Import of pipe operator works if importing "magrittr", but not if using "tidyverse"
mpettis opened this issue · comments
In my usual scripts, I do a library(tidyverse) call, and I get things like the magrittr pipe (%>%). But when using modules, if I import("tidyverse"), the pipe operator is not found. However, it does work if i do import("magrittr"). Reprex below.
library(modules)
#> Warning: package 'modules' was built under R version 3.6.3
## Can find the pipe operator if I call magrittr directly
m <- module({
import("magrittr")
foo <- function() { 1:3 %>% mean() }
})
m$foo()
#> [1] 2
## Cannot find pipe operator if imported via tidyverse package
q <- module({
import("tidyverse")
foo <- function() { 1:3 %>% mean() }
})
q$foo()
#> Error in 1:3 %>% mean(): could not find function "%>%"
## Session info
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 3.6.1 (2019-07-05)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/Chicago
#> date 2020-08-06
#>
#> - Packages -------------------------------------------------------------------
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
#> backports 1.1.7 2020-05-13 [1] CRAN (R 3.6.3)
#> broom 0.5.6 2020-04-20 [1] CRAN (R 3.6.3)
#> cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.6.1)
#> cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.3)
#> colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
#> DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.3)
#> dbplyr 1.4.3 2020-04-19 [1] CRAN (R 3.6.3)
#> digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.3)
#> dplyr 1.0.0 2020-05-29 [1] CRAN (R 3.6.3)
#> ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.1)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.3)
#> forcats 0.5.0 2020-03-01 [1] CRAN (R 3.6.3)
#> fs 1.4.1 2020-04-04 [1] CRAN (R 3.6.3)
#> generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.1)
#> ggplot2 3.3.0 2020-03-05 [1] CRAN (R 3.6.3)
#> glue 1.4.1 2020-05-13 [1] CRAN (R 3.6.3)
#> gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
#> haven 2.2.0 2019-11-08 [1] CRAN (R 3.6.1)
#> highr 0.8 2019-03-20 [1] CRAN (R 3.6.1)
#> hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.3)
#> htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.1)
#> httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.1)
#> jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.3)
#> knitr 1.28 2020-02-06 [1] CRAN (R 3.6.3)
#> lattice 0.20-41 2020-04-02 [1] CRAN (R 3.6.3)
#> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.3)
#> lubridate 1.7.8 2020-04-06 [1] CRAN (R 3.6.3)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
#> modelr 0.1.7 2020-04-30 [1] CRAN (R 3.6.3)
#> modules * 0.8.0 2019-02-10 [1] CRAN (R 3.6.3)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.1)
#> nlme 3.1-147 2020-04-13 [1] CRAN (R 3.6.3)
#> pillar 1.4.4 2020-05-05 [1] CRAN (R 3.6.3)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 3.6.3)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
#> Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.3)
#> readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
#> readxl 1.3.1 2019-03-13 [1] CRAN (R 3.6.1)
#> reprex 0.3.0 2019-05-16 [1] CRAN (R 3.6.1)
#> rlang 0.4.6 2020-05-02 [1] CRAN (R 3.6.3)
#> rmarkdown 2.1 2020-01-20 [1] CRAN (R 3.6.3)
#> rvest 0.3.5 2019-11-08 [1] CRAN (R 3.6.1)
#> scales 1.1.1 2020-05-11 [1] CRAN (R 3.6.3)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
#> stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.2)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
#> tibble 3.0.1 2020-04-20 [1] CRAN (R 3.6.3)
#> tidyr 1.0.3 2020-05-07 [1] CRAN (R 3.6.3)
#> tidyselect 1.1.0 2020-05-11 [1] CRAN (R 3.6.3)
#> tidyverse 1.3.0 2019-11-21 [1] CRAN (R 3.6.3)
#> vctrs 0.3.0 2020-05-11 [1] CRAN (R 3.6.3)
#> withr 2.2.0 2020-04-20 [1] CRAN (R 3.6.3)
#> xfun 0.13 2020-04-13 [1] CRAN (R 3.6.3)
#> xml2 1.3.2 2020-04-23 [1] CRAN (R 3.6.3)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.3)
#>
#> [1] C:/Users/IRINZN/Documents/R/R-3.6.1/libraryCreated on 2020-08-06 by the reprex package (v0.3.0)
Thanks for taking the time to report this issue.
The modules package will import all names/objects that are exported by a package. So using dplyr in your example will work, because dplyr correctly re-exports the pipe operator. You can see how that works here: https://github.com/tidyverse/dplyr/blob/f08991955f7bb76ad7f7f2364dbe90699a123d68/R/utils.r#L3
The package tidyverse does not re-export any objects; as far as I can tell. It also circumvents Rs build-in mechanism for attaching dependencies - the Depends field in the Description of the package; see: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies - that may have presented a way for a fix for your use-case. Instead, in the tidyverse package a custom function is being called (https://github.com/tidyverse/tidyverse/blob/8a0bb998e92fb61339d555f22d8bf7314c625700/R/attach.R#L18) when you attach the tidyverse package (https://github.com/tidyverse/tidyverse/blob/8a0bb998e92fb61339d555f22d8bf7314c625700/R/zzz.R#L1). Attaching is nothing else then calling library. There you find the lines where library is called and attaches all other tidyverse packages as a side-effect.
I do not see any sane way to figure out which objects need to be imported from the outside. At the same time I would like to encourage you to be more explicit when importing objects into a module. It was one of the design goals of the modules package to be able to import single objects from a package. Nonetheless, here is how I would hack my way around it, when I really do not want to spell it out:
imports <- modules::module({
tidyverse <- function(where = parent.frame()) {
## Import all packages that are usually attached by the tidyverse package.
## where (environment) the environment where you want attach the pkgs.
## Usually the calling environment of this function.
for (pkg in tidyverse:::core) {
suppressPackageStartupMessages(
eval(substitute(modules::import(pkg)), envir = where)
)
}
}
})
q <- modules::module({
use(imports)$tidyverse()
foo <- function() { 1:3 %>% mean() }
})
q$foo()You may want to put the imports module into a separate file, so you do not have to care about it anymore; in that case just refer to the filename in use.
Hope this is somehow helpful.
Thank you, this was helpful! I was ok explicitly importing magrittr, but I just wanted to report this in case this wasn't intended behavior for, say, tidyverse. I'm good now, and your comment above was helpful beyond the original question. Thank you.