FIELDimageR: A R package to analyze orthomosaic images from agricultural field trials. This package is a compilation of functions to analyze pos-mosaicking images from research fields, and allows to: crop the image; remove soil effect; build vegetation indices; rotate the image; build the plot shapefile; extract information for each plot; and evaluate stand count, canopy percentage, and plant height.
GNU General Public License v2.0
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Problem to install FIELDImageR in costum dockerfile #41
Dear Authors,
First of all thanks to make pubblic availble this package case is really usefull.
This isssue is related to #32
I would like to add the package to a docker container but i am getting a lot of problem
This is my dockerfile.
FROM rocker/verse:4.2.0
RUN groupadd -g 61000 docker
RUN useradd -g 61000 -l -M -s /bin/false -u 61000 docker
RUN apt-get update && apt-get install -y curl gdal-bin git-core imagemagick libcurl4-openssl-dev libfontconfig1-dev libgdal-dev libgeos-dev libgeos++-dev libgit2-dev libicu-dev libjq-dev libpng-dev libpq-dev libproj-dev libprotobuf-dev libsasl2-dev libssl-dev libudunits2-dev libsqlite3-dev libv8-dev libxml2-dev make pandoc pandoc-citeproc protobuf-compiler libprotoc-dev zlib1g-dev libfftw3-dev && rm -rf /var/lib/apt/lists/*
RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" >> /usr/local/lib/R/etc/Rprofile.site
RUN curl -LO https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb && \
apt-get update -qq && \
apt-get -y install \
./google-chrome-stable_current_amd64.deb && \
rm google-chrome-stable_current_amd64.deb
RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
RUN R -e 'install.packages("remotes")'
RUN Rscript -e 'remotes::install_version("htmltools",upgrade="never", version = "0.5.3")'
RUN Rscript -e 'remotes::install_version("stringr",upgrade="never", version = "1.5.0")'
RUN Rscript -e 'remotes::install_version("processx",upgrade="never", version = "3.8.0")'
RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.18")'
RUN Rscript -e 'remotes::install_version("knitr",upgrade="never", version = "1.41")'
RUN Rscript -e 'remotes::install_version("glue",upgrade="never", version = "1.6.2")'
RUN Rscript -e 'remotes::install_version("data.table",upgrade="never", version = "1.14.6")'
RUN Rscript -e 'remotes::install_version("DBI",upgrade="never", version = "1.1.3")'
RUN Rscript -e 'remotes::install_version("lubridate",upgrade="never", version = "1.9.0")'
RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.4.0")'
RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.7.3")'
RUN Rscript -e 'remotes::install_version("e1071",upgrade="never", version = "1.7-12")'
RUN Rscript -e 'remotes::install_version("sp",upgrade="never", version = "1.5-0")'
RUN Rscript -e 'remotes::install_version("sf",upgrade="never", version = "1.0-9")'
RUN Rscript -e 'remotes::install_version("raster",upgrade="never", version = "3.6-11")'
RUN Rscript -e 'remotes::install_version("forecast",upgrade="never", version = "8.19")'
RUN Rscript -e 'remotes::install_version("plotly",upgrade="never", version = "4.10.1")'
RUN Rscript -e 'remotes::install_version("viridis",upgrade="never", version = "0.6.2")'
RUN Rscript -e 'remotes::install_version("leaflet",upgrade="never", version = "2.1.1")'
RUN Rscript -e 'remotes::install_version("xml2",upgrade="never", version = "1.3.3")'
RUN Rscript -e 'remotes::install_version("zip",upgrade="never", version = "2.2.2")'
RUN Rscript -e 'remotes::install_version("pkgload",upgrade="never", version = "1.3.2")'
RUN Rscript -e 'remotes::install_version("plotrix",upgrade="never", version = "3.8-2")'
RUN Rscript -e 'remotes::install_version("rvest",upgrade="never", version = "1.0.3")'
RUN Rscript -e 'remotes::install_version("readxl",upgrade="never", version = "1.4.1")'
RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.26")'
RUN Rscript -e 'remotes::install_version("rgdal",upgrade="never", version = "1.6-3")'
RUN Rscript -e 'remotes::install_version("rgeos",upgrade="never", version = "0.6-1")'
RUN Rscript -e 'remotes::install_version("reshape",upgrade="never", version = "0.8.9")'
