search

andrewzm / FRK

Fixed Rank Kriging with big data
https://andrewzm.github.io/FRK/
66 stars 20 forks source link

Running docker images issue #3

Closed agronomofiorentini closed 2 years ago

agronomofiorentini commented 2 years ago

Dear contributors,

I have created a docker image in which I insert the gstat as package to install.

During the creation of the docker image everything works perfectly, but when I go to run the docker image I have the follow error report

Warning: Error in : package or namespace load failed for ‘FRK’: package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick cannot use with duplicate class names (the package may need to be re-installed) 55: stop 54: value[[3L]] 53: tryCatchOne 52: tryCatchList 51: tryCatch 50: library 49: server Error : package or namespace load failed for ‘FRK’: package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick

When i am running the same code on the r installed locally it is working perfectly.

This issue started yesterday, only after installing sen2r github version devel

I don't know how to fix it, but i will report my Dockerfile

FROM rocker/r-ver:4.0.5
RUN apt-get update && apt-get install -y  gdal-bin git-core imagemagick libcurl4-openssl-dev libfontconfig1-dev libgdal-dev libgeos-dev libgeos++-dev libgit2-dev libicu-dev libpng-dev libpq-dev libproj-dev libsasl2-dev libssl-dev libudunits2-dev libxml2-dev make pandoc pandoc-citeproc zlib1g-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 R -e 'install.packages("remotes")'
RUN Rscript -e 'remotes::install_version("lubridate",upgrade="never", version = "1.8.0")'
RUN Rscript -e 'remotes::install_version("glue",upgrade="never", version = "1.6.0")'
RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.3.5")'
RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.7.1")'
RUN Rscript -e 'remotes::install_version("htmltools",upgrade="never", version = "0.5.2")'
RUN Rscript -e 'remotes::install_version("DBI",upgrade="never", version = "1.1.2")'
RUN Rscript -e 'remotes::install_version("xml2",upgrade="never", version = "1.3.2")'
RUN Rscript -e 'remotes::install_version("processx",upgrade="never", version = "3.5.2")'
RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.11")'
RUN Rscript -e 'remotes::install_version("knitr",upgrade="never", version = "1.37")'
RUN Rscript -e 'remotes::install_version("data.table",upgrade="never", version = "1.14.2")'
RUN Rscript -e 'remotes::install_version("sp",upgrade="never", version = "1.4-6")'
RUN Rscript -e 'remotes::install_version("e1071",upgrade="never", version = "1.7-9")'
RUN Rscript -e 'remotes::install_version("plotly",upgrade="never", version = "4.10.0")'
RUN Rscript -e 'remotes::install_version("raster",upgrade="never", version = "3.5-11")'
RUN Rscript -e 'remotes::install_version("sf",upgrade="never", version = "1.0-5")'
RUN Rscript -e 'remotes::install_version("viridis",upgrade="never", version = "0.6.1")'
RUN Rscript -e 'remotes::install_version("leaflet",upgrade="never", version = "2.0.4.1")'
RUN Rscript -e 'remotes::install_version("zip",upgrade="never", version = "2.2.0")'
RUN Rscript -e 'remotes::install_version("pkgload",upgrade="never", version = "1.2.2")'
RUN Rscript -e 'remotes::install_version("attempt",upgrade="never", version = "0.3.1")'
RUN Rscript -e 'remotes::install_version("plotrix",upgrade="never", version = "3.8-2")'
RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.20")'
RUN Rscript -e 'remotes::install_version("rvest",upgrade="never", version = "1.0.2")'
RUN Rscript -e 'remotes::install_version("readxl",upgrade="never", version = "1.3.1")'
