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robjhyndman / forecast

Forecasting Functions for Time Series and Linear Models
http://pkg.robjhyndman.com/forecast
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ERROR: loading failed while installing forecast package, R version 4.1.0 inside python 3.8-slim-buster docker container #888

Closed santhisenan closed 2 years ago

santhisenan commented 3 years ago

Note: This issue went away when I tried it once more, however, posting here to know why it occurred.

I am trying to install R packages on Docker container using renv. I am getting the following error when it tries to install forecast package.

Error Logs

#15 1617.6 Installing forecast [8.15] ...
#15 1681.7  FAILED
#15 1681.7 Error installing package 'forecast':
#15 1681.7 ====================================
#15 1681.7
#15 1681.7 * installing to library ‘/usr/local/lib/R/site-library/.renv/1’
#15 1681.7 * installing *source* package ‘forecast’ ...
#15 1681.7 ** package ‘forecast’ successfully unpacked and MD5 sums checked
#15 1681.7 ** using staged installation
#15 1681.7 ** libs
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c calcBATS.cpp -o calcBATS.o
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c calcTBATS.cpp -o calcTBATS.o
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c etsTargetFunction.cpp -o etsTargetFunction.o
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c etsTargetFunctionWrapper.cpp -o etsTargetFunctionWrapper.o
#15 1681.7 gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c etscalc.c -o etscalc.o
#15 1681.7 gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c etspolyroot.c -o etspolyroot.o
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c makeBATSMatrices.cpp -o makeBATSMatrices.o
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c makeTBATSMatrices.cpp -o makeTBATSMatrices.o
#15 1681.7 gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c updateMatrices.cpp -o updateMatrices.o
#15 1681.7 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/.renv/1/Rcpp/include' -I'/usr/local/lib/R/site-library/.renv/1/RcppArmadillo/include'   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c updateTBATSMatrices.cpp -o updateTBATSMatrices.o
#15 1681.7 g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o forecast.so calcBATS.o calcTBATS.o etsTargetFunction.o etsTargetFunctionWrapper.o etscalc.o etspolyroot.o makeBATSMatrices.o makeTBATSMatrices.o registerDynamicSymbol.o updateMatrices.o updateTBATSMatrices.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
#15 1681.7 installing to /usr/local/lib/R/site-library/.renv/1/00LOCK-forecast/00new/forecast/libs
#15 1681.7 ** R
#15 1681.7 ** data
#15 1681.7 *** moving datasets to lazyload DB
#15 1681.7 ** inst
#15 1681.7 ** byte-compile and prepare package for lazy loading
#15 1681.7 ** help
#15 1681.7 *** installing help indices
#15 1681.7 *** copying figures
#15 1681.7 ** building package indices
#15 1681.7 ** installing vignettes
#15 1681.7 ** testing if installed package can be loaded from temporary location
#15 1681.7 ** checking absolute paths in shared objects and dynamic libraries
#15 1681.7 ** testing if installed package can be loaded from final location
#15 1681.7 Error in base::serialize(base::as.list(base::getNamespace("forecast"),  :
#15 1681.7   error writing to connection
#15 1681.7 Calls: <Anonymous> -> withCallingHandlers -> <Anonymous>
#15 1681.7 Execution halted
#15 1681.7 ERROR: loading failed
#15 1681.7 * removing ‘/usr/local/lib/R/site-library/.renv/1/forecast’
#15 1681.7 Error: install of package 'forecast' failed [error code 1]
#15 1681.7 Traceback (most recent calls last):
#15 1681.7 12: renv::restore(exclude = c("renv"), repos = c(CRAN = "https://cran.rstudio.com"))
#15 1681.7 11: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
#15 1681.7 10: renv_install_impl(records)
#15 1681.7  9: renv_install_staged(records)
#15 1681.7  8: renv_install_default(records)
#15 1681.7  7: handler(package, renv_install_package(record))
#15 1681.7  6: renv_install_package(record)
#15 1681.7  5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
#15 1681.7         vwritef("\tFAILED")
#15 1681.7         writef(e$output)
#15 1681.7     })
#15 1681.7  4: renv_install_package_impl(record)
#15 1681.7  3: r_cmd_install(package, path)
#15 1681.7  2: r_exec_error(package, output, "install", status)
#15 1681.7  1: stop(error)
#15 1683.1 Execution halted

Environment

I am using R 4.1.0 inside a python 3.8-slim-buster container.

mitchelloharawild commented 2 years ago

Are you able to install other packages which require compiled code? This looks like an issue with your docker container configuration rather than the forecast package.