trying to install package "bayesrules"

maranz · June 21, 2023, 8:55pm

install.packages(bayesrules)
Exits with this error:

Warning in install.packages :
installation of package ‘rstanarm’ had non-zero exit status

I tried installing 'rstanarm' separately and it exits with the same error.

Appreciate any help

technocrat · June 22, 2023, 1:10am

If you see

A binary version is available but a source version is later

and have been choosing the “Yes” option, try “No

Gabor · June 22, 2023, 7:06am

Can you copy here the complete output of

install.packages(bayesrules)

? Thanks!

maranz · June 22, 2023, 3:54pm

Thanks for your help...

install.packages("bayesrules")
Installing package into ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘fs’, ‘diffobj’, ‘rematch2’, ‘rappdirs’, ‘highr’, ‘tinytex’, ‘numDeriv’, ‘brio’, ‘evaluate’, ‘pkgload’, ‘praise’, ‘ps’, ‘waldo’, ‘memoise’, ‘sass’, ‘yaml’, ‘knitr’, ‘rmarkdown’, ‘lazyeval’, ‘colorspace’, ‘abind’, ‘tensorA’, ‘distributional’, ‘testthat’, ‘callr’, ‘crayon’, ‘prettyunits’, ‘processx’, ‘rprojroot’, ‘httpuv’, ‘mime’, ‘jsonlite’, ‘fontawesome’, ‘htmltools’, ‘sourcetools’, ‘later’, ‘promises’, ‘fastmap’, ‘commonmark’, ‘bslib’, ‘cachem’, ‘ellipsis’, ‘htmlwidgets’, ‘miniUI’, ‘crosstalk’, ‘jquerylib’, ‘zoo’, ‘xfun’, ‘digest’, ‘igraph’, ‘base64enc’, ‘farver’, ‘labeling’, ‘munsell’, ‘RColorBrewer’, ‘viridisLite’, ‘fansi’, ‘pkgconfig’, ‘timechange’, ‘cpp11’, ‘utf8’, ‘ggridges’, ‘posterior’, ‘reshape2’, ‘minqa’, ‘nloptr’, ‘matrixStats’, ‘inline’, ‘gridExtra’, ‘pkgbuild’, ‘desc’, ‘shiny’, ‘colourpicker’, ‘DT’, ‘dygraphs’, ‘gtools’, ‘markdown’, ‘shinyjs’, ‘shinythemes’, ‘threejs’, ‘xtable’, ‘xts’, ‘backports’, ‘cli’, ‘glue’, ‘gtable’, ‘isoband’, ‘lifecycle’, ‘rlang’, ‘scales’, ‘tibble’, ‘vctrs’, ‘withr’, ‘hms’, ‘lubridate’, ‘stringi’, ‘stringr’, ‘snakecase’, ‘tidyselect’, ‘tidyr’, ‘generics’, ‘pillar’, ‘R6’, ‘Rcpp’, ‘bayesplot’, ‘lme4’, ‘loo’, ‘rstan’, ‘rstantools’, ‘shinystan’, ‘RcppParallel’, ‘StanHeaders’, ‘BH’, ‘RcppEigen’, ‘proxy’, ‘checkmate’, ‘numbers’, ‘plyr’, ‘rearrr’, ‘ggplot2’, ‘janitor’, ‘magrittr’, ‘dplyr’, ‘purrr’, ‘rstanarm’, ‘e1071’, ‘groupdata2’