RUN Rscript -e 'remotes::install_version("googlesheets4",upgrade="never", version = "1.0.0")'
RUN Rscript -e 'remotes::install_version("rgdal",upgrade="never", version = "1.5-28")'
RUN Rscript -e 'remotes::install_version("rgeos",upgrade="never", version = "0.5-9")'
RUN Rscript -e 'remotes::install_version("timetk",upgrade="never", version = "2.6.1")'
RUN Rscript -e 'remotes::install_version("mapview",upgrade="never", version = "2.10.0")'
RUN Rscript -e 'remotes::install_version("leaflet.extras",upgrade="never", version = "1.0.0")'
RUN Rscript -e 'remotes::install_version("testthat",upgrade="never", version = "3.1.0")'
RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.1")'
RUN Rscript -e 'remotes::install_version("tidymodels",upgrade="never", version = "0.1.4")'
RUN Rscript -e 'remotes::install_version("shinymanager",upgrade="never", version = "1.0.400")'
RUN Rscript -e 'remotes::install_version("tidyverse",upgrade="never", version = "1.3.1")'
RUN Rscript -e 'remotes::install_version("spelling",upgrade="never", version = "2.2")'
RUN Rscript -e 'remotes::install_version("writexl",upgrade="never", version = "1.4.0")'
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("SpatialPosition",upgrade="never", version = "2.1.1")'
RUN Rscript -e 'remotes::install_version("skimr",upgrade="never", version = "2.1.3")'
RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.6.2")'
RUN Rscript -e 'remotes::install_version("shinyvalidate",upgrade="never", version = "0.1.1")'
RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.0.0")'
RUN Rscript -e 'remotes::install_version("shinyalert",upgrade="never", version = "2.0.0")'
RUN Rscript -e 'remotes::install_version("sever",upgrade="never", version = "0.0.7")'
RUN Rscript -e 'remotes::install_version("rtsdata",upgrade="never", version = "0.1.2")'
RUN Rscript -e 'remotes::install_version("RStoolbox",upgrade="never", version = "0.2.6")'
RUN Rscript -e 'remotes::install_version("RPostgres",upgrade="never", version = "1.4.1")'
RUN Rscript -e 'remotes::install_version("randomForest",upgrade="never", version = "4.6-14")'
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")'
RUN Rscript -e 'remotes::install_version("nasapower",upgrade="never", version = "4.0.0")'
RUN Rscript -e 'remotes::install_version("modeltime",upgrade="never", version = "1.1.1")'
RUN Rscript -e 'remotes::install_version("measurements",upgrade="never", version = "1.4.0")'
RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.3.1")'
RUN Rscript -e 'remotes::install_version("glmnet",upgrade="never", version = "4.1-2")'
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 = "2.0.3")'
RUN Rscript -e 'remotes::install_version("FRK",upgrade="never", version = "2.0.3")'
RUN Rscript -e 'remotes::install_github("r-lib/rlang@dc03e4473000d0424dacd4c8cf08211b7fb8bc97")'
RUN Rscript -e 'remotes::install_github("JohnCoene/waiter@ce5fdaa1fc1224ba657c0906c7900b275cfee1d7")'
RUN Rscript -e 'remotes::install_github("mablab/rpostgis@74a6ac71bcc21b7b5edf0ed6b59dcbfd4d7bfc59")'
RUN Rscript -e 'remotes::install_github("r-spatial/mapedit@8328411a45513f788dc25e6b4214df53363d6494")'
RUN mkdir /build_zone
ADD . /build_zone
WORKDIR /build_zone
RUN R -e 'options(warn = 2);remotes::install_local(upgrade="never")'
EXPOSE 80
CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');webapp::run_app()"
andrewzm commented 2 years ago

Hi, Unfortunately I don't have an answer to this, but it would help to know if this also happened with FRK v1.x. Can you try that out? Thanks.

Best, Andrew

On Thu, Jan 20, 2022 at 1:41 AM agronomofiorentini @.***> wrote:

Dear contributors,

I have created a docker image in which I insert the gstat as package to install.

