From 6bd7dfa4733f3bdeec8ee2045a920c522305e380 Mon Sep 17 00:00:00 2001 From: Laurence James-Woodley Date: Wed, 14 Dec 2022 20:14:28 -0500 Subject: [PATCH 1/5] add latex packages --- latex_packages.csv | 85 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 latex_packages.csv diff --git a/latex_packages.csv b/latex_packages.csv new file mode 100644 index 0000000..1f8a5fb --- /dev/null +++ b/latex_packages.csv @@ -0,0 +1,85 @@ +package +amscls +amsfonts +amsmath +babel +bibtex +booktabs +caption +cm +colortbl +dehyph +dvipdfmx +dvips +ec +environ +etex +etoolbox +euenc +fancyvrb +float +fontspec +framed +geometry +glyphlist +graphics +graphics-cfg +graphics-def +gsftopk +helvetic +hyperref +hyphen-base +ifluatex +iftex +ifxetex +inconsolata +knuth-lib +kpathsea +l3kernel +l3packages +latex +latex-bin +latex-fonts +latexconfig +latexmk +lm +lualibs +luaotfload +luatex +makecell +makeindex +mathspec +metafont +mfware +multirow +natbib +oberdiek +pdftex +plain +scheme-infraonly +tabu +tetex +tex +tex-ini-files +texlive.infra +threeparttable +threeparttablex +times +tipa +titling +tools +trimspaces +ulem +unicode-data +upquote +url +varwidth +wrapfig +xcolor +xetex +xetexconfig +xkeyval +xunicode +zapfding +pdflscape +epstopdf-pkg \ No newline at end of file From fb4a48e27c05e9939ec8faf8583e25b049d81d08 Mon Sep 17 00:00:00 2001 From: Laurence James-Woodley Date: Wed, 14 Dec 2022 20:26:43 -0500 Subject: [PATCH 2/5] add install_latex_packages.R --- install_latex_packages.R | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 install_latex_packages.R diff --git a/install_latex_packages.R b/install_latex_packages.R new file mode 100644 index 0000000..1adf20c --- /dev/null +++ b/install_latex_packages.R @@ -0,0 +1,2 @@ +packages_to_install <- read.csv("https://raw.githubusercontent.com/ljwoodley/redcapcustodian/add_latex_packages/latex_packages.csv") +tinytex::tlmgr_install(packages_to_install$package) From cbac6857882e3a50e365edef1ffc09d39b05dedb Mon Sep 17 00:00:00 2001 From: Laurence James-Woodley Date: Wed, 14 Dec 2022 21:24:10 -0500 Subject: [PATCH 3/5] install latex packages in dockerfile --- Dockerfile | 18 ++++++++- install_latex_packages.R | 2 - latex_packages.csv | 85 ---------------------------------------- 3 files changed, 17 insertions(+), 88 deletions(-) delete mode 100644 install_latex_packages.R delete mode 100644 latex_packages.csv diff --git a/Dockerfile b/Dockerfile index 899e485..915368d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -25,7 +25,23 @@ RUN R -e "install.packages(c( \ ))" RUN R -e "devtools::install_github('allanvc/mRpostman')" -RUN wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh +RUN R -e "tinytex::tlmgr_install(c(\ + 'amscls', 'amsfonts', 'amsmath', 'babel', 'bibtex', 'booktabs', \ + 'caption', 'cm', 'colortbl', 'dehyph', 'dvipdfmx', 'dvips', \ + 'ec', 'environ', 'epstopdf-pkg', 'etex', 'etoolbox', 'euenc', \ + 'fancyvrb', 'float', 'fontspec', 'framed', 'geometry', 'glyphlist', \ + 'graphics', 'graphics-cfg', 'graphics-def', 'gsftopk', 'helvetic', \ + 'hyperref', 'hyphen-base', 'ifluatex', 'iftex', 'ifxetex', 'inconsolata', \ + 'knuth-lib', 'kpathsea', 'l3kernel', 'l3packages', 'latex', 'latex-bin', \ + 'latex-fonts', 'latexconfig', 'latexmk', 'lm', 'lualibs', 'luaotfload', \ + 'luatex', 'makecell', 'makeindex', 'mathspec', 'metafont', 'mfware', \ + 'multirow', 'natbib', 'oberdiek', 'pdflscape', 'pdftex', 'plain', \ + 'scheme-infraonly', 'tabu', 'tetex', 'tex', 'tex-ini-files', 'texlive.infra', \ + 'threeparttable', 'threeparttablex', 'times', 'tipa', 'titling', \ + 'tools', 'trimspaces', 'ulem', 'unicode-data', 'upquote', 