installing binary package ‘fs’ ...
DONE (fs)
installing binary package ‘rappdirs’ ...
DONE (rappdirs)
installing binary package ‘numDeriv’ ...
DONE (numDeriv)
installing binary package ‘brio’ ...
DONE (brio)
installing binary package ‘evaluate’ ...
DONE (evaluate)
installing binary package ‘praise’ ...
DONE (praise)
installing binary package ‘ps’ ...
DONE (ps)
installing binary package ‘yaml’ ...
DONE (yaml)
installing binary package ‘lazyeval’ ...
DONE (lazyeval)
installing binary package ‘colorspace’ ...
DONE (colorspace)
installing binary package ‘abind’ ...
DONE (abind)
installing binary package ‘tensorA’ ...
DONE (tensorA)
installing binary package ‘crayon’ ...
DONE (crayon)
installing binary package ‘prettyunits’ ...
DONE (prettyunits)
installing binary package ‘rprojroot’ ...
DONE (rprojroot)
installing binary package ‘mime’ ...
DONE (mime)
installing binary package ‘jsonlite’ ...
DONE (jsonlite)
installing binary package ‘sourcetools’ ...
DONE (sourcetools)
installing binary package ‘fastmap’ ...
DONE (fastmap)
installing binary package ‘commonmark’ ...
DONE (commonmark)
installing binary package ‘zoo’ ...
DONE (zoo)
installing binary package ‘xfun’ ...
DONE (xfun)
installing binary package ‘digest’ ...
DONE (digest)
installing binary package ‘base64enc’ ...
DONE (base64enc)
installing binary package ‘farver’ ...
DONE (farver)
installing binary package ‘labeling’ ...
DONE (labeling)
installing binary package ‘RColorBrewer’ ...
DONE (RColorBrewer)
installing binary package ‘viridisLite’ ...
DONE (viridisLite)
installing binary package ‘fansi’ ...
DONE (fansi)
installing binary package ‘pkgconfig’ ...
DONE (pkgconfig)
installing binary package ‘cpp11’ ...
DONE (cpp11)
installing binary package ‘utf8’ ...
DONE (utf8)
installing binary package ‘matrixStats’ ...
DONE (matrixStats)
installing binary package ‘inline’ ...
DONE (inline)
installing binary package ‘gtools’ ...
DONE (gtools)
installing binary package ‘xtable’ ...
DONE (xtable)
installing binary package ‘backports’ ...
DONE (backports)
installing binary package ‘cli’ ...
DONE (cli)
installing binary package ‘glue’ ...
DONE (glue)
installing binary package ‘isoband’ ...
DONE (isoband)
installing binary package ‘rlang’ ...
DONE (rlang)
installing binary package ‘withr’ ...
DONE (withr)
installing binary package ‘stringi’ ...
DONE (stringi)
installing binary package ‘generics’ ...
DONE (generics)
installing binary package ‘R6’ ...
DONE (R6)
installing binary package ‘Rcpp’ ...
DONE (Rcpp)
installing binary package ‘RcppParallel’ ...
DONE (RcppParallel)
installing binary package ‘BH’ ...
DONE (BH)
installing binary package ‘proxy’ ...
DONE (proxy)
installing binary package ‘numbers’ ...
DONE (numbers)
installing binary package ‘magrittr’ ...
DONE (magrittr)
installing binary package ‘diffobj’ ...
DONE (diffobj)
installing binary package ‘highr’ ...
DONE (highr)
installing binary package ‘tinytex’ ...
DONE (tinytex)
installing binary package ‘processx’ ...
DONE (processx)
installing binary package ‘later’ ...
DONE (later)
installing binary package ‘cachem’ ...
DONE (cachem)
installing binary package ‘ellipsis’ ...
DONE (ellipsis)
installing binary package ‘igraph’ ...
DONE (igraph)
installing binary package ‘munsell’ ...
DONE (munsell)
installing binary package ‘timechange’ ...
DONE (timechange)
installing binary package ‘minqa’ ...
DONE (minqa)
installing binary package ‘desc’ ...
DONE (desc)
installing binary package ‘markdown’ ...
DONE (markdown)
installing binary package ‘xts’ ...
DONE (xts)
installing binary package ‘lifecycle’ ...
DONE (lifecycle)
installing binary package ‘RcppEigen’ ...
DONE (RcppEigen)
installing binary package ‘checkmate’ ...
DONE (checkmate)
installing binary package ‘plyr’ ...
DONE (plyr)
installing binary package ‘e1071’ ...
DONE (e1071)
installing binary package ‘pkgload’ ...
DONE (pkgload)
installing binary package ‘memoise’ ...
DONE (memoise)
installing binary package ‘knitr’ ...
DONE (knitr)
installing binary package ‘callr’ ...
DONE (callr)
installing binary package ‘htmltools’ ...
DONE (htmltools)
installing binary package ‘promises’ ...
DONE (promises)
installing binary package ‘gtable’ ...
DONE (gtable)
installing binary package ‘scales’ ...
DONE (scales)
installing binary package ‘vctrs’ ...
DONE (vctrs)
installing binary package ‘lubridate’ ...
DONE (lubridate)
installing binary package ‘loo’ ...
DONE (loo)
installing binary package ‘rstantools’ ...
DONE (rstantools)
installing binary package ‘StanHeaders’ ...
DONE (StanHeaders)
installing binary package ‘sass’ ...
DONE (sass)
installing binary package ‘httpuv’ ...
DONE (httpuv)
installing binary package ‘fontawesome’ ...
DONE (fontawesome)
installing binary package ‘crosstalk’ ...
DONE (crosstalk)
installing binary package ‘jquerylib’ ...
DONE (jquerylib)
installing binary package ‘gridExtra’ ...
DONE (gridExtra)
installing binary package ‘pkgbuild’ ...
DONE (pkgbuild)
installing binary package ‘hms’ ...
DONE (hms)
installing binary package ‘stringr’ ...
DONE (stringr)
installing binary package ‘tidyselect’ ...
DONE (tidyselect)
installing binary package ‘pillar’ ...
DONE (pillar)
installing binary package ‘purrr’ ...
DONE (purrr)
installing binary package ‘bslib’ ...
DONE (bslib)
installing binary package ‘reshape2’ ...
DONE (reshape2)
installing binary package ‘tibble’ ...
DONE (tibble)
installing binary package ‘snakecase’ ...
DONE (snakecase)
installing binary package ‘rematch2’ ...
DONE (rematch2)
installing binary package ‘rmarkdown’ ...
DONE (rmarkdown)
installing binary package ‘shiny’ ...
DONE (shiny)
installing binary package ‘ggplot2’ ...
DONE (ggplot2)
installing binary package ‘dplyr’ ...
DONE (dplyr)
installing binary package ‘waldo’ ...
DONE (waldo)
installing binary package ‘distributional’ ...
DONE (distributional)
installing binary package ‘htmlwidgets’ ...
DONE (htmlwidgets)
installing binary package ‘miniUI’ ...
DONE (miniUI)
installing binary package ‘ggridges’ ...
DONE (ggridges)
installing binary package ‘shinyjs’ ...
DONE (shinyjs)
installing binary package ‘shinythemes’ ...
DONE (shinythemes)
installing binary package ‘tidyr’ ...
DONE (tidyr)
installing binary package ‘rstan’ ...
DONE (rstan)
installing binary package ‘rearrr’ ...
DONE (rearrr)
installing binary package ‘testthat’ ...
DONE (testthat)
installing binary package ‘posterior’ ...
DONE (posterior)
installing binary package ‘colourpicker’ ...
DONE (colourpicker)
installing binary package ‘DT’ ...
DONE (DT)
installing binary package ‘dygraphs’ ...
DONE (dygraphs)
installing binary package ‘threejs’ ...
DONE (threejs)
installing binary package ‘janitor’ ...
DONE (janitor)
installing binary package ‘groupdata2’ ...
DONE (groupdata2)
installing binary package ‘nloptr’ ...
DONE (nloptr)
installing binary package ‘bayesplot’ ...
DONE (bayesplot)
installing binary package ‘lme4’ ...
DONE (lme4)
installing binary package ‘shinystan’ ...
DONE (shinystan)
installing source package ‘rstanarm’ ...
** package ‘rstanarm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
using C++17
"/opt/R/4.3.0/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/jm.stan
Wrote C++ file "stan_files/jm.cc"