During the creation of the docker image everything works perfectly, but when I go to run the docker image I have the follow error report

Warning: Error in : package or namespace load failed for ‘FRK’: package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick cannot use with duplicate class names (the package may need to be re-installed) 55: stop 54: value[[3L]] 53: tryCatchOne 52: tryCatchList 51: tryCatch 50: library 49: server Error : package or namespace load failed for ‘FRK’: package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick

When i am running the same code on the r installed locally it is working perfectly.

This issue started yesterday, only after installing sen2r github version devel

I don't know how to fix it, but i will report my Dockerfile

FROM rocker/r-ver:4.0.5

RUN apt-get update && apt-get install -y gdal-bin git-core imagemagick libcurl4-openssl-dev libfontconfig1-dev libgdal-dev libgeos-dev libgeos++-dev libgit2-dev libicu-dev libpng-dev libpq-dev libproj-dev libsasl2-dev libssl-dev libudunits2-dev libxml2-dev make pandoc pandoc-citeproc zlib1g-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 R -e 'install.packages("remotes")'

RUN Rscript -e 'remotes::install_version("lubridate",upgrade="never", version = "1.8.0")'

RUN Rscript -e 'remotes::install_version("glue",upgrade="never", version = "1.6.0")'

RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.3.5")'

RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.7.1")'

RUN Rscript -e 'remotes::install_version("htmltools",upgrade="never", version = "0.5.2")'

RUN Rscript -e 'remotes::install_version("DBI",upgrade="never", version = "1.1.2")'

RUN Rscript -e 'remotes::install_version("xml2",upgrade="never", version = "1.3.2")'

RUN Rscript -e 'remotes::install_version("processx",upgrade="never", version = "3.5.2")'

RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.11")'

RUN Rscript -e 'remotes::install_version("knitr",upgrade="never", version = "1.37")'

RUN Rscript -e 'remotes::install_version("data.table",upgrade="never", version = "1.14.2")'

RUN Rscript -e 'remotes::install_version("sp",upgrade="never", version = "1.4-6")'

RUN Rscript -e 'remotes::install_version("e1071",upgrade="never", version = "1.7-9")'

RUN Rscript -e 'remotes::install_version("plotly",upgrade="never", version = "4.10.0")'

RUN Rscript -e 'remotes::install_version("raster",upgrade="never", version = "3.5-11")'

RUN Rscript -e 'remotes::install_version("sf",upgrade="never", version = "1.0-5")'

RUN Rscript -e 'remotes::install_version("viridis",upgrade="never", version = "0.6.1")'

RUN Rscript -e 'remotes::install_version("leaflet",upgrade="never", version = "2.0.4.1")'

RUN Rscript -e 'remotes::install_version("zip",upgrade="never", version = "2.2.0")'

RUN Rscript -e 'remotes::install_version("pkgload",upgrade="never", version = "1.2.2")'

RUN Rscript -e 'remotes::install_version("attempt",upgrade="never", version = "0.3.1")'

RUN Rscript -e 'remotes::install_version("plotrix",upgrade="never", version = "3.8-2")'

RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.20")'

RUN Rscript -e 'remotes::install_version("rvest",upgrade="never", version = "1.0.2")'

RUN Rscript -e 'remotes::install_version("readxl",upgrade="never", version = "1.3.1")'

RUN Rscript -e 'remotes::install_version("googlesheets4",upgrade="never", version = "1.0.0")'

RUN Rscript -e 'remotes::install_version("rgdal",upgrade="never", version = "1.5-28")'

RUN Rscript -e 'remotes::install_version("rgeos",upgrade="never", version = "0.5-9")'

RUN Rscript -e 'remotes::install_version("timetk",upgrade="never", version = "2.6.1")'

RUN Rscript -e 'remotes::install_version("mapview",upgrade="never", version = "2.10.0")'

RUN Rscript -e 'remotes::install_version("leaflet.extras",upgrade="never", version = "1.0.0")'

