elfatherbrown
commented
3 years ago BTW. This does exactly the same thing for thematic from rstudio/thematic or install.packages("thematic").
I have tested this in two boxes, both versions.
Closed elfatherbrown closed 3 years ago
elfatherbrown
commented
3 years ago BTW. This does exactly the same thing for thematic from rstudio/thematic or install.packages("thematic").
I have tested this in two boxes, both versions.
cpsievert
commented
3 years ago Interesting, thanks for the report. Is your package publicly available?
cpsievert
commented
3 years ago Could you also include sessioninfo::session_info()?
cpsievert
commented
3 years ago Ahh, interesting, I can replicate with just this:
library(survMisc)
#> Loading required package: survival
thematic::thematic_on()And it appears {survMisc} isn't doing anything crazy in .onLoad() or .onAttach() 😬
elfatherbrown
commented
3 years ago Yes. Thanks for your atention. Sessioninfo at the end.
survminer does the same. I cant think off the top of my head of other packages that import ggplot. My own package is a mess, i'm learning. I hope it will be public quality some day. Thankfully I could reproduce it with something else.
Session info:
> sessioninfo::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.6.3 (2020-02-29)
os Ubuntu 20.04.2 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Mazatlan
date 2021-02-16
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [3] CRAN (R 3.5.0)
assertthat 0.2.1 2019-03-21 [3] CRAN (R 3.6.1)
backports 1.1.5 2019-10-02 [3] CRAN (R 3.6.1)
broom 0.7.4 2021-01-29 [1] CRAN (R 3.6.3)
callr 3.5.1 2020-10-13 [1] CRAN (R 3.6.3)
car 3.0-10 2020-09-29 [1] CRAN (R 3.6.3)
carData 3.0-4 2020-05-22 [1] CRAN (R 3.6.3)
cellranger 1.1.0 2016-07-27 [3] CRAN (R 3.5.0)
cli 2.3.0 2021-01-31 [1] CRAN (R 3.6.3)
clipr 0.7.0 2019-07-23 [3] CRAN (R 3.6.1)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 3.6.3)
crayon 1.4.1 2021-02-08 [1] CRAN (R 3.6.3)
curl 4.3 2019-12-02 [3] CRAN (R 3.6.1)
data.table 1.12.8 2019-12-09 [3] CRAN (R 3.6.2)
DBI 1.1.0 2019-12-15 [3] CRAN (R 3.6.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 3.6.3)
dplyr 1.0.4 2021-02-02 [1] CRAN (R 3.6.3)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 3.6.3)
evaluate 0.14 2019-05-28 [3] CRAN (R 3.6.1)
forcats 0.4.0 2019-02-17 [3] CRAN (R 3.6.1)
foreign 0.8-76 2020-03-03 [4] CRAN (R 3.6.3)
fs 1.3.1 2019-05-06 [3] CRAN (R 3.6.3)
generics 0.0.2 2018-11-29 [3] CRAN (R 3.5.1)
ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 3.6.3)
ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 3.6.3)
ggsignif 0.6.0 2019-08-08 [1] CRAN (R 3.6.3)
glue 1.4.2 2020-08-27 [1] CRAN (R 3.6.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.3)
gtable 0.3.0 2019-03-25 [3] CRAN (R 3.6.1)
haven 2.2.0 2019-11-08 [3] CRAN (R 3.6.3)
highr 0.8 2019-03-20 [3] CRAN (R 3.6.1)
hms 0.5.3 2020-01-08 [3] CRAN (R 3.6.2)
htmltools 0.4.0 2019-10-04 [3] CRAN (R 3.6.3)
km.ci 0.5-2 2009-08-30 [1] CRAN (R 3.6.3)
KMsurv 0.1-5 2012-12-03 [1] CRAN (R 3.6.3)
knitr 1.28 2020-02-06 [3] CRAN (R 3.6.2)