'url', \ + 'varwidth', 'wrapfig', 'xcolor', 'xetex', 'xetexconfig', 'xkeyval', \ + 'xunicode', 'zapfding' \ +))" # build and install this package ADD . /home/rocker/redcapcustodian diff --git a/install_latex_packages.R b/install_latex_packages.R deleted file mode 100644 index 1adf20c..0000000 --- a/install_latex_packages.R +++ /dev/null @@ -1,2 +0,0 @@ -packages_to_install <- read.csv("https://raw.githubusercontent.com/ljwoodley/redcapcustodian/add_latex_packages/latex_packages.csv") -tinytex::tlmgr_install(packages_to_install$package) diff --git a/latex_packages.csv b/latex_packages.csv deleted file mode 100644 index 1f8a5fb..0000000 --- a/latex_packages.csv +++ /dev/null @@ -1,85 +0,0 @@ -package -amscls -amsfonts -amsmath -babel -bibtex -booktabs -caption -cm -colortbl -dehyph -dvipdfmx -dvips -ec -environ -etex -etoolbox -euenc -fancyvrb -float -fontspec -framed -geometry -glyphlist -graphics -graphics-cfg -graphics-def -gsftopk -helvetic -hyperref -hyphen-base -ifluatex -iftex -ifxetex -inconsolata -knuth-lib -kpathsea -l3kernel -l3packages -latex -latex-bin -latex-fonts -latexconfig -latexmk -lm -lualibs -luaotfload -luatex -makecell -makeindex -mathspec -metafont -mfware -multirow -natbib -oberdiek -pdftex -plain -scheme-infraonly -tabu -tetex -tex -tex-ini-files -texlive.infra -threeparttable -threeparttablex -times -tipa -titling -tools -trimspaces -ulem -unicode-data -upquote -url -varwidth -wrapfig -xcolor -xetex -xetexconfig -xkeyval -xunicode -zapfding -pdflscape -epstopdf-pkg \ No newline at end of file From fee6f5c398ec6edb40226b56a4cb9fb96353213d Mon Sep 17 00:00:00 2001 From: Laurence James-Woodley Date: Wed, 14 Dec 2022 21:41:11 -0500 Subject: [PATCH 4/5] add mdwtools package --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 915368d..d18ab2b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,7 +35,7 @@ RUN R -e "tinytex::tlmgr_install(c(\ 'knuth-lib', 'kpathsea', 'l3kernel', 'l3packages', 'latex', 'latex-bin', \ 'latex-fonts', 'latexconfig', 'latexmk', 'lm', 'lualibs', 'luaotfload', \ 'luatex', 'makecell', 'makeindex', 'mathspec', 'metafont', 'mfware', \ - 'multirow', 'natbib', 'oberdiek', 'pdflscape', 'pdftex', 'plain', \ + 'mdwtools', 'multirow', 'natbib', 'oberdiek', 'pdflscape', 'pdftex', 'plain', \ 'scheme-infraonly', 'tabu', 'tetex', 'tex', 'tex-ini-files', 'texlive.infra', \ 'threeparttable', 'threeparttablex', 'times', 'tipa', 'titling', \ 'tools', 'trimspaces', 'ulem', 'unicode-data', 'upquote', 'url', \ From b33da6083ead82aeb05f3da5bb1aecda597aa0c5 Mon Sep 17 00:00:00 2001 From: Philip Chase Date: Thu, 15 Dec 2022 11:25:53 -0500 Subject: [PATCH 5/5] Bump VERSION and update NEWS.md for release 1.4.1 --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ VERSION | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7389adf..01b7fa0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: redcapcustodian Type: Package Title: System data cleaning for REDCap -Version: 1.4.0 +Version: 1.4.1 Authors@R: c( person("Philip", "Chase", email = "pbc@ufl.edu", diff --git a/NEWS.md b/NEWS.md index a51e1b0..94de4b3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,6 +3,11 @@ All notable changes to the redcapcustodian package and its contained scripts wil This project adheres to [Semantic Versioning](http://semver.org/). +## [1.4.1] - 2022-12-15 +### Changed +- Install latex packages directly in Dockerfile (Laurence James-Woodley) + + ## [1.4.0] - 2022-12-13 ### Added - Switch Dockerfile from tidyverse to verse (Laurence James-Woodley) diff --git a/VERSION b/VERSION index 88c5fb8..347f583 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.4.0 +1.4.1