RUN Rscript -e 'remotes::install_version("testthat",upgrade="never", version = "3.1.0")'

RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.1")'

RUN Rscript -e 'remotes::install_version("tidymodels",upgrade="never", version = "0.1.4")'

RUN Rscript -e 'remotes::install_version("shinymanager",upgrade="never", version = "1.0.400")'

RUN Rscript -e 'remotes::install_version("tidyverse",upgrade="never", version = "1.3.1")'

RUN Rscript -e 'remotes::install_version("spelling",upgrade="never", version = "2.2")'

RUN Rscript -e 'remotes::install_version("writexl",upgrade="never", version = "1.4.0")'

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("SpatialPosition",upgrade="never", version = "2.1.1")'

RUN Rscript -e 'remotes::install_version("skimr",upgrade="never", version = "2.1.3")'

RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.6.2")'

RUN Rscript -e 'remotes::install_version("shinyvalidate",upgrade="never", version = "0.1.1")'

RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.0.0")'

RUN Rscript -e 'remotes::install_version("shinyalert",upgrade="never", version = "2.0.0")'

RUN Rscript -e 'remotes::install_version("sever",upgrade="never", version = "0.0.7")'

RUN Rscript -e 'remotes::install_version("rtsdata",upgrade="never", version = "0.1.2")'

RUN Rscript -e 'remotes::install_version("RStoolbox",upgrade="never", version = "0.2.6")'

RUN Rscript -e 'remotes::install_version("RPostgres",upgrade="never", version = "1.4.1")'

RUN Rscript -e 'remotes::install_version("randomForest",upgrade="never", version = "4.6-14")'

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")'

RUN Rscript -e 'remotes::install_version("nasapower",upgrade="never", version = "4.0.0")'

RUN Rscript -e 'remotes::install_version("modeltime",upgrade="never", version = "1.1.1")'

RUN Rscript -e 'remotes::install_version("measurements",upgrade="never", version = "1.4.0")'

RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.3.1")'

RUN Rscript -e 'remotes::install_version("glmnet",upgrade="never", version = "4.1-2")'

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 = "2.0.3")'

RUN Rscript -e 'remotes::install_version("FRK",upgrade="never", version = "2.0.3")'

RUN Rscript -e @.***")'

RUN Rscript -e @.***")'

RUN Rscript -e @.***")'

RUN Rscript -e @.***")'

RUN mkdir /build_zone

ADD . /build_zone

WORKDIR /build_zone

RUN R -e 'options(warn = 2);remotes::install_local(upgrade="never")'

EXPOSE 80

CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');webapp::run_app()"

— Reply to this email directly, view it on GitHub https://github.com/andrewzm/FRK/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABEU3LD7WMBRAMDM7SUYR3UW3ESJANCNFSM5MKD3ZMA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

agronomofiorentini commented 2 years ago

A update of this issue is the follow. i have removed and installed again the FRK package.

But when i tried to load it, i have the follow error

Error: caricamento pacchetto o namespace fallito per ‘FRK’: package slot missing from signature for generic ‘coerce’ and classes STFDF, RasterBrick cannot use with duplicate class names (the package may need to be re-installed)

The same issue is on the gstat package.

agronomofiorentini commented 2 years ago

I have solve this problem just by copy and paste the df_to_SpatialPolygons function beacuse id the function that i need.

Thanks

andrewzm commented 2 years ago

Glad you found a workaround -- Andrew

On Fri, Jan 21, 2022 at 2:41 AM agronomofiorentini @.***> wrote:

I have solve this problem just by copy and paste the df_to_SpatialPolygons function beacuse id the function that i need.

Thanks

— Reply to this email directly, view it on GitHub https://github.com/andrewzm/FRK/issues/3#issuecomment-1017636836, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABEU3MKUVBRHAH4I4JP6E3UXAUJBANCNFSM5MKD3ZMA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you commented.Message ID: @.***>