:20:02 UTC
* Number of recursive dependencies: 86
Run `cloud_details(, "bayesdfa")` for more info
</details>
## In both
* checking whether package bayesdfa can be installed ... ERROR
```
Installation failed.
See /tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out for details.
```
## Installation
### Devel
```
* installing *source* package bayesdfa ...
** package bayesdfa successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++17 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.1.1/lib/R/site-library/BH/include' -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.1.1/lib/R/site-library/rstan/include' -I'/opt/R/4.1.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.1.1/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/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
...
/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Options = 0; Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::XprType = Eigen::Product<Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>, Eigen::Matrix<double, -1, 1>, 0>]
/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::operator const Scalar() const [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Option = 0; Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::Scalar = double]
/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]
/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument Eigen::internal::packet_traits<double>::type {aka __vector(2) double} [-Wignored-attributes]
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stanExports_dfa.o] Error 1
ERROR: compilation failed for package bayesdfa
* removing /tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa
```
### CRAN
```
* installing *source* package bayesdfa ...
** package bayesdfa successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++17 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.1.1/lib/R/site-library/BH/include' -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.1.1/lib/R/site-library/rstan/include' -I'/opt/R/4.1.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.1.1/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/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
...
/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Options = 0; Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::XprType = Eigen::Product<Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>, Eigen::Matrix<double, -1, 1>, 0>]
/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::operator const Scalar() const [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Option = 0; Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::Scalar = double]
/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]
/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument Eigen::internal::packet_traits<double>::type {aka __vector(2) double} [-Wignored-attributes]
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stanExports_dfa.o] Error 1
ERROR: compilation failed for package bayesdfa
* removing /tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# BrailleR
<details>
* Version: 1.0.2
* GitHub: https://github.com/ajrgodfrey/BrailleR
* Source code: https://github.com/cran/BrailleR
* Date/Publication: 2023-07-10 19:10:12 UTC
* Number of recursive dependencies: 196
Run `cloud_details(, "BrailleR")` for more info
</details>
## In both
* checking whether package BrailleR can be installed ... ERROR
```
Installation failed.
See /tmp/workdir/BrailleR/new/BrailleR.Rcheck/00install.out for details.
```
## Installation
### Devel
```
* installing *source* package BrailleR ...
** package BrailleR successfully unpacked and MD5 sums checked
** using staged installation
** R
Error in parse(outFile) :
/tmp/workdir/BrailleR/new/BrailleR.Rcheck/00_pkg_src/BrailleR/R/AddXMLInternal.R:398:48: unexpected input
397: group_split() |>
398: Filter(function(x) nrow(x) >= 2, x = _
^
ERROR: unable to collate and parse R files for package BrailleR
* removing /tmp/workdir/BrailleR/new/BrailleR.Rcheck/BrailleR
```
### CRAN
```
* installing *source* package BrailleR ...
** package BrailleR successfully unpacked and MD5 sums checked
** using staged installation
** R
Error in parse(outFile) :
/tmp/workdir/BrailleR/old/BrailleR.Rcheck/00_pkg_src/BrailleR/R/AddXMLInternal.R:398:48: unexpected input
397: group_split() |>
398: Filter(function(x) nrow(x) >= 2, x = _
^
ERROR: unable to collate and parse R files for package BrailleR
* removing /tmp/workdir/BrailleR/old/BrailleR.Rcheck/BrailleR
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
@ -117,7 +451,7 @@ Status: 1 NOTE
* GitHub: NA
* Source code: https://github.com/cran/CausalImpact
* Date/Publication: 2022-11-09 08:40:40 UTC
* Number of recursive dependencies: 79
* Number of recursive dependencies: 81
Run `cloud_details(, "CausalImpact")` for more info
@ -379,26 +713,306 @@ Run `cloud_details(, "NA")` for more info
```
# ctsem
# NA
<details>
* Version: 3.7.6
* GitHub: https://github.com/cdriveraus/ctsem
* Source code: https://github.com/cran/ctsem
* Date/Publication: 2023-03-26 17:10:02 UTC
* Number of recursive dependencies: 137
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "ctsem")` for more info
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# fdacluster
<details>
* Version: 0.3.0
* GitHub: https://github.com/astamm/fdacluster
* Source code: https://github.com/cran/fdacluster
* Date/Publication: 2023-07-04 15:53:04 UTC
* Number of recursive dependencies: 121
Run `cloud_details(, "fdacluster")` for more info
</details>
## In both
* checking whether package ctsem can be installed ... ERROR
* checking whether package fdacluster can be installed ... ERROR
```
Installation failed.
