Turn into notebooks R scripts 000, 010, 020, 030

Just a note about the JupyterLab Git extension (a little bug we can report)

Look the displayed names of git branches have a little bug we can report in the official repo :

Note also as a team, we have the opportunity to propose an awesome new feature for the extnesion: add github login, which should be configurable with our own teams JupyterlLab Github OAuth2 App, so that we don't have to manually create a personal access token ourselves anymore, we just github login. Also extensible to Gitea / Gitlab / Keycloak OAuth2

@JeanGarf I have issues installing devtools package, that i 'd like to discuss with you:

@JeanGarf I have issues installing devtools package, that i 'd like to discuss with you:

Additionnally, there are many other error messages stating the package is not available for our version of R, 3.5.0. Now, in the logs of my Jupyterlab docker container, i found one interesting error, thrown right after resolving the remotes package, and related to the installation of the systemfonts package :

jupyter_deno_1       | [I 2024-03-10 15:53:22.645 ServerApp] Connecting to kernel ab5660d2-fd1b-45ac-a04c-b6e627331fb6.
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/remotes_2.4.2.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 152560 bytes (148 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 148 KB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���remotes��� ...
jupyter_deno_1       | ** package ���remotes��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** R
jupyter_deno_1       | ** inst
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** installing vignettes
jupyter_deno_1       | ** testing if installed package can be loaded
jupyter_deno_1       | * DONE (remotes)
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/RtmporcoBv/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/systemfonts_1.0.6.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 80844 bytes (78 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 78 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/textshaping_0.3.7.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 35100 bytes (34 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 34 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/pillar_1.9.0.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 444528 bytes (434 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 434 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/shiny_1.8.0.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 2826485 bytes (2.7 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 2.7 MB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/bslib_0.6.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 6059587 bytes (5.8 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 5.8 MB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/downlit_0.4.3.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 36888 bytes (36 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 36 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/purrr_1.0.2.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 220868 bytes (215 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 215 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/ragg_1.2.7.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 425500 bytes (415 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 415 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/rmarkdown_2.26.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 2189506 bytes (2.1 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 2.1 MB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/tibble_3.2.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 565982 bytes (552 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 552 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/htmlwidgets_1.6.4.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 868895 bytes (848 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 848 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/vctrs_0.6.5.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 969066 bytes (946 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 946 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 97958 bytes (95 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 95 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/pkgdown_2.0.7.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 871465 bytes (851 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 851 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/profvis_0.3.8.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 149012 bytes (145 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 145 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/rversions_2.1.2.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 42135 bytes (41 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 41 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/urlchecker_1.0.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 13340 bytes (13 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 13 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/devtools_2.4.5.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 374718 bytes (365 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 365 KB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���systemfonts��� ...
jupyter_deno_1       | ** package ���systemfonts��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | Using PKG_CFLAGS=
jupyter_deno_1       | Using PKG_LIBS=-lfontconfig -lfreetype
jupyter_deno_1       | ** libs
jupyter_deno_1       | rm -f systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c caches.cpp -o caches.o
jupyter_deno_1       | In file included from caches.h:7:0,
jupyter_deno_1       |                  from caches.cpp:1:
jupyter_deno_1       | ft_cache.h:9:10: fatal error: ft2build.h: No such file or directory
jupyter_deno_1       |  #include <ft2build.h>
jupyter_deno_1       |           ^~~~~~~~~~~~
jupyter_deno_1       | compilation terminated.
jupyter_deno_1       | make: *** [/root/anaconda3/lib/R/etc/Makeconf:167: caches.o] Error 1
jupyter_deno_1       | ERROR: compilation failed for package ���systemfonts���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/systemfonts���
jupyter_deno_1       | ERROR: dependency ���lifecycle��� is not available for package ���bslib���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/bslib���
jupyter_deno_1       | ERROR: dependency ���lifecycle��� is not available for package ���vctrs���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/vctrs���
jupyter_deno_1       | ERROR: dependency ���xml2��� is not available for package ���rversions���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/rversions���
jupyter_deno_1       | ERROR: dependency ���xml2��� is not available for package ���urlchecker���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/urlchecker���
jupyter_deno_1       | ERROR: dependency ���systemfonts��� is not available for package ���textshaping���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/textshaping���
jupyter_deno_1       | ERROR: dependencies ���lifecycle���, ���vctrs��� are not available for package ���pillar���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/pillar���
jupyter_deno_1       | ERROR: dependencies ���bslib���, ���lifecycle��� are not available for package ���shiny���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/shiny���
jupyter_deno_1       | ERROR: dependencies ���brio���, ���vctrs��� are not available for package ���downlit���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/downlit���
jupyter_deno_1       | ERROR: dependencies ���lifecycle���, ���vctrs��� are not available for package ���purrr���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/purrr���
jupyter_deno_1       | ERROR: dependency ���bslib��� is not available for package ���rmarkdown���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/rmarkdown���
jupyter_deno_1       | ERROR: dependencies ���systemfonts���, ���textshaping��� are not available for package ���ragg���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/ragg���
jupyter_deno_1       | ERROR: dependencies ���lifecycle���, ���pillar���, ���vctrs��� are not available for package ���tibble���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/tibble���
jupyter_deno_1       | ERROR: dependency ���rmarkdown��� is not available for package ���htmlwidgets���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/htmlwidgets���
jupyter_deno_1       | ERROR: dependency ���shiny��� is not available for package ���miniUI���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/miniUI���
jupyter_deno_1       | ERROR: dependencies ���bslib���, ���downlit���, ���purrr���, ���ragg���, ���rmarkdown���, ���tibble���, ���xml2��� are not available for package ���pkgdown���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/pkgdown���
jupyter_deno_1       | ERROR: dependencies ���htmlwidgets���, ���purrr���, ���vctrs��� are not available for package ���profvis���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/profvis���
jupyter_deno_1       | ERROR: dependencies ���usethis���, ���lifecycle���, ���miniUI���, ���pkgdown���, ���profvis���, ���roxygen2���, ���rversions���, ���testthat���, ���urlchecker��� are not available for package ���devtools���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/devtools���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/RtmporcoBv/downloaded_packages���
jupyter_deno_1       | [I 2024-03-10 15:55:20.933 ServerApp] Saving file at /jb/reload_deces_europe/decoderleco_deces_europe_reloaded/notebooks/Dependencies.ipynb

I try installing the libfontconfig1-dev linux package to fix that systemfonts error, according https://stackoverflow.com/questions/68094530/fatal-error-installing-systemfonts-in-jupyter-r-docker , the result is that indeed, the fix is confirmed:

jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 365 KB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���systemfonts��� ...
jupyter_deno_1       | ** package ���systemfonts��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | Found pkg-config cflags and libs!
jupyter_deno_1       | Using PKG_CFLAGS=-I/usr/include/freetype2 -I/usr/include/libpng16
jupyter_deno_1       | Using PKG_LIBS=-lfontconfig -lfreetype
jupyter_deno_1       | ** libs
jupyter_deno_1       | rm -f systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c caches.cpp -o caches.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c cpp11.cpp -o cpp11.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c dev_metrics.cpp -o dev_metrics.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c font_matching.cpp -o font_matching.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c font_registry.cpp -o font_registry.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c ft_cache.cpp -o ft_cache.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c string_shape.cpp -o string_shape.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/cpp11/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/root/anaconda3/include   -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/root/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c font_metrics.cpp -o font_metrics.o
jupyter_deno_1       | x86_64-conda_cos6-linux-gnu-c++  -I/root/anaconda3/lib/R/include -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16  -I"/root/anaconda3/lib/R/library/

I then get another error, which suggests to install additionnal linux packages libharfbuzz-dev libfribidi-dev:

jupyter_deno_1       | ERROR: dependency ���lifecycle��� is not available for package ���bslib���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/bslib���
jupyter_deno_1       | ERROR: dependency ���lifecycle��� is not available for package ���vctrs���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/vctrs���
jupyter_deno_1       | ERROR: dependency ���xml2��� is not available for package ���rversions���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/rversions���
jupyter_deno_1       | ERROR: dependency ���xml2��� is not available for package ���urlchecker���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/urlchecker���
jupyter_deno_1       | * installing *source* package ���textshaping��� ...
jupyter_deno_1       | ** package ���textshaping��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | Package harfbuzz was not found in the pkg-config search path.
jupyter_deno_1       | Perhaps you should add the directory containing `harfbuzz.pc'
jupyter_deno_1       | to the PKG_CONFIG_PATH environment variable
jupyter_deno_1       | Package 'harfbuzz', required by 'virtual:world', not found
jupyter_deno_1       | Package 'fribidi', required by 'virtual:world', not found
jupyter_deno_1       | Using PKG_CFLAGS=
jupyter_deno_1       | Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng
jupyter_deno_1       | --------------------------- [ANTICONF] --------------------------------
jupyter_deno_1       | Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
jupyter_deno_1       |  * deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
jupyter_deno_1       |  * rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
jupyter_deno_1       |  * csw: libharfbuzz_dev libfribidi_dev (Solaris)
jupyter_deno_1       |  * brew: harfbuzz fribidi (OSX)
jupyter_deno_1       | If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in your
jupyter_deno_1       | PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-config
jupyter_deno_1       | is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
jupyter_deno_1       | R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
jupyter_deno_1       | -------------------------- [ERROR MESSAGE] ---------------------------
jupyter_deno_1       | <stdin>:1:10: fatal error: hb-ft.h: No such file or directory
jupyter_deno_1       | compilation terminated.
jupyter_deno_1       | --------------------------------------------------------------------
jupyter_deno_1       | ERROR: configuration failed for package ���textshaping���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/textshaping���
jupyter_deno_1       | ERROR: dependencies ���lifecycle���, ���vctrs��� are not available for package ���pillar���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/pillar���
jupyter_deno_1       | ERROR: dependencies ���bslib���, ���lifecycle��� are not available for package ���shiny���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/shiny���
jupyter_deno_1       | ERROR: dependencies ���lifecycle���, ���vctrs��� are not available for package ���purrr���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/purrr���
jupyter_deno_1       | ERROR: dependency ���bslib��� is not available for package ���rmarkdown���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/rmarkdown���
jupyter_deno_1       | ERROR: dependency ���textshaping��� is not available for package ���ragg���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/ragg���
jupyter_deno_1       | ERROR: dependency ���rmarkdown��� is not available for package ���htmlwidgets���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/htmlwidgets���
jupyter_deno_1       | ERROR: dependency ���shiny��� is not available for package ���miniUI���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/miniUI���
jupyter_deno_1       | ERROR: dependencies ���bslib���, ���downlit���, ���purrr���, ���ragg���, ���rmarkdown���, ���tibble���, ���xml2��� are not available for package ���pkgdown���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/pkgdown���
jupyter_deno_1       | ERROR: dependencies ���htmlwidgets���, ���purrr���, ���vctrs��� are not available for package ���profvis���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/profvis���
jupyter_deno_1       | ERROR: dependencies ���usethis���, ���lifecycle���, ���miniUI���, ���pkgdown���, ���profvis���, ���roxygen2���, ���rversions���, ���testthat���, ���urlchecker��� are not available for package ���devtools���
jupyter_deno_1       | * removing ���/root/anaconda3/lib/R/library/devtools���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/RtmporcoBv/downloaded_packages���

