-
Notifications
You must be signed in to change notification settings - Fork 6
/
Dockerfile
194 lines (188 loc) · 12 KB
/
Dockerfile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
# Generated by packamon: do not edit by hand
# Instead of modifying this file, you can modify a template. See ?init for details.
FROM registry.openanalytics.eu/openanalytics/r-ver:4.4.0
# System libraries (incl. system requirements for R packages)
RUN apt-get update && apt-get install --no-install-recommends -y \
libcairo2-dev \
libcurl4-openssl-dev \
libfontconfig1-dev \
libfreetype6-dev \
libfribidi-dev \
libharfbuzz-dev \
libicu-dev \
libjpeg-dev \
libnode-dev \
libpng-dev \
libssl-dev \
libtiff-dev \
libv8-dev \
libxml2-dev \
make \
pandoc \
texlive \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
RUN apt-get update && apt-get install --no-install-recommends -y \
texinfo \
texlive-latex-base \
texlive-latex-recommended \
texlive-latex-extra \
# for creation manual (R CMD check)
texlive-fonts-recommended \
texlive-fonts-extra \
# to check size reduction of PDFs
qpdf \
&& rm -rf /var/lib/apt/lists/*
RUN echo \
'options(repos = c(CRAN = gsub("/([0-9-]*)$", "/latest", Sys.getenv("CRAN", "https://cloud.r-project.org")), CRAN.source = "https://cloud.r-project.org"))' \
>> $(R RHOME)/etc/Rprofile.site
# install dependencies
RUN R -q -e "options(warn = 2); \
install.packages('remotes'); \
remotes::install_version('base64enc', version = '0.1-3', upgrade = FALSE); \
remotes::install_version('bit', version = '4.0.5', upgrade = FALSE); \
remotes::install_version('brew', version = '1.0-10', upgrade = FALSE); \
remotes::install_version('brio', version = '1.1.5', upgrade = FALSE); \
remotes::install_version('cli', version = '3.6.2', upgrade = FALSE); \
remotes::install_version('clipr', version = '0.8.0', upgrade = FALSE); \
remotes::install_version('colorspace', version = '2.1-0', upgrade = FALSE); \
remotes::install_version('commonmark', version = '1.9.1', upgrade = FALSE); \
remotes::install_version('countrycode', version = '1.6.0', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('cpp11', version = '0.4.7', upgrade = FALSE); \
remotes::install_version('crayon', version = '1.5.2', upgrade = FALSE); \
remotes::install_version('curl', version = '5.2.1', upgrade = FALSE); \
remotes::install_version('data.table', version = '1.15.4', upgrade = FALSE); \
remotes::install_version('digest', version = '0.6.35', upgrade = FALSE); \
remotes::install_version('evaluate', version = '0.24.0', upgrade = FALSE); \
remotes::install_version('fansi', version = '1.0.6', upgrade = FALSE); \
remotes::install_version('farver', version = '2.1.2', upgrade = FALSE); \
remotes::install_version('fastmap', version = '1.2.0', upgrade = FALSE); \
remotes::install_version('fontBitstreamVera', version = '0.1.1', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('fontLiberation', version = '0.1.0', upgrade = FALSE); \
remotes::install_version('fs', version = '1.6.4', upgrade = FALSE); \
remotes::install_version('generics', version = '0.1.3', upgrade = FALSE); \
remotes::install_version('glue', version = '1.7.0', upgrade = FALSE); \
remotes::install_version('httpcode', version = '0.3.0', upgrade = FALSE); \
remotes::install_version('isoband', version = '0.2.7', upgrade = FALSE); \
remotes::install_version('jsonlite', version = '1.8.8', upgrade = FALSE); \
remotes::install_version('labeling', version = '0.4.3', upgrade = FALSE); \
remotes::install_version('lattice', version = '0.22-6', upgrade = FALSE); \
remotes::install_version('lazyeval', version = '0.2.2', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('magrittr', version = '2.0.3', upgrade = FALSE); \
remotes::install_version('MASS', version = '7.3-60.0.1', upgrade = FALSE); \
remotes::install_version('mime', version = '0.12', upgrade = FALSE); \