See /tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out for details.
See /tmp/workdir/fdacluster/new/fdacluster.Rcheck/00install.out for details.
```
## Installation
@ -406,264 +1020,54 @@ Run `cloud_details(, "ctsem")` for more info
### Devel
```
* installing *source* package ctsem ...
** package ctsem successfully unpacked and MD5 sums checked
* installing *source* package fdacluster ...
** package fdacluster successfully unpacked and MD5 sums checked
** using staged installation
DIAGNOSTIC(S) FROM PARSER:
Info: integer division implicitly rounds to integer. Found int division: d * d - d / 2
Positive values rounded down, negative values rounded up or down in platform-dependent way.
Info: integer division implicitly rounds to integer. Found int division: d * d - d / 2
Positive values rounded down, negative values rounded up or down in platform-dependent way.
DIAGNOSTIC(S) FROM PARSER:
** libs
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c affineWarpingClass.cpp -o affineWarpingClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseDissimilarityClass.cpp -o baseDissimilarityClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseOptimizerClass.cpp -o baseOptimizerClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseWarpingClass.cpp -o baseWarpingClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c bobyqaOptimizerClass.cpp -o bobyqaOptimizerClass.o
...
In file included from stanExports_ctsm.cc:5:
stanExports_ctsm.h: In member function T__ model_ctsm_namespace::model_ctsm::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = true; T__ = double]:
stanExports_ctsm.h:2091:9: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
2091 | T__ log_prob(std::vector<T__>& params_r__,
| ^~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stanExports_ctsm.o] Error 1
ERROR: compilation failed for package ctsem
* removing /tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem
g++ -std=gnu++14 -shared -L/opt/R/4.1.1/lib/R/lib -L/usr/local/lib -o fdacluster.so RcppExports.o affineWarpingClass.o baseDissimilarityClass.o baseOptimizerClass.o baseWarpingClass.o bobyqaOptimizerClass.o dilationWarpingClass.o kmaModelClass.o kmap.o kumaraswamyWarpingClass.o l2DissimilarityClass.o lowessCenterClass.o meanCenterClass.o medianCenterClass.o medoidCenterClass.o noWarpingClass.o pearsonDissimilarityClass.o polyCenterClass.o shiftWarpingClass.o utilityFunctions.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.1.1/lib/R/lib -lR
installing to /tmp/workdir/fdacluster/new/fdacluster.Rcheck/00LOCK-fdacluster/00new/fdacluster/libs
** R
Error in parse(outFile) :
/tmp/workdir/fdacluster/new/fdacluster.Rcheck/00_pkg_src/fdacluster/R/utils.R:132:31: unexpected input
131: purrr::imap(\(values, id) stats::approx(x@argvals[[id]], values, n = M)$y) |>
132: do.call(rbind, args = _
^
ERROR: unable to collate and parse R files for package fdacluster
* removing /tmp/workdir/fdacluster/new/fdacluster.Rcheck/fdacluster
```
### CRAN
```
* installing *source* package ctsem ...
** package ctsem successfully unpacked and MD5 sums checked
* installing *source* package fdacluster ...
** package fdacluster successfully unpacked and MD5 sums checked
** using staged installation
DIAGNOSTIC(S) FROM PARSER:
Info: integer division implicitly rounds to integer. Found int division: d * d - d / 2
Positive values rounded down, negative values rounded up or down in platform-dependent way.
Info: integer division implicitly rounds to integer. Found int division: d * d - d / 2
Positive values rounded down, negative values rounded up or down in platform-dependent way.
DIAGNOSTIC(S) FROM PARSER:
** libs
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c affineWarpingClass.cpp -o affineWarpingClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseDissimilarityClass.cpp -o baseDissimilarityClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseOptimizerClass.cpp -o baseOptimizerClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseWarpingClass.cpp -o baseWarpingClass.o
g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c bobyqaOptimizerClass.cpp -o bobyqaOptimizerClass.o
...
In file included from stanExports_ctsm.cc:5:
stanExports_ctsm.h: In member function T__ model_ctsm_namespace::model_ctsm::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = true; T__ = double]:
stanExports_ctsm.h:2091:9: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
2091 | T__ log_prob(std::vector<T__>& params_r__,
| ^~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stanExports_ctsm.o] Error 1
ERROR: compilation failed for package ctsem
* removing /tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation
### Devel
```
```
### CRAN
```
```
# NA
<details>
* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/NA
* Number of recursive dependencies: 0
Run `cloud_details(, "NA")` for more info
</details>
## Error before installation