An interesting point

I noticed something very interesting and important:

First, according the above logs, devtools is indeed resolved and downloaded successfully
but devtools is after that removed: why ? because of errors occuring after devtools resolution, like the systemfonts package error, and the others i am debugging one after the other.
that is really important: R has a rollback mechanism, when performing packages installation!
This also means that despite of the error messages tating that the packages are not available for our R version, the desired R packages might be available, but they require devtools to successfully be installed.
Finally, what i just said about devtools is also true for the remotes package, which obviously is require for further package resolution!
We are on the good path, I think, wdyt @JeanGarf ?

Unstacking all missing linux packages errors

Following error, after error, the instructions given in stderr/stdout logs:

I installed libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev, and then ANTICONF tells me this in logs:

jupyter_deno_1       | -----------------------------[ ANTICONF ]-------------------------------
jupyter_deno_1       | Configuration failed to find one of freetype2 libpng libtiff-4 libjpeg. Try installing:
jupyter_deno_1       |  * deb: libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev (Debian, Ubuntu, etc)
jupyter_deno_1       |  * rpm: freetype-devel libpng-devel libtiff-devel libjpeg-devel (Fedora, CentOS, RHEL)
jupyter_deno_1       |  * csw: libfreetype_dev libpng16_dev libtiff_dev libjpeg_dev (Solaris)
jupyter_deno_1       | If freetype2 libpng libtiff-4 libjpeg is already installed, check that 'pkg-config' is in your
jupyter_deno_1       | PATH and PKG_CONFIG_PATH contains a freetype2 libpng libtiff-4 libjpeg.pc file. If pkg-config
jupyter_deno_1       | is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
jupyter_deno_1       | R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
jupyter_deno_1       | -------------------------- [ERROR MESSAGE] ---------------------------

Okay, so the previous error fix is kind of a bit complex, as suggesed by ANTICONF. Now, I found a stackoverflow page, where a ery interesting fact is stated:
- quote _if you install devtools just for having install_github() function, you can just use remotes::install_github() instead_
- and indeed, our source code only adds devtools as dependency, for making use of install_github() (thank you for well docuementing that in comments @JeanGarf )
- so i comented all commands referencing devtools in source code and replaced all occurences of install_github() by remotes::install_github()
- Ok, so now that i did that, i have no more errors, only the one stating that glue is not available for R 3.5.0: and ideed, in the glue package page, we can read that the glue package requires R version 3.6 or above!

So now I need to upgrade the installed version of R. how do I do that? :
- I installed R using conda, so the question is how do i install a conda package in a specific version ?
- plus, when installing R with conda, i installed it with the r package, instead of the r-base package, like mentioned here, and here in the official r-notebook dockerfile
- Exactly, i installed r and the R kernel for Jupyter, like this: conda install -y -c r r-irkernel. It is now time to change that, to install all linux packages and conda packages just like here in the official r-notebook dockerfile, and to remove the installation of apt-get packages I did above in the analysis ( libxrender1 libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev ). Maybe I'll just keep libxrender1, i'll try without it first.
- result: awsome, it all works, glue package was installed without any issue (i could retry adding again the devtools package, but i'll do that later maybe). Note I end up with R version 4.2.2 Patched (2022-11-10 r83330)

The next R packages installation

As I executed the installation of all remaining packages, I noted the following errors, which were inside the log of one single execution:

The below Errors caused the tidyr, vroom, httr, classInt, regions, readr, RefManageR, and eurostat packages to be removed:


jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** checking absolute paths in shared objects and dynamic libraries
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (lubridate)
jupyter_deno_1       | ERROR: dependencies ���dplyr���, ���tibble��� are not available for package ���tidyr���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/tidyr���
jupyter_deno_1       | ERROR: dependency ���tibble��� is not available for package ���vroom���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/vroom���
jupyter_deno_1       | ERROR: dependency ���curl��� is not available for package ���httr���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/httr���
jupyter_deno_1       | ERROR: dependency ���KernSmooth��� is not available for package ���classInt���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/classInt���
jupyter_deno_1       | ERROR: dependencies ���dplyr���, ���tidyr���, ���readxl���, ���tibble��� are not available for package ���regions���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/regions���
jupyter_deno_1       | ERROR: dependencies ���tibble���, ���vroom��� are not available for package ���readr���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/readr���
jupyter_deno_1       | ERROR: dependency ���httr��� is not available for package ���RefManageR���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/RefManageR���
jupyter_deno_1       | ERROR: dependencies ���classInt���, ���curl���, ���dplyr���, ���httr2���, ���ISOweek���, ���readr���, ���RefManageR���, ���regions���, ���tibble���, ���tidyr��� are not available for package ���eurostat���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/eurostat���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/maps_3.4.2.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 2278051 bytes (2.2 MB)
jupyter_deno_1       | ==================================================

