minimise dependencies

[ValentineHerr]

@cpiponiot (and @VincyaneBadouard )

The installation of the package is too daunting because of all the dependencies and how high the required version are. I'd like to simplify that by :

• removing unnecessary dependencies
• lowering required version

First step here is to identify the packages that are used in the package, the function they need and the frequency those functions are used (this is excluding c("base", "utils", "TreeData", "stats", "shiny", "shinydashboard", "tools", "shinyjs", "shinyWidgets")):

pkgs	funs	Freq
XML	xmlAttrs	3
XML	xmlChildren	3
XML	xmlGetAttr	2
XML	xmlName	3
XML	xmlParse	3
XML	xmlValue	3
xml	read_html	1
WorldFlora	WFO.match	1
usethis	use_data	11
units	install_unit	2
units	remove_unit	2
testthat	expect_equal	3
testthat	expect_error	14
testthat	expect_false	2
testthat	expect_message	1
testthat	expect_true	14
testthat	expect_warning	4
testthat	test_check	1
testthat	test_that	18
Taxonstand	TPL	1
stringr	str_count	1
stringr	str_replace_all	1
stringr	str_wrap	1
stringdist	stringdistmatrix	1
shinytest	testApp	1
shinycssloaders	withSpinner	1
rvest	html_nodes	1
rlist	list.flatten	3
rlang	is_complex	3
rlang	link	1
pkgbuild	style	3
methods	new	6
lubridate	date_decimal	1
lubridate	decimal_date	2
htmltools	withTags	1
htmlTable	.	5
grDevices	dev.new	2
graphics	box	4
glue	glue	2
ggrepel	geom_text_repel	1
ggplot2	aes	2
ggplot2	geom_line	2
ggplot2	geom_point	2
ggplot2	ggplot	2
ggplot2	labs	2
ggplot2	scale_colour_manual	2
ggplot2	theme_minimal	2
ggforce	facet_wrap_paginate	2
ggforce	firstUpper	1
DT	datatable	2
DT	DTOutput	3
DT	JS	1
DT	renderDT	2
DT	tableFooter	1
DT	tableHeader	1
dplyr	select	1
dplyr	vars	2
data.tree	Do	1
data.tree	FindNode	1
data.tree	ToDataFrameTable	1
data.tree	ToDataFrameTypeCol	1
data.table	copy	11
data.table	data.table	11
data.table	dcast	2
data.table	melt	1
data.table	rbindlist	5
data.table	setDF	4
data.table	setDT	10
data.table	setnames	10
data.table	tstrsplit	2
data	fread	4
data	FromDataFrameNetwork	3
BIOMASS	getTaxonomy	1
(unknown)	:=	18
(unknown)	AddChild	1
(unknown)	AddChildNode	2
(unknown)	compareNA	3
(unknown)	FotterWithHeader	1
(unknown)	get_annotation	2
(unknown)	Guyafor2df	1
(unknown)	textarea	1
(unknown)	uploadFile	4

[ValentineHerr]

one of the most annoying package dependency is grDevices which seems to only be used for dev.new. @VincyaneBadouard, do you remember why you specifically added geDevices in the imports? This is a package that gets loaded with R.

[ValentineHerr]

This is what I get when I install this package (I always skip all but should update all at some point):