remotes::install_version('pkgconfig', version = '2.0.3', upgrade = FALSE); \
remotes::install_version('praise', version = '1.0.0', upgrade = FALSE); \
remotes::install_version('prettyunits', version = '1.2.0', upgrade = FALSE); \
remotes::install_version('ps', version = '1.7.6', upgrade = FALSE); \
remotes::install_version('R6', version = '2.5.1', upgrade = FALSE); \
remotes::install_version('rappdirs', version = '0.3.3', upgrade = FALSE); \
remotes::install_version('RColorBrewer', version = '1.1-3', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('Rcpp', version = '1.0.12', upgrade = FALSE); \
remotes::install_version('rlang', version = '1.1.4', upgrade = FALSE); \
remotes::install_version('rprojroot', version = '2.0.4', upgrade = FALSE); \
remotes::install_version('sourcetools', version = '0.1.7-1', upgrade = FALSE); \
remotes::install_version('stringi', version = '1.8.4', upgrade = FALSE); \
remotes::install_version('sys', version = '3.4.2', upgrade = FALSE); \
remotes::install_version('utf8', version = '1.2.4', upgrade = FALSE); \
remotes::install_version('uuid', version = '1.2-0', upgrade = FALSE); \
remotes::install_version('viridisLite', version = '0.4.2', upgrade = FALSE); \
remotes::install_version('withr', version = '3.0.0', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('xfun', version = '0.45', upgrade = FALSE); \
remotes::install_version('xtable', version = '1.8-4', upgrade = FALSE); \
remotes::install_version('yaml', version = '2.3.8', upgrade = FALSE); \
remotes::install_version('zip', version = '2.3.1', upgrade = FALSE); \
remotes::install_version('askpass', version = '1.2.0', upgrade = FALSE); \
remotes::install_version('bit64', version = '4.0.5', upgrade = FALSE); \
remotes::install_version('cachem', version = '1.1.0', upgrade = FALSE); \
remotes::install_version('desc', version = '1.4.3', upgrade = FALSE); \
remotes::install_version('diffobj', version = '0.3.5', upgrade = FALSE); \
remotes::install_version('fontquiver', version = '0.2.1', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('highr', version = '0.11', upgrade = FALSE); \
remotes::install_version('htmltools', version = '0.5.8.1', upgrade = FALSE); \
remotes::install_version('later', version = '1.3.2', upgrade = FALSE); \
remotes::install_version('lifecycle', version = '1.0.4', upgrade = FALSE); \
remotes::install_version('Matrix', version = '1.6-5', upgrade = FALSE); \
remotes::install_version('munsell', version = '0.5.1', upgrade = FALSE); \
remotes::install_version('nlme', version = '3.1-165', upgrade = FALSE); \
remotes::install_version('plyr', version = '1.8.9', upgrade = FALSE); \
remotes::install_version('processx', version = '3.8.4', upgrade = FALSE); \
remotes::install_version('rex', version = '1.2.1', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('tinytex', version = '0.51', upgrade = FALSE); \
remotes::install_version('triebeard', version = '0.4.1', upgrade = FALSE); \
remotes::install_version('tzdb', version = '0.4.0', upgrade = FALSE); \
remotes::install_version('V8', version = '4.4.2', upgrade = FALSE); \
remotes::install_version('xml2', version = '1.3.6', upgrade = FALSE); \
remotes::install_version('callr', version = '3.7.6', upgrade = FALSE); \
remotes::install_version('crosstalk', version = '1.2.1', upgrade = FALSE); \
remotes::install_version('fontawesome', version = '0.5.2', upgrade = FALSE); \
remotes::install_version('gtable', version = '0.3.5', upgrade = FALSE); \
remotes::install_version('jquerylib', version = '0.1.4', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('jsonvalidate', version = '1.3.2', upgrade = FALSE); \
remotes::install_version('knitr', version = '1.47', upgrade = FALSE); \
remotes::install_version('memoise', version = '2.0.1', upgrade = FALSE); \
remotes::install_version('mgcv', version = '1.9-1', upgrade = FALSE); \
remotes::install_version('openssl', version = '2.2.0', upgrade = FALSE); \