* The below Errors caused the `mgcv`, `knitr`, `raster`, `ggplot2`, `htmlwidgets`, and `leaflet` packages to be removed:

```bash
jupyter_deno_1       | ERROR: dependency ���Matrix��� is not available for package ���mgcv���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/mgcv���
jupyter_deno_1       | ERROR: dependency ���yaml��� is not available for package ���knitr���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/knitr���
jupyter_deno_1       | ERROR: dependency ���terra��� is not available for package ���raster���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/raster���
jupyter_deno_1       | * installing *source* package ���scales��� ...
jupyter_deno_1       | ** package ���scales��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** R
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | *** copying figures
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (scales)
jupyter_deno_1       | ERROR: dependency ���mgcv��� is not available for package ���ggplot2���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/ggplot2���
jupyter_deno_1       | ERROR: dependencies ���knitr���, ���rmarkdown���, ���yaml��� are not available for package ���htmlwidgets���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/htmlwidgets���
jupyter_deno_1       | ERROR: dependency ���ggplot2��� is not available for package ���viridis���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/viridis���
jupyter_deno_1       | ERROR: dependencies ���htmlwidgets���, ���raster���, ���viridis��� are not available for package ���leaflet���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/leaflet���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/vroom_1.6.5.tar.gz'
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 24131 bytes (23 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 23 KB

The below Errors caused the classInt, shiny, labelled, miniUI, and questionr, packages to be removed:

jupyter_deno_1       | * DONE (tidyr)
jupyter_deno_1       | ERROR: dependency ���KernSmooth��� is not available for package ���classInt���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/classInt���
jupyter_deno_1       | * installing *source* package ���R.utils��� ...
jupyter_deno_1       | ** package ���R.utils��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** R
jupyter_deno_1       | ** inst
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
jupyter_deno_1       |   Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils.
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (R.utils)
jupyter_deno_1       | ERROR: dependencies ���httpuv���, ���xtable��� are not available for package ���shiny���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/shiny���
jupyter_deno_1       | ERROR: dependency ���haven��� is not available for package ���labelled���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/labelled���
jupyter_deno_1       | * installing *source* package ���R.cache��� ...
jupyter_deno_1       | ** package ���R.cache��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** R
jupyter_deno_1       | ** inst
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (R.cache)
jupyter_deno_1       | ERROR: dependency ���shiny��� is not available for package ���miniUI���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/miniUI���
jupyter_deno_1       | * installing *source* package ���styler��� ...
jupyter_deno_1       | ** package ���styler��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** R
jupyter_deno_1       | ** inst
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** installing vignettes
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (styler)
jupyter_deno_1       | ERROR: dependencies ���shiny���, ���miniUI���, ���classInt���, ���labelled��� are not available for package ���questionr���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/questionr���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/Matrix_1.6-5.tar.gz'
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/mgcv_1.9-1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 1083217 bytes (1.0 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 1.0 MB

Then I got a noticeable error about the KernSmooth package:

sstdiag.o
jupyter_deno_1       | gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
jupyter_deno_1       | /usr/bin/ld: cannot find -lblas: No such file or directory
jupyter_deno_1       | collect2: error: ld returned 1 exit status
jupyter_deno_1       | make: *** [/usr/share/R/share/make/shlib.mk:10: KernSmooth.so] Error 1
jupyter_deno_1       | ERROR: compilation failed for package ���KernSmooth���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/KernSmooth���
jupyter_deno_1       | * installing *source* package ���wk��� ...
jupyter_deno_1       | ** package ���wk��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** libs

Then another error, which this time suggests to install an additional linux packe for debian, the libudunits2-dev package:

jupyter_deno_1       | --------------------------------------------------------------------------------
jupyter_deno_1       |   Configuration failed because libudunits2.so was not found. Try installing:
jupyter_deno_1       |     * deb: libudunits2-dev (Debian, Ubuntu, ...)
jupyter_deno_1       |     * rpm: udunits2-devel (Fedora, EPEL, ...)
jupyter_deno_1       |     * brew: udunits (OSX)
jupyter_deno_1       |   If udunits2 is already installed in a non-standard location, use:
jupyter_deno_1       |     --configure-args='--with-udunits2-lib=/usr/local/lib'
jupyter_deno_1       |   if the library was not found, and/or:
jupyter_deno_1       |     --configure-args='--with-udunits2-include=/usr/include/udunits2'
jupyter_deno_1       |   if the header was not found, replacing paths with appropriate values.
jupyter_deno_1       |   You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
jupyter_deno_1       | --------------------------------------------------------------------------------
jupyter_deno_1       |
jupyter_deno_1       | See `config.log' for more details
jupyter_deno_1       | ERROR: configuration failed for package ���units���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/units���
jupyter_deno_1       | * installing *source* package ���terra��� ...
jupyter_deno_1       | ** package ���terra��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | configure: CC: gcc
jupyter_deno_1       | configure: CXX: g++ -std=gnu++14
jupyter_deno_1       | checking for gdal-config... no
jupyter_deno_1       | no
jupyter_deno_1       | configure: error: gdal-config not found or not executable.
jupyter_deno_1       | ERROR: configuration failed for package ���terra���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/terra���
jupyter_deno_1       | ERROR: dependency ���KernSmooth��� is not available for package ���classInt���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/classInt���
jupyter_deno_1       | * installing *source* package ���s2��� ...
jupyter_deno_1       | ** package ���s2��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | Testing compiler using PKG_CFLAGS=
jupyter_deno_1       | Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3
jupyter_deno_1       | Using PKG_CFLAGS= -DOPENSSL_SUPPRESS_DEPRECATED -DIS_LITTLE_ENDIAN
jupyter_deno_1       | ** libs
jupyter_deno_1       | g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/wk/include'   -DOPENSSL_SUPPRESS_DEPRECATED -DIS_LITTLE_ENDIAN -pthread -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c absl/base/internal/cycleclock.cc -o absl/base/internal/cycleclock.o

I then saw and copied the following output:

jupyter_deno_1       | installing to /usr/local/lib/R/site-library/00LOCK-s2/00new/s2/libs
jupyter_deno_1       | ** R
jupyter_deno_1       | ** data
jupyter_deno_1       | *** moving datasets to lazyload DB
jupyter_deno_1       | ** inst
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | *** copying figures
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** checking absolute paths in shared objects and dynamic libraries
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (s2)
jupyter_deno_1       | ERROR: dependencies ���classInt���, ���units��� are not available for package ���sf���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/sf���
jupyter_deno_1       | ERROR: dependencies ���httr���, ���sf���, ���terra��� are not available for package ���rnaturalearth���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/rnaturalearth���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/rnaturalearthdata_1.0.0.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 3313555 bytes (3.2 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 3.2 MB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���rnaturalearthdata��� ...
jupyter_deno_1       | ** package ���rnaturalearthdata��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** R
jupyter_deno_1       | ** data
jupyter_deno_1       | *** moving datasets to lazyload DB
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (rnaturalearthdata)
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/vroom_1.6.5.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 750416 bytes (732 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 732 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/readr_2.1.5.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 298065 bytes (291 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 291 KB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���vroom��� ...
jupyter_deno_1       | ** package ���vroom��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** libs

Then I catched another part of the logs, which suggests to install another linux package libcurl4-openssl-dev:

jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/RColorBrewer_1.1-3.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 11638 bytes (11 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 11 KB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���RColorBrewer��� ...
jupyter_deno_1       | ** package ���RColorBrewer��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** R
jupyter_deno_1       | ** inst
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (RColorBrewer)
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/curl_5.2.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 716695 bytes (699 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 699 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/httr_1.4.7.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 118500 bytes (115 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 115 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/insee_1.1.5.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 3749953 bytes (3.6 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 3.6 MB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���curl��� ...
jupyter_deno_1       | ** package ���curl��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | Using PKG_CFLAGS=
jupyter_deno_1       | Using PKG_LIBS=-lcurl
jupyter_deno_1       | --------------------------- [ANTICONF] --------------------------------
jupyter_deno_1       | Configuration failed because libcurl was not found. Try installing:
jupyter_deno_1       |  * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
jupyter_deno_1       |  * rpm: libcurl-devel (Fedora, CentOS, RHEL)
jupyter_deno_1       | If libcurl is already installed, check that 'pkg-config' is in your
jupyter_deno_1       | PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
jupyter_deno_1       | is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
jupyter_deno_1       | R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
jupyter_deno_1       | -------------------------- [ERROR MESSAGE] ---------------------------
jupyter_deno_1       | <stdin>:1:10: fatal error: curl/curl.h: No such file or directory
jupyter_deno_1       | compilation terminated.
jupyter_deno_1       | --------------------------------------------------------------------
jupyter_deno_1       | ERROR: configuration failed for package ���curl���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/curl���
jupyter_deno_1       | ERROR: dependency ���curl��� is not available for package ���httr���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/httr���
jupyter_deno_1       | ERROR: dependency ���httr��� is not available for package ���insee���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/insee���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/curl_5.2.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 716695 bytes (699 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 699 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/httr_1.4.7.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 118500 bytes (115 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 115 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/selectr_0.4-2.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 41371 bytes (40 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 40 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/rvest_1.0.4.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 115876 bytes (113 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 113 KB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���curl��� ...