lattice 0.20-41 2020-04-02 [4] CRAN (R 3.6.3)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 3.6.3)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 3.6.3)
Matrix 1.3-2 2021-01-06 [4] CRAN (R 3.6.3)
munsell 0.5.0 2018-06-12 [3] CRAN (R 3.5.0)
openxlsx 4.2.3 2020-10-27 [1] CRAN (R 3.6.3)
pillar 1.4.7 2020-11-20 [1] CRAN (R 3.6.3)
pkgconfig 2.0.3 2019-09-22 [3] CRAN (R 3.6.1)
processx 3.4.5 2020-11-30 [1] CRAN (R 3.6.3)
ps 1.5.0 2020-12-05 [1] CRAN (R 3.6.3)
purrr 0.3.3 2019-10-18 [3] CRAN (R 3.6.1)
R6 2.5.0 2020-10-28 [1] CRAN (R 3.6.3)
Rcpp 1.0.3 2019-11-08 [3] CRAN (R 3.6.3)
readxl 1.3.1 2019-03-13 [3] CRAN (R 3.6.3)
reprex 1.0.0 2021-01-27 [1] CRAN (R 3.6.3)
rio 0.5.16 2018-11-26 [1] CRAN (R 3.6.3)
rlang 0.4.10 2020-12-30 [1] CRAN (R 3.6.3)
rmarkdown 2.1 2020-01-20 [3] CRAN (R 3.6.2)
rstatix 0.7.0 2021-02-13 [1] CRAN (R 3.6.3)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 3.6.3)
scales 1.1.1 2020-05-11 [1] CRAN (R 3.6.3)
sessioninfo 1.1.1 2018-11-05 [3] CRAN (R 3.5.1)
stringi 1.4.6 2020-02-17 [3] CRAN (R 3.6.3)
survival 3.2-7 2020-09-28 [4] CRAN (R 3.6.3)
survminer * 0.4.8 2020-07-25 [1] CRAN (R 3.6.3)
survMisc 0.5.5 2018-07-05 [1] CRAN (R 3.6.3)
thematic * 0.1.1.9000 2021-02-16 [1] Github (rstudio/thematic@03b8c7b)
tibble 3.0.6 2021-01-29 [1] CRAN (R 3.6.3)
tidyr 1.0.2 2020-01-24 [3] CRAN (R 3.6.3)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 3.6.3)
vctrs 0.3.6 2020-12-17 [1] CRAN (R 3.6.3)
withr 2.4.1 2021-01-26 [1] CRAN (R 3.6.3)
xfun 0.12 2020-01-13 [3] CRAN (R 3.6.2)
xtable 1.8-4 2019-04-21 [3] CRAN (R 3.6.1)
yaml 2.2.1 2020-02-01 [3] CRAN (R 3.6.2)
zip 2.1.1 2020-08-27 [1] CRAN (R 3.6.3)
zoo 1.8-8 2020-05-02 [1] CRAN (R 3.6.3) My hunch was that this is related to the way that survMisc::autoplot works, but even after removing it, I still see this, which is super weird:
> .getNamespaceInfo(asNamespace("ggplot2"), "S3methods")[1:5, 3]
[1] "$.ggproto" "$.ggproto_parent" "$<-.uneval"
[4] "+.gg" "[.mapped_discrete"
> library(survMisc)
Loading required package: survival
Registered S3 method overwritten by 'survMisc':
method from
plot.Surv survival
survMisc0.5.1
> .getNamespaceInfo(asNamespace("ggplot2"), "S3methods")[1:5, 3]
[[1]]
[1] "$.ggproto"
[[2]]
[1] "$.ggproto_parent"
[[3]]
[1] "$<-.uneval"
[[4]]
[1] "+.gg"
[[5]]
[1] "[.mapped_discrete"But check it out. Also the survminer package, not survMisc, shows the same problem:
library(thematic)
#> This version of thematic is designed to work with rmarkdown version 2.6.6 or higher. Consider upgrading via remotes::install_github('rstudio/rmarkdown')
thematic::thematic_on()
thematic::thematic_off()
library(survminer)
#> Loading required package: ggplot2
#> Loading required package: ggpubr
thematic::thematic_on()
#> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()): invalid first argumentThis is how i rewrote ggplot_build_set to debug it, but i have no idea if its meaningful (probably not):
ggplot_build_set <- function() {
browser()
if (!is_installed("ggplot2")) return(NULL)
ggplot_build_restore()