These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                         
 2: CRAN packages only                          
 3: None                                        
 4: digest       (0.6.27    -> 0.6.30   ) [CRAN]
 5: rappdirs     (0.3.1     -> 0.3.3    ) [CRAN]
 6: R6           (2.5.0     -> 2.5.1    ) [CRAN]
 7: htmltools    (0.5.2     -> 0.5.3    ) [CRAN]
 8: rlang        (1.0.2     -> 1.0.6    ) [CRAN]
 9: fs           (1.5.0     -> 1.5.2    ) [CRAN]
10: BH           (1.75.0-0  -> 1.78.0-0 ) [CRAN]
11: Rcpp         (1.0.7     -> 1.0.9    ) [CRAN]
12: magrittr     (2.0.1     -> 2.0.3    ) [CRAN]
13: cli          (3.2.0     -> 3.4.1    ) [CRAN]
14: memoise      (1.1.0     -> 2.0.1    ) [CRAN]
15: jquerylib    (0.1.3     -> 0.1.4    ) [CRAN]
16: sass         (0.4.0     -> 0.4.4    ) [CRAN]
17: lifecycle    (1.0.1     -> 1.0.3    ) [CRAN]
18: cachem       (1.0.1     -> 1.0.6    ) [CRAN]
19: bslib        (0.3.1     -> 0.4.1    ) [CRAN]
20: commonmark   (1.7       -> 1.8.1    ) [CRAN]
21: withr        (2.3.0     -> 2.5.0    ) [CRAN]
22: crayon       (1.3.4     -> 1.5.2    ) [CRAN]
23: promises     (1.1.1     -> 1.2.0.1  ) [CRAN]
24: later        (1.1.0.1   -> 1.3.0    ) [CRAN]
25: fontawesome  (0.2.2     -> 0.4.0    ) [CRAN]
26: jsonlite     (1.7.1     -> 1.8.3    ) [CRAN]
27: mime         (0.9       -> 0.12     ) [CRAN]
28: httpuv       (1.5.5     -> 1.6.6    ) [CRAN]
29: terra        (1.5-21    -> 1.6-41   ) [CRAN]
30: sp           (1.4-5     -> 1.5-1    ) [CRAN]
31: cpp11        (0.3.1     -> 0.4.3    ) [CRAN]
32: vctrs        (0.3.8     -> 0.5.1    ) [CRAN]
33: farver       (2.0.3     -> 2.1.1    ) [CRAN]
34: utf8         (1.1.4     -> 1.2.2    ) [CRAN]
35: colorspace   (2.0-0     -> 2.0-3    ) [CRAN]
36: pillar       (1.7.0     -> 1.8.1    ) [CRAN]
37: fansi        (0.4.1     -> 1.0.3    ) [CRAN]
38: viridisLite  (0.4.0     -> 0.4.1    ) [CRAN]
39: RColorBrewer (1.1-2     -> 1.1-3    ) [CRAN]
40: tibble       (3.1.6     -> 3.1.8    ) [CRAN]
41: scales       (1.1.1     -> 1.2.1    ) [CRAN]
42: isoband      (0.2.3     -> 0.2.6    ) [CRAN]
43: gtable       (0.3.0     -> 0.3.1    ) [CRAN]
44: yaml         (2.2.1     -> 2.3.6    ) [CRAN]
45: backports    (1.2.1     -> 1.4.1    ) [CRAN]
46: systemfonts  (1.0.1     -> 1.0.4    ) [CRAN]
47: ps           (1.4.0     -> 1.7.2    ) [CRAN]
48: processx     (3.4.5     -> 3.8.0    ) [CRAN]
49: callr        (3.5.1     -> 3.7.3    ) [CRAN]
50: stringi      (1.5.3     -> 1.7.8    ) [CRAN]
51: highr        (0.8       -> 0.9      ) [CRAN]
52: xfun         (0.30      -> 0.35     ) [CRAN]
53: tinytex      (0.38      -> 0.42     ) [CRAN]
54: stringr      (1.4.0     -> 1.4.1    ) [CRAN]
55: knitr        (1.38      -> 1.41     ) [CRAN]
56: evaluate     (0.15      -> 0.18     ) [CRAN]
57: sys          (3.4       -> 3.4.1    ) [CRAN]
58: openssl      (1.4.3     -> 2.0.4    ) [CRAN]
59: curl         (4.3       -> 4.3.3    ) [CRAN]
60: xml2         (1.3.2     -> 1.3.3    ) [CRAN]
61: httr         (1.4.2     -> 1.4.4    ) [CRAN]
62: shiny        (1.7.1     -> 1.7.3    ) [CRAN]
63: crosstalk    (1.1.1     -> 1.2.0    ) [CRAN]
64: htmlwidgets  (1.5.3     -> 1.5.4    ) [CRAN]
65: data.table   (1.14.2    -> 1.14.6   ) [CRAN]
66: proj4        (1.0-10.1  -> 1.0-12   ) [CRAN]
67: raster       (3.4-5     -> 3.6-11   ) [CRAN]
68: minpack.lm   (1.2-1     -> 1.2-2    ) [CRAN]
69: pbapply      (1.5-0     -> 1.6-0    ) [CRAN]
70: ggplot2      (3.3.5     -> 3.4.0    ) [CRAN]
71: RcppEigen    (0.3.3.9.1 -> 0.3.3.9.3) [CRAN]
72: tidyselect   (1.1.2     -> 1.2.0    ) [CRAN]
73: polyclip     (1.10-0    -> 1.10-4   ) [CRAN]
74: tweenr       (1.0.2     -> 2.0.2    ) [CRAN]
75: rstudioapi   (0.13      -> 0.14     ) [CRAN]
76: checkmate    (2.0.0     -> 2.1.0    ) [CRAN]
77: svglite      (2.0.0     -> 2.1.0    ) [CRAN]
78: webshot      (0.5.2     -> 0.5.4    ) [CRAN]
79: rmarkdown    (2.14      -> 2.18     ) [CRAN]
80: rvest        (0.3.6     -> 1.0.3    ) [CRAN]
81: shinyWidgets (0.7.0     -> 0.7.5    ) [CRAN]
82: shinyjs      (2.0.0     -> 2.1.0    ) [CRAN]
83: DT           (0.23      -> 0.26     ) [CRAN]
84: WorldFlora   (1.10      -> 1.11     ) [CRAN]
85: stringdist   (0.9.8     -> 0.9.10   ) [CRAN]
86: ggrepel      (0.9.1     -> 0.9.2    ) [CRAN]
87: ggforce      (0.3.4     -> 0.4.1    ) [CRAN]
88: htmlTable    (2.2.1     -> 2.4.1    ) [CRAN]

[VincyaneBadouard]

Hi! ah sorry dev.new() allows to open the correction plots in different windows to allow the user to have time to look at them. If I didn't do this, the plots would follow each other in the same window and therefore disappear as soon as another one replaced it. Maybe there is another way to do this. The only other method I knew of was to produce a pdf without viewing in Rstudio