jupyter_deno_1       | ** package ���curl��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | Using PKG_CFLAGS=
jupyter_deno_1       | Using PKG_LIBS=-lcurl
jupyter_deno_1       | --------------------------- [ANTICONF] --------------------------------
jupyter_deno_1       | Configuration failed because libcurl was not found. Try installing:
jupyter_deno_1       |  * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
jupyter_deno_1       |  * rpm: libcurl-devel (Fedora, CentOS, RHEL)
jupyter_deno_1       | If libcurl is already installed, check that 'pkg-config' is in your
jupyter_deno_1       | PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
jupyter_deno_1       | is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
jupyter_deno_1       | R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
jupyter_deno_1       | -------------------------- [ERROR MESSAGE] ---------------------------
jupyter_deno_1       | <stdin>:1:10: fatal error: curl/curl.h: No such file or directory
jupyter_deno_1       | compilation terminated.
jupyter_deno_1       | --------------------------------------------------------------------
jupyter_deno_1       | ERROR: configuration failed for package ���curl���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/curl���
jupyter_deno_1       | * installing *source* package ���selectr��� ...
jupyter_deno_1       | ** package ���selectr��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** R
jupyter_deno_1       | ** inst
jupyter_deno_1       | ** byte-compile and prepare package for lazy loading
jupyter_deno_1       | ** help
jupyter_deno_1       | *** installing help indices
jupyter_deno_1       | ** building package indices
jupyter_deno_1       | ** testing if installed package can be loaded from temporary location
jupyter_deno_1       | ** testing if installed package can be loaded from final location
jupyter_deno_1       | ** testing if installed package keeps a record of temporary installation path
jupyter_deno_1       | * DONE (selectr)
jupyter_deno_1       | ERROR: dependency ���curl��� is not available for package ���httr���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/httr���
jupyter_deno_1       | ERROR: dependency ���httr��� is not available for package ���rvest���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/rvest���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/ucminf_1.2.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 16586 bytes (16 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 16 KB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/numDeriv_2016.8-1.1.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 76053 bytes (74 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 74 KB
jupyter_deno_1       |

# ... Then it continues downloading, installing, at this stage, the 
# insee R package was already computed by package resolution process...

Then:

jupyter_deno_1       | /usr/bin/ld: cannot find -llapack: No such file or directory
jupyter_deno_1       | /usr/bin/ld: cannot find -lblas: No such file or directory
jupyter_deno_1       | collect2: error: ld returned 1 exit status
jupyter_deno_1       | make: *** [/usr/share/R/share/make/shlib.mk:10: RcppEigen.so] Error 1
jupyter_deno_1       | ERROR: compilation failed for package ���RcppEigen���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/RcppEigen���
jupyter_deno_1       | ERROR: dependencies ���ucminf���, ���Matrix��� are not available for package ���ordinal���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/ordinal���
jupyter_deno_1       | * installing *source* package ���processx��� ...
jupyter_deno_1       | ** package ���processx��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** libs
jupyter_deno_1       | gcc -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wl,-z,relro -Wall tools/px.c -o tools/px
jupyter_deno_1       | gcc -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wl,-z,relro -I../inst/include -Wall tools/sock.c -o tools/sock

Then:

jupyter_deno_1       | --------------------------- [ANTICONF] --------------------------------
jupyter_deno_1       | Configuration failed because libcurl was not found. Try installing:
jupyter_deno_1       |  * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
jupyter_deno_1       |  * rpm: libcurl-devel (Fedora, CentOS, RHEL)
jupyter_deno_1       | If libcurl is already installed, check that 'pkg-config' is in your
jupyter_deno_1       | PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
jupyter_deno_1       | is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
jupyter_deno_1       | R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
jupyter_deno_1       | -------------------------- [ERROR MESSAGE] ---------------------------
jupyter_deno_1       | <stdin>:1:10: fatal error: curl/curl.h: No such file or directory
jupyter_deno_1       | compilation terminated.
jupyter_deno_1       | --------------------------------------------------------------------
jupyter_deno_1       | ERROR: configuration failed for package ���curl���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/curl���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/gsl_2.1-8.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 217997 bytes (212 KB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 212 KB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���gsl��� ...
jupyter_deno_1       | ** package ���gsl��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | checking for gcc... gcc
jupyter_deno_1       | checking whether the C compiler works... yes
jupyter_deno_1       | checking for C compiler default output file name... a.out
jupyter_deno_1       | checking for suffix of executables...
jupyter_deno_1       | checking whether we are cross compiling... no
jupyter_deno_1       | checking for suffix of object files... o
jupyter_deno_1       | checking whether the compiler supports GNU C... yes
jupyter_deno_1       | checking whether gcc accepts -g... yes
jupyter_deno_1       | checking for gcc option to enable C11 features... none needed
jupyter_deno_1       | checking for gsl-config... no
jupyter_deno_1       | configure: error: gsl-config not found, is GSL installed?
jupyter_deno_1       | ERROR: configuration failed for package ���gsl���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/gsl���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/Matrix_1.6-5.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 2883851 bytes (2.8 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 2.8 MB
jupyter_deno_1       |
jupyter_deno_1       | trying URL 'http://cloud.r-project.org/src/contrib/igraph_2.0.2.tar.gz'
jupyter_deno_1       | Content type 'application/x-gzip' length 4965448 bytes (4.7 MB)
jupyter_deno_1       | ==================================================
jupyter_deno_1       | downloaded 4.7 MB
jupyter_deno_1       |
jupyter_deno_1       | * installing *source* package ���Matrix��� ...
jupyter_deno_1       | ** package ���Matrix��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** libs
jupyter_deno_1       | gcc -I"/usr/share/R/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Csparse.c -o Csparse.o
jupyter_deno_1       | gcc -I"/usr/share/R/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER    -fvisibility=hidden -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c abIndex.c -o abIndex.o

Then :

rmat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SuiteSparse_config.c -o SuiteSparse_config.o
jupyter_deno_1       | ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
jupyter_deno_1       | ar: `u' modifier ignored since `D' is the default (see `U')
jupyter_deno_1       | make[1]: Leaving directory '/tmp/RtmprprYVZ/R.INSTALL51a347520eec/Matrix/src/SuiteSparse_config'
jupyter_deno_1       | gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o Matrix.so Csparse.o abIndex.o attrib.o bind.o chm_common.o cholmod-etc.o coerce.o cs.o cs-etc.o dense.o determinant.o dgCMatrix.o dgeMatrix.o factorizations.o idz.o init.o kappa.o objects.o perm.o products.o solve.o sparse.o sparseVector.o subscript.o utils-R.o utils.o validity.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
jupyter_deno_1       | /usr/bin/ld: cannot find -llapack: No such file or directory
jupyter_deno_1       | /usr/bin/ld: cannot find -lblas: No such file or directory
jupyter_deno_1       | collect2: error: ld returned 1 exit status
jupyter_deno_1       | make: *** [/usr/share/R/share/make/shlib.mk:10: Matrix.so] Error 1
jupyter_deno_1       | ERROR: compilation failed for package ���Matrix���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/Matrix���
jupyter_deno_1       | * installing *source* package ���tweenr��� ...
jupyter_deno_1       | ** package ���tweenr��� successfully unpacked and MD5 sums checked
jupyter_deno_1       | ** using staged installation
jupyter_deno_1       | ** libs
jupyter_deno_1       | g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/cpp11/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c along.cpp -o along.o
jupyter_deno_1       | g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/cpp11/include'    -fpic  -g -O2 -ffile-prefix-map=/build/r-base-wZDgjM/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c at.cpp -o at.o

Then:

jupyter_deno_1       | ../inst/include/Eigen/src/Core/CoreEvaluators.h:1071:54: warning: ignoring attributes on template argument ���Eigen::internal::packet_traits<double>::type��� {aka ���__m128d���} [-Wignored-attributes]
jupyter_deno_1       |  1071 |     PacketAlignment = unpacket_traits<PacketScalar>::alignment,
jupyter_deno_1       |       |                                                      ^~~~~~~~~
jupyter_deno_1       | g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
jupyter_deno_1       | /usr/bin/ld: cannot find -llapack: No such file or directory
jupyter_deno_1       | /usr/bin/ld: cannot find -lblas: No such file or directory
jupyter_deno_1       | collect2: error: ld returned 1 exit status
jupyter_deno_1       | make: *** [/usr/share/R/share/make/shlib.mk:10: RcppEigen.so] Error 1
jupyter_deno_1       | ERROR: compilation failed for package ���RcppEigen���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/RcppEigen���
jupyter_deno_1       | ERROR: dependency ���Matrix��� is not available for package ���mgcv���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/mgcv���
jupyter_deno_1       | ERROR: dependency ���mgcv��� is not available for package ���ggplot2���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/ggplot2���
jupyter_deno_1       | ERROR: dependencies ���ggplot2���, ���systemfonts���, ���RcppEigen��� are not available for package ���ggforce���
jupyter_deno_1       | * removing ���/usr/local/lib/R/site-library/ggforce���
jupyter_deno_1       |
jupyter_deno_1       | The downloaded source packages are in
jupyter_deno_1       |  ���/tmp/Rtmpa6pPR4/downloaded_packages���
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jupyter_deno_1       | ** package ���pyramid��� successfully unpacked and MD5 sums checked
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jupyter_deno_1       | ** R
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jupyter_deno_1       | *** installing help indices
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I have successfully resolved absolutely all dependencies required to execute the very little code to download all eurostat data. That's my commit commithash.

Now when I execute the code, @decoderleco here is the error I get :

Now yesterday Pierre gave us one indication that definitely will help solving the error:

and also yesterday Pierre git pushed those fixes he talked about on github, directly on the main git branch (c'est pas bien de push directement sur main Pierre ;) ) of https://github.com/decoderleco/deces_europe/ : the git commit hash is a9326ae9f1ca0641cc3d5cc8d17ce698cc87893d.

There, I can find which files changed, just with a git diff between the git commit a9326ae9f1ca0641cc3d5cc8d17ce698cc87893d and its predecessor 527682e60da1a0eaa019842c7e47b403a87b5da8, like this 👍 :


export COMMIT_WITH_FIX="a9326ae9f1ca0641cc3d5cc8d17ce698cc87893d"

export COMMIT_BEFORE_FIX="527682e60da1a0eaa019842c7e47b403a87b5da8"

git clone git@github.com:decoderleco/deces_europe ./pierre_c_pas_bien_10_pompes_pr_avoir_commit_sur_main/

cd ./pierre_c_pas_bien_10_pompes_pr_avoir_commit_sur_main/

# git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX}
git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX} --name-only

And here is the output:

$ git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX} --name-only
010_eurostat_creation_tables_deces_europe.R
030_eurostat_analyses_deces_std_hebdo.R
src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R
src/files/files.R

Le détail de changement dans les fichiers:


$ git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX}
diff --git a/010_eurostat_creation_tables_deces_europe.R b/010_eurostat_creation_tables_deces_europe.R
index afb236a..80015a3 100644
--- a/010_eurostat_creation_tables_deces_europe.R
+++ b/010_eurostat_creation_tables_deces_europe.R
@@ -90,10 +90,10 @@ a__original_es_proj <- read.csv("data/csv/proj_19np__custom_2224172_linear.csv")
# Initialiser avec les données d'origine d'EuroStat
es_pjan <- a__original_es_pjan_le2020