# Note that assignInNamespace() does S3 method registration, but to
# find the relevant generic, it looks in the parent.frame()...
# so this line here is prevent that from failing if ggplot2 hasn't been attached
# https://github.com/wch/r-source/blob/d0ede8/src/library/utils/R/objects.R#L472
ggplot_build <- getFromNamespace("ggplot_build", "ggplot2")
.globals$ggplot_build <- getFromNamespace("ggplot_build.ggplot", "ggplot2")
assign_in_namespace<-function (x, value, ns, pos = -1, envir = as.environment(pos))
{
browser()
nf <- sys.nframe()
if (missing(ns)) {
nm <- attr(envir, "name", exact = TRUE)
if (is.null(nm) || substr(nm, 1L, 8L) != "package:")
stop("environment specified is not a package")
ns <- asNamespace(substring(nm, 9L))
}
else ns <- asNamespace(ns)
ns_name <- getNamespaceName(ns)
if (nf > 1L) {
if (ns_name %in% tools:::.get_standard_package_names()$base)
stop("locked binding of ", sQuote(x), " cannot be changed",
domain = NA)
}
if (bindingIsLocked(x, ns)) {
in_load <- Sys.getenv("_R_NS_LOAD_")
if (nzchar(in_load)) {
if (in_load != ns_name) {
msg <- gettextf("changing locked binding for %s in %s whilst loading %s",
sQuote(x), sQuote(ns_name), sQuote(in_load))
if (!in_load %in% c("Matrix", "SparseM"))
warning(msg, call. = FALSE, domain = NA, immediate. = TRUE)
}
}
else if (nzchar(Sys.getenv("_R_WARN_ON_LOCKED_BINDINGS_"))) {
warning(gettextf("changing locked binding for %s in %s",
sQuote(x), sQuote(ns_name)), call. = FALSE, domain = NA,
immediate. = TRUE)
}
unlockBinding(x, ns)
assign(x, value, envir = ns, inherits = FALSE)
w <- options("warn")
on.exit(options(w))
options(warn = -1)
lockBinding(x, ns)
}
else {
assign(x, value, envir = ns, inherits = FALSE)
}
if (!isBaseNamespace(ns)) {
S3 <- .getNamespaceInfo(ns, "S3methods")
if (!length(S3))
return(invisible(NULL))
S3names <- S3[, 3L]
if (x %in% S3names) {
i <- match(x, S3names)
browser()
#This is where the error happens
genfun <- get(S3[i, 1L], mode = "function", envir = parent.frame())
# If you change the S3 access to: S3[i, 1L][[1]], then the get succeeds.
if (.isMethodsDispatchOn() && methods::is(genfun,
"genericFunction"))
genfun <- methods::slot(genfun, "default")@methods$ANY
defenv <- if (typeof(genfun) == "closure")
environment(genfun)
else .BaseNamespaceEnv
S3Table <- get(".__S3MethodsTable__.", envir = defenv)
remappedName <- paste(S3[i, 1L], S3[i, 2L], sep = ".")
if (exists(remappedName, envir = S3Table, inherits = FALSE))
assign(remappedName, value, S3Table)
}
}
invisible(NULL)
}
assign_in_namespace("ggplot_build.ggplot", ggthematic_build, "ggplot2")
}Looks like the problem derives from the zoo package (a dependency of these packages):
> library(zoo); thematic::thematic_on()
Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) :
invalid first argumentTurns out that library(zoo) causes this problem since it's calling registerS3method() in an .onLoad() hook, which unfortunately causes assignInNamespace() to no longer work (this seems like a bug in R itself). A minimal example:
library(ggplot2)
# works
ggplotBuild <- getFromNamespace("ggplot_build.ggplot", "ggplot2")
assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2")
qplot(1:10)
# doesn't work
library(zoo)
assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2")
#> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) :
#> invalid first argumentAnd this happens because the S3 lookup matrix turns into a list when registerS3method() happens:
is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods"))
#> TRUE
library(zoo)
is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods"))
#> FALSEI may submit a bug to R core for this, but in the meantime, I think I can have thematic workaround this
elfatherbrown
commented
3 years ago Tested s3methods-matrix branch. My problem has gone away. Thanks!