RUN Rscript -e 'remotes::install_version("gstat",upgrade="never", version = "2.1-0")'
RUN Rscript -e 'remotes::install_version("gt",upgrade="never", version = "0.8.0")'
RUN Rscript -e 'remotes::install_version("timetk",upgrade="never", version = "2.8.2")'
RUN Rscript -e 'remotes::install_version("mapview",upgrade="never", version = "2.11.0")'
RUN Rscript -e 'remotes::install_version("leaflet.extras",upgrade="never", version = "1.0.0")'
RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.1")'
RUN Rscript -e 'remotes::install_version("attempt",upgrade="never", version = "0.3.1")'
RUN Rscript -e 'remotes::install_version("waiter",upgrade="never", version = "0.2.5")'
RUN Rscript -e 'remotes::install_version("tidyverse",upgrade="never", version = "1.3.2")'
RUN Rscript -e 'remotes::install_version("tidymodels",upgrade="never", version = "1.0.0")'
RUN Rscript -e 'remotes::install_version("SpatialPosition",upgrade="never", version = "2.1.1")'
RUN Rscript -e 'remotes::install_version("shinymanager",upgrade="never", version = "1.0.410")'
RUN Rscript -e 'remotes::install_version("RStoolbox",upgrade="never", version = "0.3.0")'
RUN Rscript -e 'remotes::install_version("rpostgis",upgrade="never", version = "1.4.3")'
RUN Rscript -e 'remotes::install_version("testthat",upgrade="never", version = "3.1.5")'
RUN Rscript -e 'remotes::install_version("spelling",upgrade="never", version = "2.2")'
RUN Rscript -e 'remotes::install_version("ranger",upgrade="never", version = "0.14.1")'
RUN Rscript -e 'remotes::install_version("collapse",upgrade="never", version = "1.8.9")'
RUN Rscript -e 'remotes::install_version("cubeview",upgrade="never", version = "0.2.0")'
RUN Rscript -e 'remotes::install_version("echarts4r",upgrade="never", version = "0.4.4")'
RUN Rscript -e 'remotes::install_version("automap",upgrade="never", version = "1.0-16")'
RUN Rscript -e 'remotes::install_version("writexl",upgrade="never", version = "1.4.1")'
RUN Rscript -e 'remotes::install_version("weathermetrics",upgrade="never", version = "1.2.2")'
RUN Rscript -e 'remotes::install_version("SPEI",upgrade="never", version = "1.7")'
RUN Rscript -e 'remotes::install_version("spdplyr",upgrade="never", version = "0.4.0")'
RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.7.5")'
RUN Rscript -e 'remotes::install_version("shinyvalidate",upgrade="never", version = "0.1.2")'
RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.0.0")'
RUN Rscript -e 'remotes::install_version("shinyalert",upgrade="never", version = "3.0.0")'
RUN Rscript -e 'remotes::install_version("sever",upgrade="never", version = "0.0.7")'
RUN Rscript -e 'remotes::install_version("rtsdata",upgrade="never", version = "0.1.3")'
RUN Rscript -e 'remotes::install_version("RPostgres",upgrade="never", version = "1.4.4")'
RUN Rscript -e 'remotes::install_version("RMySQL",upgrade="never", version = "0.10.24")'
RUN Rscript -e 'remotes::install_version("randomForest",upgrade="never", version = "4.7-1.1")'
RUN Rscript -e 'remotes::install_version("pagedown",upgrade="never", version = "0.19")'
RUN Rscript -e 'remotes::install_version("owmr",upgrade="never", version = "0.8.2")'
RUN Rscript -e 'remotes::install_version("NbClust",upgrade="never", version = "3.0.1")'
RUN Rscript -e 'remotes::install_version("nasapower",upgrade="never", version = "4.0.8")'
RUN Rscript -e 'remotes::install_version("modeltime",upgrade="never", version = "1.2.4")'
RUN Rscript -e 'remotes::install_version("measurements",upgrade="never", version = "1.4.0")'
RUN Rscript -e 'remotes::install_version("mapedit",upgrade="never", version = "0.6.0")'
RUN Rscript -e 'remotes::install_version("leaflet.extras2",upgrade="never", version = "1.2.0")'
RUN Rscript -e 'remotes::install_version("kableExtra",upgrade="never", version = "1.3.4")'
RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.3.5")'
RUN Rscript -e 'remotes::install_version("glmnet",upgrade="never", version = "4.1-6")'
RUN Rscript -e 'remotes::install_version("geojsonlint",upgrade="never", version = "0.4.0")'
RUN Rscript -e 'remotes::install_version("geojsonio",upgrade="never", version = "0.10.0")'
RUN Rscript -e 'remotes::install_version("earth",upgrade="never", version = "5.3.1")'