-# Renommer la colonne "values" en "population" et supprimer la colonne "unit" et freq +# Renommer la colonne "values" en "population" et supprimer la colonne "unit" es_pjan <- es_pjan %>% dplyr::rename(population = values) %>%

select(-unit,-freq)
select(-unit)

Filtrer :

les totaux : sexe T (T = M+F) et age

@@ -215,7 +215,7 @@ b__es_deces_et_pop_par_annee <- a__original_es_deces_annuel_le2020

Filtrer age

b__es_deces_et_pop_par_annee <- b__es_deces_et_pop_par_annee %>% dplyr::rename(deces=values) %>%
select(-unit,-freq) %>%
select(-unit) %>% filter( sex != "T", age != "TOTAL", age != "UNK") diff --git a/030_eurostat_analyses_deces_std_hebdo.R b/030_eurostat_analyses_deces_std_hebdo.R index db82542..0bdfa09 100644 --- a/030_eurostat_analyses_deces_std_hebdo.R +++ b/030_eurostat_analyses_deces_std_hebdo.R @@ -224,7 +224,7 @@ g<-ggplot(data = france_suede_portugal) + geom_area(aes(x = numSemaineDepuis2013, y = deces_france), color="#CC0000",fill="#CC0000",size=1,alpha=1/2) +
geom_vline(xintercept = seq(from=0, to=550, by = 52),linetype = "dashed",color="steelblue")+
geom_vline(xintercept = seq(from=0, to=500, by = 52),linetype = "dashed",color="steelblue")+ theme(axis.title.x = element_blank(), axis.text.x = element_blank(), axis.title.y = element_text(color="#000000", size=20 ), @@ -241,7 +241,6 @@ g<-ggplot(data = france_suede_portugal) + geom_text(x=391, y=1000, label="2020",size=10)+ geom_text(x=443, y=1000, label="2021",size=10)+ geom_text(x=495, y=1000, label="2022",size=10)+
geom_text(x=547, y=1000, label="2023",size=10)+ annotate(geom = "text", x = 50, y = 30000, label = "Portugal", color = "#006600", angle = 0, size = 15)+ annotate(geom = "text", x = 50, y = 28000, label = "Suède", color = "#0066CC", @@ -267,7 +266,7 @@ g<-ggplot(data = france_suede_portugal) + geom_area(aes(x = numSemaineDepuis2013, y = deces_france), color="#000000",fill="#000000",size=1,alpha=1/2) +
geom_vline(xintercept = seq(from=0, to=550, by = 52),linetype = "dashed",color="steelblue")+
geom_vline(xintercept = seq(from=0, to=500, by = 52),linetype = "dashed",color="steelblue")+ theme(axis.title.x = element_blank(), axis.text.x = element_blank(), axis.title.y = element_text(color="#000000", size=20 ), @@ -282,9 +281,7 @@ g<-ggplot(data = france_suede_portugal) + geom_text(x=287, y=1000, label="2018",size=10)+ geom_text(x=339, y=1000, label="2019",size=10)+ geom_text(x=391, y=1000, label="2020",size=10)+
geom_text(x=443, y=1000, label="2021",size=10)+
geom_text(x=495, y=1000, label="2022",size=10)+
geom_text(x=547, y=1000, label="2023",size=10)+
geom_text(x=440, y=1000, label="2021",size=10)+ annotate(geom = "text", x = 50, y = 30000, label = "Portugal", color = "#999999", angle = 0, size = 15)+ annotate(geom = "text", x = 50, y = 28000, label = "Suède", color = "#666666", diff --git a/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R b/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R index a4f32ff..23af0dc 100644 --- a/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R +++ b/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R @@ -214,9 +214,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s text(287, 0, "2018", cex=1.2) text(339, 0, "2019", cex=1.2) text(391, 0, "2020", cex=1.2)
text(443, 0, "2021", cex=1.2)
text(495, 0, "2022", cex=1.2)
text(547, 0, "2023", cex=1.2)
text(440, 0, "2021", cex=1.2)
text(492, 0, "2022", cex=1.2)
```
#text(26, 22000, nomPays, cex=1.2)
```

@@ -353,9 +352,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s text(287, base::min(essai$deces_standardises_si_pop_2020_15_24), "2018", cex=1.2) text(339, base::min(essai$deces_standardises_si_pop_2020_15_24), "2019", cex=1.2) text(391, base::min(essai$deces_standardises_si_pop_2020_15_24), "2020", cex=1.2)

text(443, base::min(essai$deces_standardises_si_pop_2020_15_24), "2021", cex=1.2)
text(495, base::min(essai$deces_standardises_si_pop_2020_15_24), "2022", cex=1.2)
text(547, base::min(essai$deces_standardises_si_pop_2020_15_24), "2023", cex=1.2)
text(440, base::min(essai$deces_standardises_si_pop_2020_15_24), "2021", cex=1.2)
text(492, base::min(essai$deces_standardises_si_pop_2020_15_24), "2022", cex=1.2)
```
        # Superposer la moyenne mobile
        par(new=T)
```
@@ -486,9 +484,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s text(287, base::min(essai$deces_standardises_si_pop_2020_25_49), "2018", cex=1.2) text(339, base::min(essai$deces_standardises_si_pop_2020_25_49), "2019", cex=1.2) text(391, base::min(essai$deces_standardises_si_pop_2020_25_49), "2020", cex=1.2)
text(443, base::min(essai$deces_standardises_si_pop_2020_25_49), "2021", cex=1.2)
text(495, base::min(essai$deces_standardises_si_pop_2020_25_49), "2022", cex=1.2)
text(547, base::min(essai$deces_standardises_si_pop_2020_25_49), "2023", cex=1.2)
text(440, base::min(essai$deces_standardises_si_pop_2020_25_49), "2021", cex=1.2)
text(492, base::min(essai$deces_standardises_si_pop_2020_25_49), "2022", cex=1.2)
```
        #text(26, 22000, nomPays, cex=1.2)
```

@@ -622,9 +619,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s text(287, base::min(essai$deces_standardises_si_pop_2020_50_59), "2018", cex=1.2) text(339, base::min(essai$deces_standardises_si_pop_2020_50_59), "2019", cex=1.2) text(391, base::min(essai$deces_standardises_si_pop_2020_50_59), "2020", cex=1.2)

text(443, base::min(essai$deces_standardises_si_pop_2020_50_59), "2021", cex=1.2)
text(495, base::min(essai$deces_standardises_si_pop_2020_50_59), "2022", cex=1.2)
text(547, base::min(essai$deces_standardises_si_pop_2020_50_59), "2023", cex=1.2)
text(440, base::min(essai$deces_standardises_si_pop_2020_50_59), "2021", cex=1.2)
text(492, base::min(essai$deces_standardises_si_pop_2020_50_59), "2022", cex=1.2)
```
#text(26, 22000, nomPays, cex=1.2)
```

@@ -757,9 +753,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s text(287, base::min(essai$deces_standardises_si_pop_2020_60_69), "2018", cex=1.2) text(339, base::min(essai$deces_standardises_si_pop_2020_60_69), "2019", cex=1.2) text(391, base::min(essai$deces_standardises_si_pop_2020_60_69), "2020", cex=1.2)

text(443, base::min(essai$deces_standardises_si_pop_2020_60_69), "2021", cex=1.2)
text(495, base::min(essai$deces_standardises_si_pop_2020_60_69), "2022", cex=1.2)
text(547, base::min(essai$deces_standardises_si_pop_2020_60_69), "2023", cex=1.2)
text(440, base::min(essai$deces_standardises_si_pop_2020_60_69), "2021", cex=1.2)
text(492, base::min(essai$deces_standardises_si_pop_2020_60_69), "2022", cex=1.2)
```
#text(26, 22000, nomPays, cex=1.2)
```

@@ -892,9 +887,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s text(287, base::min(essai$deces_standardises_si_pop_2020_70_79), "2018", cex=1.2) text(339, base::min(essai$deces_standardises_si_pop_2020_70_79), "2019", cex=1.2) text(391, base::min(essai$deces_standardises_si_pop_2020_70_79), "2020", cex=1.2)

text(443, base::min(essai$deces_standardises_si_pop_2020_70_79), "2021", cex=1.2)
text(495, base::min(essai$deces_standardises_si_pop_2020_70_79), "2022", cex=1.2)
text(547, base::min(essai$deces_standardises_si_pop_2020_70_79), "2023", cex=1.2)
text(440, base::min(essai$deces_standardises_si_pop_2020_70_79), "2021", cex=1.2)
text(492, base::min(essai$deces_standardises_si_pop_2020_70_79), "2022", cex=1.2)
```
#text(26, 22000, nomPays, cex=1.2)
```

@@ -1029,9 +1023,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s text(287, base::min(essai$deces_standardises_si_pop_2020_ge80), "2018", cex=1.2) text(339, base::min(essai$deces_standardises_si_pop_2020_ge80), "2019", cex=1.2) text(391, base::min(essai$deces_standardises_si_pop_2020_ge80), "2020", cex=1.2)

text(443, base::min(essai$deces_standardises_si_pop_2020_ge80), "2021", cex=1.2)
text(495, base::min(essai$deces_standardises_si_pop_2020_ge80), "2022", cex=1.2)
text(547, base::min(essai$deces_standardises_si_pop_2020_ge80), "2023", cex=1.2)
text(440, base::min(essai$deces_standardises_si_pop_2020_ge80), "2021", cex=1.2)
text(492, base::min(essai$deces_standardises_si_pop_2020_ge80), "2022", cex=1.2)
```
#text(26, 22000, nomPays, cex=1.2)
```

@@ -1174,10 +1167,9 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s geom_text(x=287, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2018",size=6)+ geom_text(x=339, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2019",size=6)+ geom_text(x=391, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2020",size=6)+

geom_text(x=443, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
geom_text(x=495, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+
geom_text(x=547, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2023",size=6)+
geom_text(x=440, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
geom_text(x=492, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+
```
          geom_text(x=base::min(es_deces_standard_pays_semaine$numSemaineDepuis2013+26),
                    y=(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020_15_24[1]+
                         es_deces_standard_pays_semaine$deces_standardises_si_pop_2020_25_49[1]+
```
@@ -1278,9 +1270,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s geom_text(x=287, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2018",size=6)+ geom_text(x=339, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2019",size=6)+ geom_text(x=391, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2020",size=6)+
geom_text(x=443, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
geom_text(x=495, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+
geom_text(x=547, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2023",size=6)+
geom_text(x=440, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
geom_text(x=492, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+
```
    geom_text(x=base::min(es_deces_standard_pays_semaine$numSemaineDepuis2013+26),
              y=(
```
@@ -2042,7 +2033,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema paste0( "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_15_24_2021)," (",floor(part_surmortalite_15_24_2021),"%)",
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_15_24_2020), " même période en 2019 : ", @@ -2356,7 +2347,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_25_49_2021), " (",floor(part_surmortalite_25_49_2021),"%)",
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_25_49_2020), " même période en 2019 : ", @@ -2605,7 +2596,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_50_59_2021), " (",floor(part_surmortalite_50_59_2021),"%)",
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_50_59_2020), " même période en 2019 : ", @@ -2856,7 +2847,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_60_69_2021), " (",floor(part_surmortalite_60_69_2021),"%)",
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_60_69_2020), " même période en 2019 : ", @@ -3105,7 +3096,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_70_79_2021), " (",floor(part_surmortalite_70_79_2021),"%)",
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_70_79_2020), " même période en 2019 : ", @@ -3328,7 +3319,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema geom_text(x=floor(date_debut_2021_ge80), y=base::max(essai_court$diff_deces_tot_predit_stand_ge80), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021), " (",floor(part_surmortalite_ge80_2021),"%)",
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_ge80_2020), " même période en 2019 : ",floor(surmortalite_ge80_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ @@ -4366,7 +4357,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa paste0( "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_15_24_2021)," (",floor(part_surmortalite_15_24_2021),"%)",
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_15_24_2020), " même période en 2019 : ", @@ -4681,7 +4672,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_25_49_2021), " (",floor(part_surmortalite_25_49_2021),"%)",
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_25_49_2020), " même période en 2019 : ", @@ -4931,7 +4922,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_50_59_2021), " (",floor(part_surmortalite_50_59_2021),"%)",
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_50_59_2020), " même période en 2019 : ", @@ -5183,7 +5174,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_60_69_2021), " (",floor(part_surmortalite_60_69_2021),"%)",
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_60_69_2020), " même période en 2019 : ", @@ -5433,7 +5424,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_70_79_2021), " (",floor(part_surmortalite_70_79_2021),"%)",
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_70_79_2020), " même période en 2019 : ", @@ -5656,7 +5647,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa geom_text(x=floor(date_debut_2021_ge80), y=base::max(essai_court$diff_ge80), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021), " (",floor(part_surmortalite_ge80_2021),"%)",
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_ge80_2020), " même période en 2019 : ",floor(surmortalite_ge80_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ @@ -7041,7 +7032,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standardpays paste0( "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_15_24_2021)," (",floor(part_surmortalite_15_24_2021),"%)",