g++ -std=gnu++17 -I"/opt/R/4.3.0/lib/R/include" -DNDEBUG -I"../inst/include" -I"/cloud/lib/x86_64-pc-linux-gnu-library/4.3/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -D_HAS_AUTO_PTR_ETC=0 -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/StanHeaders/include' -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/rstan/include' -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/BH/include' -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/RcppEigen/include' -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/RcppParallel/include' -I/usr/local/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -D_HAS_AUTO_PTR_ETC=0 -fpic -g -O2 -c stan_files/jm.cc -o stan_files/jm.o
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.0/lib/R/etc/Makeconf:198: stan_files/jm.o] Error 1
rm stan_files/jm.cc
ERROR: compilation failed for package ‘rstanarm’

removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.3/rstanarm’
Warning in install.packages :
installation of package ‘rstanarm’ had non-zero exit status
installing binary package ‘bayesrules’ ...
DONE (bayesrules)

The downloaded source packages are in
‘/tmp/RtmpPMehtF/downloaded_packages’

Gabor · June 22, 2023, 4:09pm

This seems like the Out-Of-Memory killer. C++ compilation often needs a lot of memory. How much memory do you have? Can you use a swap file?

maranz · June 22, 2023, 4:59pm

Memory = 1G
I installed on a different VM with 4G -- no problem.

Thanks for your help!

technocrat · June 22, 2023, 7:34pm

I don’t have the metrics to back up my hunch, but that seems too stingy to work very well for anything other than just familiarization use of R in general, let alone any heavy duty compilation work, given that the VM has other demands that reduce how much of the 1GB is available.

system · August 3, 2023, 7:34pm

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