RUN Rscript -e 'remotes::install_version("climatol",upgrade="never", version = "3.1.2")'
RUN Rscript -e 'remotes::install_version("cicerone",upgrade="never", version = "1.0.4")'
RUN Rscript -e 'remotes::install_version("bs4Dash",upgrade="never", version = "2.1.0")'
RUN Rscript -e 'remotes::install_version("shiny.pwa",upgrade="never", version = "0.2.1")'
RUN Rscript -e 'remotes::install_version("httr",upgrade="never", version = "1.4.4")'
RUN Rscript -e 'remotes::install_version("jsonlite",upgrade="never", version = "1.8.4")'
RUN Rscript -e 'remotes::install_version("agroclim",upgrade="never", version = "0.3.0")'
RUN Rscript -e 'remotes::install_version("pollen",upgrade="never", version = "0.82.0")'
RUN Rscript -e 'remotes::install_github("rfortherestofus/pagedreport@ace07abe531009a3d675bfbb36c63adc20e3482f")'
RUN Rscript -e 'remotes::install_github("Appsilon/shiny.i18n@e11ea740994be5787066e29d4f9e17dee3772da5")'
RUN Rscript -e 'remotes::install_github("filipematias23/cleanRfield@ce8edc5ceaf3cd82f620702be965f623ff1951b0")'
RUN Rscript -e 'remotes::install_github("ropensci/skimr@4c48f8e1c7dd6f58c7eabf178fbbd1e664793591")'
RUN Rscript -e 'remotes::install_github("MichelNivard/gptstudio@055558509abdc7140ea9801140753be49e436d05")'
RUN Rscript -e 'install.packages("emayili")'
RUN Rscript -e 'install.packages("devtools")'
RUN R -e 'devtools::install_github("OpenDroneMap/FIELDimageR"); if (!library(FIELDimageR, logical.return=T)) quit(status=10);'
RUN mkdir /build_zone
ADD . /build_zone
WORKDIR /build_zone
RUN R -e 'options(warn = 2);remotes::install_local(upgrade="never")'
EXPOSE 587/tcp
EXPOSE 80
CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');webapp4::run_app()"
And when i am checking if the package is installed with the following command
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
#107 183.3 call: dyn.load(file, DLLpath = DLLpath, ...)
#107 183.3 error: unable to load shared object '/usr/local/lib/R/library/tcltk/libs/tcltk.so':
#107 183.3 libtcl8.6.so: cannot open shared object file: No such file or directory
#107 183.3 Execution halted
#107 183.3 ERROR: lazy loading failed for package ‘misc3d’
#107 183.3 * removing ‘/usr/local/lib/R/site-library/misc3d’
#107 183.3 cat: plot3D.out: No such file or directory
#107 183.3 cat: ks.out: No such file or directory
#107 183.3 cat: spatialEco.out: No such file or directory
#107 183.3
#107 183.3 The downloaded source packages are in
#107 183.3 ‘/tmp/Rtmp84B6zK/downloaded_packages’
#107 183.5 * checking for file ‘/tmp/Rtmp84B6zK/remotes7692aef91/OpenDroneMap-FIELDimageR-c0a3f92/DESCRIPTION’ ... OK
#107 183.5 * preparing ‘FIELDimageR’:
#107 183.5 * checking DESCRIPTION meta-information ... OK
#107 183.6 * checking for LF line-endings in source and make files and shell scripts
#107 183.6 * checking for empty or unneeded directories
#107 183.6 Omitted ‘LazyData’ from DESCRIPTION
#107 183.6 * building ‘FIELDimageR_0.3.3.tar.gz’
#107 183.6
#107 183.6 Installing package into ‘/usr/local/lib/R/site-library’
#107 183.6 (as ‘lib’ is unspecified)
#107 183.8 ERROR: dependency ‘spatialEco’ is not available for package ‘FIELDimageR’
#107 183.8 * removing ‘/usr/local/lib/R/site-library/FIELDimageR’
#107 183.8 Warning messages:
#107 183.8 1: In i.p(...) : installation of one or more packages failed,
#107 183.8 probably ‘misc3d’, ‘plot3D’, ‘ks’, ‘spatialEco’
#107 183.8 2: In i.p(...) :
#107 183.8 installation of package ‘/tmp/Rtmp84B6zK/file74ef0e5a6/FIELDimageR_0.3.3.tar.gz’ had non-zero exit status
#107 183.8 Warning message:
#107 183.8 In library(FIELDimageR, logical.return = T) :
#107 183.8 there is no package called ‘FIELDimageR’
------
executor failed running [/bin/sh -c R -e 'devtools::install_github("OpenDroneMap/FIELDimageR"); if (!library(FIELDimageR, logical.return=T)) quit(status=10);']: exit code: 10
Dear Authors, First of all thanks to make pubblic availble this package case is really usefull.
This isssue is related to #32
I would like to add the package to a docker container but i am getting a lot of problem
This is my dockerfile.
And when i am checking if the package is installed with the following command
I have the following error output