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_15_24_2020), " même période en 2019 : ", @@ -7344,7 +7335,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standardpays "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_25_49_2021), " (",floor(part_surmortalite_25_49_2021),"%)",
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_25_49_2020), " même période en 2019 : ", @@ -7583,7 +7574,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standardpays "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_50_59_2021), " (",floor(part_surmortalite_50_59_2021),"%)",
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_50_59_2020), " même période en 2019 : ", @@ -7824,7 +7815,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standardpays "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_60_69_2021), " (",floor(part_surmortalite_60_69_2021),"%)",
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_60_69_2020), " même période en 2019 : ", @@ -8063,7 +8054,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standardpays "surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_70_79_2021), " (",floor(part_surmortalite_70_79_2021),"%)",
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ", floor(surmortalite_70_79_2020), " même période en 2019 : ", @@ -8278,7 +8269,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standardpays geom_text(x=floor(date_debut_2021_ge80), y=base::max(essai_court$diff_ge80), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021), " (",floor(part_surmortalite_ge80_2021),"%)",
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_ge80_2020), " même période en 2019 : ",floor(surmortalite_ge80_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ @@ -8994,7 +8985,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand geom_text(x=194, y=base::min(essai_nouv$diff_15_24), label="2020")+ geom_text(x=220, y=base::min(essai_nouv$diff_15_24), label="2021")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_15_24_2021),
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_nouv$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_15_24_2021/base::max(essai_nouv$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_15_24_2020), " même période en 2019 : ",floor(surmortalite_15_24_2019)))+ ylab("Différence décès constatés \n décès attendus")+ @@ -9101,7 +9092,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand geom_vline(xintercept = floor(date_debut_2021_25_49/2), colour="#336666", linetype = "longdash")+ geom_text(x=floor(date_debut_2021_25_49/2), y=base::max(essai_nouv$diff_25_49), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_25_49_2021),
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_nouv$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_25_49_2021/base::max(essai_nouv$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_25_49_2020), " même période en 2019 : ",floor(surmortalite_25_49_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ @@ -9201,7 +9192,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand geom_vline(xintercept = floor(date_debut_2021_50_59/2), colour="#336666", linetype = "longdash")+ geom_text(x=floor(date_debut_2021_50_59/2), y=base::max(essai_nouv$diff_50_59), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_50_59_2021),
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_nouv$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_50_59_2021/base::max(essai_nouv$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_50_59_2020), " même période en 2019 : ",floor(surmortalite_50_59_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ @@ -9303,7 +9294,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand geom_vline(xintercept = floor(date_debut_2021_60_69/2), colour="#336666", linetype = "longdash")+ geom_text(x=floor(date_debut_2021_60_69/2), y=base::max(essai_nouv$diff_60_69), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_60_69_2021),
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_nouv$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_60_69_2021/base::max(essai_nouv$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_60_69_2020), " même période en 2019 : ",floor(surmortalite_60_69_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ @@ -9407,7 +9398,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand geom_text(x=floor(date_debut_2021_70_79/2), y=base::max(essai_nouv$diff_70_79), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ", floor(surmortalite_70_79_2021),
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_nouv$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_70_79_2021/base::max(essai_nouv$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_70_79_2020), " même période en 2019 : ",floor(surmortalite_70_79_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ @@ -9509,7 +9500,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand geom_vline(xintercept = floor(date_debut_2021_ge80/2), colour="#336666", linetype = "longdash")+ geom_text(x=floor(date_debut_2021_ge80/2), y=base::max(essai_nouv$diff_ge80), label="début vaccination", color="#336666")+ xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021),
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_nouv$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
" (soit ",floor(surmortalite_ge80_2021/base::max(essai_nouv$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)", " \n même période en 2020 : ",floor(surmortalite_ge80_2020), " même période en 2019 : ",floor(surmortalite_ge80_2019)))+ ylab("Différence entre décès constatés \n et décès attendus")+ diff --git a/src/files/files.R b/src/files/files.R index 1acd893..9c0b30e 100644 --- a/src/files/files.R +++ b/src/files/files.R @@ -149,12 +149,10 @@ a__f_downloadIfNeeded <- function(sourceType = K_SOURCE_TYPE_CSV,
```
                                downloadedDatas <- downloadedDatas %>%
                                                # Reordonner les colonnes
```
select(geo, sex, age, TIME_PERIOD, everything()) %>%
select(geo, sex, age, time, everything()) %>%

Trier les lignes selon les colonnes
arrange(geo, sex, age, TIME_PERIOD)
arrange(geo, sex, age, time)
downloadedDatas <- downloadedDatas %>% rename(time=TIME_PERIOD)

                                downloaded = TRUE

                        } else {

I have successfully resolved absolutely all dependencies required to execute the very little code to download all eurostat data. That's my commit commithash.

Now when I execute the code, @decoderleco here is the error I get :

Now yesterday Pierre gave us one indication that definitely will help solving the error:

export COMMIT_WITH_FIX="a9326ae9f1ca0641cc3d5cc8d17ce698cc87893d"

export COMMIT_BEFORE_FIX="527682e60da1a0eaa019842c7e47b403a87b5da8"

git clone git@github.com:decoderleco/deces_europe ./pierre_c_pas_bien_10_pompes_pr_avoir_commit_sur_main/

cd ./pierre_c_pas_bien_10_pompes_pr_avoir_commit_sur_main/

# git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX}
git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX} --name-only

And here is the output:

$ git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX} --name-only
010_eurostat_creation_tables_deces_europe.R
030_eurostat_analyses_deces_std_hebdo.R
src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R
src/files/files.R

Le détail de changement dans les fichiers:

$ git diff ${COMMIT_WITH_FIX} ${COMMIT_BEFORE_FIX}
diff --git a/010_eurostat_creation_tables_deces_europe.R b/010_eurostat_creation_tables_deces_europe.R
index afb236a..80015a3 100644
--- a/010_eurostat_creation_tables_deces_europe.R
+++ b/010_eurostat_creation_tables_deces_europe.R
@@ -90,10 +90,10 @@ a__original_es_proj <- read.csv("data/csv/proj_19np__custom_2224172_linear.csv")
 # Initialiser avec les données d'origine d'EuroStat
 es_pjan <- a__original_es_pjan_le2020

-# Renommer la colonne "values" en "population" et supprimer la colonne "unit" et freq
+# Renommer la colonne "values" en "population" et supprimer la colonne "unit"
 es_pjan <- es_pjan %>%
   dplyr::rename(population = values) %>%
-  select(-unit,-freq)
+  select(-unit)

 # Filtrer :
 #  les totaux : sexe T (T = M+F) et age
@@ -215,7 +215,7 @@ b__es_deces_et_pop_par_annee <- a__original_es_deces_annuel_le2020
 # Filtrer age
 b__es_deces_et_pop_par_annee <- b__es_deces_et_pop_par_annee %>%
   dplyr::rename(deces=values) %>%
-               select(-unit,-freq) %>%
+               select(-unit) %>%
                filter( sex != "T",
                                age != "TOTAL",
                                age != "UNK")
diff --git a/030_eurostat_analyses_deces_std_hebdo.R b/030_eurostat_analyses_deces_std_hebdo.R
index db82542..0bdfa09 100644
--- a/030_eurostat_analyses_deces_std_hebdo.R
+++ b/030_eurostat_analyses_deces_std_hebdo.R
@@ -224,7 +224,7 @@ g<-ggplot(data = france_suede_portugal) +
   geom_area(aes(x = numSemaineDepuis2013,
                 y = deces_france),
             color="#CC0000",fill="#CC0000",size=1,alpha=1/2) +
-  geom_vline(xintercept = seq(from=0, to=550, by = 52),linetype = "dashed",color="steelblue")+
+  geom_vline(xintercept = seq(from=0, to=500, by = 52),linetype = "dashed",color="steelblue")+
   theme(axis.title.x = element_blank(),
         axis.text.x = element_blank(),
         axis.title.y = element_text(color="#000000", size=20 ),
@@ -241,7 +241,6 @@ g<-ggplot(data = france_suede_portugal) +
   geom_text(x=391, y=1000, label="2020",size=10)+
   geom_text(x=443, y=1000, label="2021",size=10)+
   geom_text(x=495, y=1000, label="2022",size=10)+
-  geom_text(x=547, y=1000, label="2023",size=10)+
   annotate(geom = "text", x = 50, y = 30000, label = "Portugal", color = "#006600",
            angle = 0, size = 15)+
   annotate(geom = "text", x = 50, y = 28000, label = "Suède", color = "#0066CC",
@@ -267,7 +266,7 @@ g<-ggplot(data = france_suede_portugal) +
   geom_area(aes(x = numSemaineDepuis2013,
                 y = deces_france),
             color="#000000",fill="#000000",size=1,alpha=1/2) +
-  geom_vline(xintercept = seq(from=0, to=550, by = 52),linetype = "dashed",color="steelblue")+
+  geom_vline(xintercept = seq(from=0, to=500, by = 52),linetype = "dashed",color="steelblue")+
   theme(axis.title.x = element_blank(),
         axis.text.x = element_blank(),
         axis.title.y = element_text(color="#000000", size=20 ),
@@ -282,9 +281,7 @@ g<-ggplot(data = france_suede_portugal) +
   geom_text(x=287, y=1000, label="2018",size=10)+
   geom_text(x=339, y=1000, label="2019",size=10)+
   geom_text(x=391, y=1000, label="2020",size=10)+
-  geom_text(x=443, y=1000, label="2021",size=10)+
-  geom_text(x=495, y=1000, label="2022",size=10)+
-  geom_text(x=547, y=1000, label="2023",size=10)+
+  geom_text(x=440, y=1000, label="2021",size=10)+
   annotate(geom = "text", x = 50, y = 30000, label = "Portugal", color = "#999999",
            angle = 0, size = 15)+
   annotate(geom = "text", x = 50, y = 28000, label = "Suède", color = "#666666",
diff --git a/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R b/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R
index a4f32ff..23af0dc 100644
--- a/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R
+++ b/src/analyses/world/eu/es/deces/hebdo/es_deces_hebdo_std.R
@@ -214,9 +214,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
        text(287, 0, "2018", cex=1.2)
        text(339, 0, "2019", cex=1.2)
        text(391, 0, "2020", cex=1.2)
-       text(443, 0, "2021", cex=1.2)
-       text(495, 0, "2022", cex=1.2)
-       text(547, 0, "2023", cex=1.2)
+       text(440, 0, "2021", cex=1.2)
+       text(492, 0, "2022", cex=1.2)

        #text(26, 22000, nomPays, cex=1.2)

@@ -353,9 +352,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
                text(287, base::min(essai$deces_standardises_si_pop_2020_15_24), "2018", cex=1.2)
                text(339, base::min(essai$deces_standardises_si_pop_2020_15_24), "2019", cex=1.2)
                text(391, base::min(essai$deces_standardises_si_pop_2020_15_24), "2020", cex=1.2)
-               text(443, base::min(essai$deces_standardises_si_pop_2020_15_24), "2021", cex=1.2)
-               text(495, base::min(essai$deces_standardises_si_pop_2020_15_24), "2022", cex=1.2)
-               text(547, base::min(essai$deces_standardises_si_pop_2020_15_24), "2023", cex=1.2)
+               text(440, base::min(essai$deces_standardises_si_pop_2020_15_24), "2021", cex=1.2)
+               text(492, base::min(essai$deces_standardises_si_pop_2020_15_24), "2022", cex=1.2)

                # Superposer la moyenne mobile
                par(new=T)
@@ -486,9 +484,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
                text(287, base::min(essai$deces_standardises_si_pop_2020_25_49), "2018", cex=1.2)
                text(339, base::min(essai$deces_standardises_si_pop_2020_25_49), "2019", cex=1.2)
                text(391, base::min(essai$deces_standardises_si_pop_2020_25_49), "2020", cex=1.2)
-               text(443, base::min(essai$deces_standardises_si_pop_2020_25_49), "2021", cex=1.2)
-               text(495, base::min(essai$deces_standardises_si_pop_2020_25_49), "2022", cex=1.2)
-               text(547, base::min(essai$deces_standardises_si_pop_2020_25_49), "2023", cex=1.2)