ghost
commented
3 years ago Turns out that
library(zoo)causes this problem since it's callingregisterS3method()in an.onLoad()hook, which unfortunately causesassignInNamespace()to no longer work (this seems like a bug in R itself). A minimal example:library(ggplot2) # works ggplotBuild <- getFromNamespace("ggplot_build.ggplot", "ggplot2") assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2") qplot(1:10) # doesn't work library(zoo) assignInNamespace("ggplot_build.ggplot", function(x) { warning("owned"); ggplotBuild(x) }, "ggplot2") #> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) : #> invalid first argumentAnd this happens because the S3 lookup matrix turns into a list when
registerS3method()happens:is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods")) #> TRUE library(zoo) is.matrix(.getNamespaceInfo(asNamespace("ggplot2"), "S3methods")) #> FALSEI may submit a bug to R core for this, but in the meantime, I think I can have thematic workaround this
Hi. I still face the same problem
#> Error in get(S3[i, 1L], mode = "function", envir = parent.frame()) :
#> invalid first argumentHere is my sessionInfo
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=Greek_Greece.1253
[2] LC_CTYPE=Greek_Greece.1253
[3] LC_MONETARY=Greek_Greece.1253
[4] LC_NUMERIC=C
[5] LC_TIME=Greek_Greece.1253
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
other attached packages:
[1] zoo_1.8-8 ggplot2_3.3.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 bslib_0.2.4 compiler_4.0.4
[4] pillar_1.5.1 jquerylib_0.1.3 tools_4.0.4
[7] odbc_1.3.0 digest_0.6.27 bit_4.0.4
[10] lattice_0.20-41 gtable_0.3.0 evaluate_0.14
[13] jsonlite_1.7.2 lifecycle_1.0.0 tibble_3.1.0
[16] debugme_1.1.0 pkgconfig_2.0.3 rlang_0.4.10
[19] DBI_1.1.1 rstudioapi_0.13 yaml_2.2.1
[22] xfun_0.21 withr_2.4.1 dplyr_1.0.5
[25] knitr_1.31 htmlwidgets_1.5.3 generics_0.1.0
[28] vctrs_0.3.6 sass_0.3.1 hms_1.0.0
[31] thematic_0.1.1 bit64_4.0.5 grid_4.0.4
[34] tidyselect_1.1.0 glue_1.4.2 R6_2.5.0
[37] fansi_0.4.2 rmarkdown_2.7 librarian_1.7.0
[40] farver_2.1.0 purrr_0.3.4 blob_1.2.1
[43] magrittr_2.0.1 scales_1.1.1 ellipsis_0.3.1
[46] htmltools_0.5.1.1 rsconnect_0.8.16 assertthat_0.2.1
[49] colorspace_2.0-0 labeling_0.4.2 utf8_1.1.4
[52] munsell_0.5.0 crayon_1.4.1 You need the development version remotes::install_github('rstudio/thematic')
michaelgaunt404
commented
3 years ago Hi, I'm still receiving this error as well. This is my yaml and first code chunk:
---
title: "ETAN Database Exploration Tool"
output:
html_document:
theme:
bg: "#002b36"
fg: "#eee8d5"
primary: "#2aa198"
font: "auto"
# runtime: shiny
---
'''{r setup, include=FALSE}
knitr::opts_chunk$set(
cache = FALSE, cache.lazy = FALSE, autodep = TRUE, warning = FALSE,
message = FALSE, echo = TRUE, dpi = 180,
fig.width = 8, fig.height = 5, echo = FALSE
)
thematic::thematic_rmd(font = "auto")
'''I'm receiving the following error both in isolated code chunks that generate ggplot visuals and during markdown knit.
> > sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.6.0 gridExtra_2.3 scales_1.1.1 ggraph_2.0.5
[5] tidygraph_1.2.0 networkD3_0.4 thematic_0.1.2.1 ggridges_0.5.3
[9] here_1.0.1 data.validator_0.1.5 skimr_2.1.2 DT_0.17
[13] lubridate_1.7.9.2 data.table_1.13.2 janitor_2.1.0 readxl_1.3.1
[17] magrittr_2.0.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.4
[21] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.0
[25] ggplot2_3.3.3 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-0 ellipsis_0.3.1 rsconnect_0.8.16 rprojroot_2.0.2
[5] snakecase_0.11.0 base64enc_0.1-3 fs_1.5.0 rstudioapi_0.13
[9] farver_2.0.3 rstan_2.21.2 graphlayouts_0.7.1 ggrepel_0.9.1
[13] fansi_0.4.2 xml2_1.3.2 codetools_0.2-16 knitr_1.31
[17] polyclip_1.10-0 jsonlite_1.7.2 packrat_0.5.0 broom_0.7.5
[21] gganimate_1.0.7 dbplyr_2.1.0 ggforce_0.3.2 compiler_3.6.2
[25] httr_1.4.2 backports_1.2.1 assertthat_0.2.1 fastmap_1.0.1
[29] cli_2.3.1 later_1.1.0.1 tweenr_1.0.1 htmltools_0.5.1.1
[33] prettyunits_1.1.1 tools_3.6.2 igraph_1.2.6 gtable_0.3.0
[37] glue_1.4.2 V8_3.4.0 Rcpp_1.0.6 jquerylib_0.1.3
[41] cellranger_1.1.0 vctrs_0.3.6 crosstalk_1.1.1 xfun_0.19
[45] ps_1.3.2 rvest_0.3.6 mime_0.9 lifecycle_1.0.0
[49] MASS_7.3-51.4 hms_1.0.0 promises_1.1.1 parallel_3.6.2
[53] inline_0.3.17 yaml_2.2.1 curl_4.3 sass_0.3.1
[57] loo_2.4.1 StanHeaders_2.21.0-6 stringi_1.5.3 gifski_0.8.6
[61] pkgbuild_1.2.0 repr_1.1.3 matrixStats_0.57.0 rlang_0.4.10
[65] pkgconfig_2.0.3 evaluate_0.14 lattice_0.20-38 htmlwidgets_1.5.3
[69] labeling_0.4.2 tidyselect_1.1.0 processx_3.4.4 plyr_1.8.6
[73] R6_2.5.0 generics_0.1.0 DBI_1.1.1 pillar_1.6.0
[77] haven_2.3.1 withr_2.4.1 modelr_0.1.8 crayon_1.4.1
[81] utf8_1.1.4 rmarkdown_2.7 viridis_0.5.1 progress_1.2.2
[85] grid_3.6.2 callr_3.5.1 reprex_1.0.0 digest_0.6.27
[89] xtable_1.8-4 httpuv_1.5.4 RcppParallel_5.0.2 stats4_3.6.2
[93] munsell_0.5.0 viridisLite_0.3.0 bslib_0.2.4 @michaelgaunt404 your theme definition is off. You probably want base_font (not font) set to a Google Font? https://rstudio.github.io/bslib/articles/bslib.html#custom-themes
cpsievert
commented
3 years ago If that doesn't fix your issues, you might need to update to a more recent version of R
The problem
I have a shiny app built as a package with golem that uses many plotting libraries including ggplot2 and as soon as I tried thematic_on or thematic_shiny I got:
"Error in get(S3[i, 1L], mode = "function", envir = parent.frame()): invalid first argument".
I digged in and discovered that the same problem that happens with my package, happens with others that include ggplot2:
Created on 2021-02-16 by the reprex package (v1.0.0)
Further digging on thematic's code
On another box I set out to debug thematic. I cloned it and this is what I did.
On this function I put a browser:
Discovered that the aforementioned "get" problem with S3 comes from assign_in_namespace("ggplot_build.ggplot", ggthematic_build, "ggplot2"). So I copied the assign_in_namespace (from assignInNamespace, as it does in the code), but set a browser on that.
What I discovered is that inside the assignInNamespace code, down by the line:
S3[i,1L] returns a list that contains the name of the function, but get wants a string. So, as you can see:
This goes away if one rewrites with:
Or at least the error does. Im not keen on hacking away at this because im pretty much a newb (i've no idea how S3 or namespaces actually work), but I think this is either a freakish mismanagement of my base packages (e.g. i carry a bug in utils::assignInNamespace), or a particular use of it that got mangled somewhere.
I LOVE the thematic idea. I want to use it! Let me know if I can help out.