remotes::install_version('promises', version = '1.3.0', upgrade = FALSE); \
remotes::install_version('sass', version = '0.4.9', upgrade = FALSE); \
remotes::install_version('scales', version = '1.3.0', upgrade = FALSE); \
remotes::install_version('systemfonts', version = '1.1.0', upgrade = FALSE); \
remotes::install_version('urltools', version = '1.7.3', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('vctrs', version = '0.6.5', upgrade = FALSE); \
remotes::install_version('bslib', version = '0.7.0', upgrade = FALSE); \
remotes::install_version('crul', version = '1.4.2', upgrade = FALSE); \
remotes::install_version('gridExtra', version = '2.3', upgrade = FALSE); \
remotes::install_version('hms', version = '1.1.3', upgrade = FALSE); \
remotes::install_version('httpuv', version = '1.6.15', upgrade = FALSE); \
remotes::install_version('httr', version = '1.4.7', upgrade = FALSE); \
remotes::install_version('pillar', version = '1.9.0', upgrade = FALSE); \
remotes::install_version('pkgbuild', version = '1.4.4', upgrade = FALSE); \
remotes::install_version('purrr', version = '1.0.2', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('stringr', version = '1.5.1', upgrade = FALSE); \
remotes::install_version('textshaping', version = '0.4.0', upgrade = FALSE); \
remotes::install_version('tidyselect', version = '1.2.1', upgrade = FALSE); \
remotes::install_version('covr', version = '3.6.4', upgrade = FALSE); \
remotes::install_version('pkgload', version = '1.3.4', upgrade = FALSE); \
remotes::install_version('progress', version = '1.2.3', upgrade = FALSE); \
remotes::install_version('ragg', version = '1.3.2', upgrade = FALSE); \
remotes::install_version('reshape2', version = '1.4.4', upgrade = FALSE); \
remotes::install_version('rmarkdown', version = '2.27', upgrade = FALSE); \
remotes::install_version('shiny', version = '1.8.1.1', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('tibble', version = '3.2.1', upgrade = FALSE); \
remotes::install_version('bookdown', version = '0.39', upgrade = FALSE); \
remotes::install_version('dplyr', version = '1.1.4', upgrade = FALSE); \
remotes::install_version('forcats', version = '1.0.0', upgrade = FALSE); \
remotes::install_version('gfonts', version = '0.2.0', upgrade = FALSE); \
remotes::install_version('ggplot2', version = '3.5.1', upgrade = FALSE); \
remotes::install_version('htmlwidgets', version = '1.6.4', upgrade = FALSE); \
remotes::install_version('officer', version = '0.6.6', upgrade = FALSE); \
remotes::install_version('rematch2', version = '2.1.2', upgrade = FALSE); \
remotes::install_version('roxygen2', version = '7.3.1', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('vroom', version = '1.6.5', upgrade = FALSE); \
remotes::install_version('cowplot', version = '1.1.3', upgrade = FALSE); \
remotes::install_version('DT', version = '0.33', upgrade = FALSE); \
remotes::install_version('gdtools', version = '0.3.7', upgrade = FALSE); \
remotes::install_version('ggrepel', version = '0.9.5', upgrade = FALSE); \
remotes::install_version('readr', version = '2.1.5', upgrade = FALSE); \
remotes::install_version('tidyr', version = '1.3.1', upgrade = FALSE); \
remotes::install_version('waldo', version = '0.5.2', upgrade = FALSE); \
remotes::install_version('flextable', version = '0.9.6', upgrade = FALSE); \
remotes::install_version('haven', version = '2.5.4', upgrade = FALSE)"
RUN R -q -e "options(warn = 2); \
remotes::install_version('plotly', version = '4.10.4', upgrade = FALSE); \
remotes::install_version('testthat', version = '3.2.1.1', upgrade = FALSE); \
remotes::install_version('clinUtils', version = '0.2.0', upgrade = FALSE); \
remotes::install_version('inTextSummaryTable', version = '3.3.3', upgrade = FALSE); \
remotes::install_version('patientProfilesVis', version = '2.0.8', upgrade = FALSE)"