+               text(440, base::min(essai$deces_standardises_si_pop_2020_25_49), "2021", cex=1.2)
+               text(492, base::min(essai$deces_standardises_si_pop_2020_25_49), "2022", cex=1.2)

                #text(26, 22000, nomPays, cex=1.2)

@@ -622,9 +619,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
        text(287, base::min(essai$deces_standardises_si_pop_2020_50_59), "2018", cex=1.2)
        text(339, base::min(essai$deces_standardises_si_pop_2020_50_59), "2019", cex=1.2)
        text(391, base::min(essai$deces_standardises_si_pop_2020_50_59), "2020", cex=1.2)
-       text(443, base::min(essai$deces_standardises_si_pop_2020_50_59), "2021", cex=1.2)
-       text(495, base::min(essai$deces_standardises_si_pop_2020_50_59), "2022", cex=1.2)
-       text(547, base::min(essai$deces_standardises_si_pop_2020_50_59), "2023", cex=1.2)
+       text(440, base::min(essai$deces_standardises_si_pop_2020_50_59), "2021", cex=1.2)
+       text(492, base::min(essai$deces_standardises_si_pop_2020_50_59), "2022", cex=1.2)

        #text(26, 22000, nomPays, cex=1.2)

@@ -757,9 +753,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
        text(287, base::min(essai$deces_standardises_si_pop_2020_60_69), "2018", cex=1.2)
        text(339, base::min(essai$deces_standardises_si_pop_2020_60_69), "2019", cex=1.2)
        text(391, base::min(essai$deces_standardises_si_pop_2020_60_69), "2020", cex=1.2)
-       text(443, base::min(essai$deces_standardises_si_pop_2020_60_69), "2021", cex=1.2)
-       text(495, base::min(essai$deces_standardises_si_pop_2020_60_69), "2022", cex=1.2)
-       text(547, base::min(essai$deces_standardises_si_pop_2020_60_69), "2023", cex=1.2)
+       text(440, base::min(essai$deces_standardises_si_pop_2020_60_69), "2021", cex=1.2)
+       text(492, base::min(essai$deces_standardises_si_pop_2020_60_69), "2022", cex=1.2)

        #text(26, 22000, nomPays, cex=1.2)

@@ -892,9 +887,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
        text(287, base::min(essai$deces_standardises_si_pop_2020_70_79), "2018", cex=1.2)
        text(339, base::min(essai$deces_standardises_si_pop_2020_70_79), "2019", cex=1.2)
        text(391, base::min(essai$deces_standardises_si_pop_2020_70_79), "2020", cex=1.2)
-       text(443, base::min(essai$deces_standardises_si_pop_2020_70_79), "2021", cex=1.2)
-       text(495, base::min(essai$deces_standardises_si_pop_2020_70_79), "2022", cex=1.2)
-       text(547, base::min(essai$deces_standardises_si_pop_2020_70_79), "2023", cex=1.2)
+       text(440, base::min(essai$deces_standardises_si_pop_2020_70_79), "2021", cex=1.2)
+       text(492, base::min(essai$deces_standardises_si_pop_2020_70_79), "2022", cex=1.2)

        #text(26, 22000, nomPays, cex=1.2)

@@ -1029,9 +1023,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
        text(287, base::min(essai$deces_standardises_si_pop_2020_ge80), "2018", cex=1.2)
        text(339, base::min(essai$deces_standardises_si_pop_2020_ge80), "2019", cex=1.2)
        text(391, base::min(essai$deces_standardises_si_pop_2020_ge80), "2020", cex=1.2)
-       text(443, base::min(essai$deces_standardises_si_pop_2020_ge80), "2021", cex=1.2)
-       text(495, base::min(essai$deces_standardises_si_pop_2020_ge80), "2022", cex=1.2)
-       text(547, base::min(essai$deces_standardises_si_pop_2020_ge80), "2023", cex=1.2)
+       text(440, base::min(essai$deces_standardises_si_pop_2020_ge80), "2021", cex=1.2)
+       text(492, base::min(essai$deces_standardises_si_pop_2020_ge80), "2022", cex=1.2)

        #text(26, 22000, nomPays, cex=1.2)

@@ -1174,10 +1167,9 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
                  geom_text(x=287, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2018",size=6)+
                  geom_text(x=339, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2019",size=6)+
                  geom_text(x=391, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2020",size=6)+
-                 geom_text(x=443, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
-                 geom_text(x=495, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+
-                 geom_text(x=547, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2023",size=6)+
-
+                 geom_text(x=440, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
+                 geom_text(x=492, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+
+
                  geom_text(x=base::min(es_deces_standard_pays_semaine$numSemaineDepuis2013+26),
                            y=(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020_15_24[1]+
                                 es_deces_standard_pays_semaine$deces_standardises_si_pop_2020_25_49[1]+
@@ -1278,9 +1270,8 @@ a__f_plot_es_deces_hebdo_std_moyenne_mobile <- function(es_deces_standard_pays_s
            geom_text(x=287, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2018",size=6)+
            geom_text(x=339, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2019",size=6)+
            geom_text(x=391, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2020",size=6)+
-           geom_text(x=443, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
-           geom_text(x=495, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+
-           geom_text(x=547, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2023",size=6)+
+           geom_text(x=440, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2021",size=6)+
+           geom_text(x=492, y=base::max(es_deces_standard_pays_semaine$deces_standardises_si_pop_2020), label="2022",size=6)+

            geom_text(x=base::min(es_deces_standard_pays_semaine$numSemaineDepuis2013+26),
                      y=(
@@ -2042,7 +2033,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema
                                                        paste0(
                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                        floor(surmortalite_15_24_2021),"  (",floor(part_surmortalite_15_24_2021),"%)",
-                                                                       "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                       "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                        "  \n même période en 2020 : ",
                                                                        floor(surmortalite_15_24_2020),
                                                                        "           même période en 2019 : ",
@@ -2356,7 +2347,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema
                                                                "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                floor(surmortalite_25_49_2021),
                                                                "  (",floor(part_surmortalite_25_49_2021),"%)",
-                                                               "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",
                                                                floor(surmortalite_25_49_2020),
                                                                "           même période en 2019 : ",
@@ -2605,7 +2596,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema
                                                                "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                floor(surmortalite_50_59_2021),
                                                                "  (",floor(part_surmortalite_50_59_2021),"%)",
-                                                               "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",
                                                                floor(surmortalite_50_59_2020),
                                                                "           même période en 2019 : ",
@@ -2856,7 +2847,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema
                                                                "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                floor(surmortalite_60_69_2021),
                                                                "  (",floor(part_surmortalite_60_69_2021),"%)",
-                                                               "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",
                                                                floor(surmortalite_60_69_2020),
                                                                "           même période en 2019 : ",
@@ -3105,7 +3096,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema
                                                                "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                floor(surmortalite_70_79_2021),
                                                                "  (",floor(part_surmortalite_70_79_2021),"%)",
-                                                               "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",
                                                                floor(surmortalite_70_79_2020),
                                                                "           même période en 2019 : ",
@@ -3328,7 +3319,7 @@ a__f_plot_es_deces_hebdo_std_vaccination <- function(es_deces_standard_pays_sema
                                geom_text(x=floor(date_debut_2021_ge80), y=base::max(essai_court$diff_deces_tot_predit_stand_ge80), label="début vaccination", color="#336666")+
                                xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021),
                                                                "  (",floor(part_surmortalite_ge80_2021),"%)",
-                                                               "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",floor(surmortalite_ge80_2020),
                                                                "           même période en 2019 : ",floor(surmortalite_ge80_2019)))+
                                ylab("Différence entre décès constatés \n et décès attendus")+
@@ -4366,7 +4357,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa
                                                                                paste0(
                                                                                                "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                                floor(surmortalite_15_24_2021),"  (",floor(part_surmortalite_15_24_2021),"%)",
-                                                                                               "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                               "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                                "  \n même période en 2020 : ",
                                                                                                floor(surmortalite_15_24_2020),
                                                                                                "           même période en 2019 : ",
@@ -4681,7 +4672,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_25_49_2021),
                                                                                        "  (",floor(part_surmortalite_25_49_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_25_49_2020),
                                                                                        "           même période en 2019 : ",
@@ -4931,7 +4922,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_50_59_2021),
                                                                                        "  (",floor(part_surmortalite_50_59_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_50_59_2020),
                                                                                        "           même période en 2019 : ",
@@ -5183,7 +5174,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_60_69_2021),
                                                                                        "  (",floor(part_surmortalite_60_69_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_60_69_2020),
                                                                                        "           même période en 2019 : ",
@@ -5433,7 +5424,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_70_79_2021),
                                                                                        "  (",floor(part_surmortalite_70_79_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_70_79_2020),
                                                                                        "           même période en 2019 : ",
@@ -5656,7 +5647,7 @@ a__f_plot_es_deces_hebdo_std_interp_vaccination <- function(es_deces_standard_pa
                                                        geom_text(x=floor(date_debut_2021_ge80), y=base::max(essai_court$diff_ge80), label="début vaccination", color="#336666")+
                                                        xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021),
                                                                                        "  (",floor(part_surmortalite_ge80_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",floor(surmortalite_ge80_2020),
                                                                                        "           même période en 2019 : ",floor(surmortalite_ge80_2019)))+
                                                        ylab("Différence entre décès constatés \n et décès attendus")+
@@ -7041,7 +7032,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standard_pays_
                                                                                paste0(
                                                                                                "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                                floor(surmortalite_15_24_2021),"  (",floor(part_surmortalite_15_24_2021),"%)",
-                                                                                               "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                               "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_court$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                                "  \n même période en 2020 : ",
                                                                                                floor(surmortalite_15_24_2020),
                                                                                                "           même période en 2019 : ",
@@ -7344,7 +7335,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standard_pays_
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_25_49_2021),
                                                                                        "  (",floor(part_surmortalite_25_49_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_court$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_25_49_2020),
                                                                                        "           même période en 2019 : ",
@@ -7583,7 +7574,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standard_pays_
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_50_59_2021),
                                                                                        "  (",floor(part_surmortalite_50_59_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_court$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_50_59_2020),
                                                                                        "           même période en 2019 : ",
@@ -7824,7 +7815,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standard_pays_
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_60_69_2021),
                                                                                        "  (",floor(part_surmortalite_60_69_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_court$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_60_69_2020),
                                                                                        "           même période en 2019 : ",
@@ -8063,7 +8054,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standard_pays_
                                                                                        "surmortalité depuis le début de la vaccination en 2021 : ",
                                                                                        floor(surmortalite_70_79_2021),
                                                                                        "  (",floor(part_surmortalite_70_79_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_court$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",
                                                                                        floor(surmortalite_70_79_2020),
                                                                                        "           même période en 2019 : ",
@@ -8278,7 +8269,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination <- function(es_deces_standard_pays_
                                                        geom_text(x=floor(date_debut_2021_ge80), y=base::max(essai_court$diff_ge80), label="début vaccination", color="#336666")+
                                                        xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021),
                                                                                        "  (",floor(part_surmortalite_ge80_2021),"%)",
-                                                                                       "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                                       "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_court$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                                        "  \n même période en 2020 : ",floor(surmortalite_ge80_2020),
                                                                                        "           même période en 2019 : ",floor(surmortalite_ge80_2019)))+
                                                        ylab("Différence entre décès constatés \n et décès attendus")+
@@ -8994,7 +8985,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand
                                        geom_text(x=194, y=base::min(essai_nouv$diff_15_24), label="2020")+
                                        geom_text(x=220, y=base::min(essai_nouv$diff_15_24), label="2021")+
                                        xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_15_24_2021),
-                                                                       "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_nouv$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                                       "          (soit ",floor(surmortalite_15_24_2021/base::max(essai_nouv$cumul_15_24_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                        "  \n même période en 2020 : ",floor(surmortalite_15_24_2020),
                                                                        "           même période en 2019 : ",floor(surmortalite_15_24_2019)))+
                                        ylab("Différence décès constatés \n décès attendus")+
@@ -9101,7 +9092,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand
                                geom_vline(xintercept = floor(date_debut_2021_25_49/2), colour="#336666", linetype = "longdash")+
                                geom_text(x=floor(date_debut_2021_25_49/2), y=base::max(essai_nouv$diff_25_49), label="début vaccination", color="#336666")+
                                xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_25_49_2021),
-                                                               "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_nouv$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_25_49_2021/base::max(essai_nouv$cumul_25_49_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",floor(surmortalite_25_49_2020),
                                                                "           même période en 2019 : ",floor(surmortalite_25_49_2019)))+
                                ylab("Différence entre décès constatés \n et décès attendus")+
@@ -9201,7 +9192,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand
                                geom_vline(xintercept = floor(date_debut_2021_50_59/2), colour="#336666", linetype = "longdash")+
                                geom_text(x=floor(date_debut_2021_50_59/2), y=base::max(essai_nouv$diff_50_59), label="début vaccination", color="#336666")+
                                xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_50_59_2021),
-                                                               "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_nouv$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_50_59_2021/base::max(essai_nouv$cumul_50_59_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",floor(surmortalite_50_59_2020),
                                                                "           même période en 2019 : ",floor(surmortalite_50_59_2019)))+
                                ylab("Différence entre décès constatés \n et décès attendus")+
@@ -9303,7 +9294,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand
                                geom_vline(xintercept = floor(date_debut_2021_60_69/2), colour="#336666", linetype = "longdash")+
                                geom_text(x=floor(date_debut_2021_60_69/2), y=base::max(essai_nouv$diff_60_69), label="début vaccination", color="#336666")+
                                xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_60_69_2021),
-                                                               "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_nouv$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_60_69_2021/base::max(essai_nouv$cumul_60_69_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",floor(surmortalite_60_69_2020),
                                                                "           même période en 2019 : ",floor(surmortalite_60_69_2019)))+
                                ylab("Différence entre décès constatés \n et décès attendus")+
@@ -9407,7 +9398,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand
                                geom_text(x=floor(date_debut_2021_70_79/2), y=base::max(essai_nouv$diff_70_79), label="début vaccination", color="#336666")+
                                xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",
                                                                floor(surmortalite_70_79_2021),
-                                                               "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_nouv$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_70_79_2021/base::max(essai_nouv$cumul_70_79_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",floor(surmortalite_70_79_2020),
                                                                "           même période en 2019 : ",floor(surmortalite_70_79_2019)))+
                                ylab("Différence entre décès constatés \n et décès attendus")+
@@ -9509,7 +9500,7 @@ a__f_plot_es_deces_hebdo_compare_vaccination_regroupe <- function(es_deces_stand
                                geom_vline(xintercept = floor(date_debut_2021_ge80/2), colour="#336666", linetype = "longdash")+
                                geom_text(x=floor(date_debut_2021_ge80/2), y=base::max(essai_nouv$diff_ge80), label="début vaccination", color="#336666")+
                                xlab(paste0("surmortalité depuis le début de la vaccination en 2021 : ",floor(surmortalite_ge80_2021),
-                                                               "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_nouv$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 doubles doses)",
+                                                               "          (soit ",floor(surmortalite_ge80_2021/base::max(essai_nouv$cumul_ge80_dose2,na.rm=TRUE)*100000)," pour 100 000 double dose)",
                                                                "  \n même période en 2020 : ",floor(surmortalite_ge80_2020),
                                                                "           même période en 2019 : ",floor(surmortalite_ge80_2019)))+
                                ylab("Différence entre décès constatés \n et décès attendus")+
diff --git a/src/files/files.R b/src/files/files.R
index 1acd893..9c0b30e 100644
--- a/src/files/files.R
+++ b/src/files/files.R
@@ -149,12 +149,10 @@ a__f_downloadIfNeeded <- function(sourceType = K_SOURCE_TYPE_CSV,

                                        downloadedDatas <- downloadedDatas %>%
                                                        # Reordonner les colonnes
-                                                       select(geo, sex, age, TIME_PERIOD, everything()) %>%
+                                                       select(geo, sex, age, time, everything()) %>%
                                                        # Trier les lignes selon les colonnes
-                                                       arrange(geo, sex, age, TIME_PERIOD)
+                                                       arrange(geo, sex, age, time)

-                                       downloadedDatas <- downloadedDatas %>% rename(time=TIME_PERIOD)
-
                                        downloaded = TRUE

                                } else {

Après ces fix appliqués, je constate:

J'ai un succès quant à juste exécuter le code nécessaire pour télécharger les données eurostat: pour les lignes 1 à 83 du fichier 010_eurostat_creation_tables_deces_europe.R
28 packages `R en dépendances directe pour juste télécharger les données eurostat: ça, il va falloir modulariser ça, c'est beaucoup trop de dépendances pour faire une si petite chose
je note, mais c'est à re-valider pour la reproductibilité, avec un environnement vierge neuf: je n'ai toujours pas eu besoin de devtools, pour l'instant.
j'ai "réparé" l'installation d'à peu près 50% des packages R de 000_install_libraries.R

note: https://github.com/decoderleco/deces_europe/blob/a9326ae9f1ca0641cc3d5cc8d17ce698cc87893d/000_install_libraries.R#L41

cette dépendance, le package R - Rtools, est spécifique windows: il doit être retiré donc, pour le notebook Jupyter

Je note une simple remarque: il existe très peu si ce n'est aucun, gros projet R qui donne un standard de projet R

decoder-leco / decoderleco_deces_europe_reloaded