Quantcast
Channel: Active questions tagged amazon-ec2 - Stack Overflow
Viewing all articles
Browse latest Browse all 29421

AWS Rsudio Server package installation issue; cannot find -lboost_filesystem and -lboost_system

$
0
0

I am using a Rstudio AMI developed by Louis Aslett and try to install R package requires lib boost-dev, the latest version of which is installed and there are Boost libraries installed in /usr/include/boost. However, the package failed to be installed with a following error;

> install_github("velocyto-team/velocyto.R", lib="/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6")Downloading GitHub repo velocyto-team/velocyto.R@masterSkipping 1 packages not available: pcaMethods✓  checking for file ‘/tmp/RtmpqEM2ow/remotes8bb32d2c94c/velocyto-team-velocyto.R-83e6ed9/DESCRIPTION’ ...─  preparing ‘velocyto.R’:✓  checking DESCRIPTION meta-information ...─  cleaning src─  checking for LF line-endings in source and make files and shell scripts─  checking for empty or unneeded directories─  building ‘velocyto.R_0.6.tar.gz’* installing *source* package ‘velocyto.R’ ...** using staged installation** libsg++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.og++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c points_within.cpp -o points_within.og++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include"  -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c routines.cpp -o routines.og++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o velocyto.R.so RcppExports.o points_within.o routines.o -lboost_filesystem -lboost_system -lstdc++ -llapack -lblas -fopenmp -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR/usr/bin/ld: cannot find -lboost_filesystem/usr/bin/ld: cannot find -lboost_systemcollect2: error: ld returned 1 exit status

I'd appreciate any workaround for this.

> session_info()─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting  value                        version  R version 3.6.0 (2019-04-26) os       Ubuntu 18.04.2 LTS           system   x86_64, linux-gnu            ui       RStudio                      language (EN)                         collate  C.UTF-8                      ctype    C.UTF-8                      tz       Etc/UTC                      date     2020-04-03                  ─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── package     * version date       lib source         assertthat    0.2.1   2019-03-21 [2] CRAN (R 3.6.0) backports     1.1.5   2019-10-02 [2] CRAN (R 3.6.0) BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 3.6.0) callr         3.4.3   2020-03-28 [1] CRAN (R 3.6.0) cli           2.0.2   2020-02-28 [1] CRAN (R 3.6.0) crayon        1.3.4   2017-09-16 [2] CRAN (R 3.6.0) curl          4.3     2019-12-02 [1] CRAN (R 3.6.0) desc          1.2.0   2018-05-01 [2] CRAN (R 3.6.0) devtools    * 2.2.2   2020-02-17 [1] CRAN (R 3.6.0) digest        0.6.25  2020-02-23 [1] CRAN (R 3.6.0) ellipsis      0.3.0   2019-09-20 [1] CRAN (R 3.6.0) fansi         0.4.1   2020-01-08 [2] CRAN (R 3.6.0) fs            1.4.0   2020-03-31 [1] CRAN (R 3.6.0) glue          1.3.2   2020-03-12 [2] CRAN (R 3.6.0) magrittr      1.5     2014-11-22 [2] CRAN (R 3.6.0) memoise       1.1.0   2017-04-21 [1] CRAN (R 3.6.0) pkgbuild      1.0.6   2019-10-09 [1] CRAN (R 3.6.0) pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.6.0) prettyunits   1.1.1   2020-01-24 [2] CRAN (R 3.6.0) processx      3.4.2   2020-02-09 [1] CRAN (R 3.6.0) ps            1.3.2   2020-02-13 [2] CRAN (R 3.6.0) R6            2.4.1   2019-11-12 [2] CRAN (R 3.6.0) remotes       2.1.1   2020-02-15 [1] CRAN (R 3.6.0) rlang         0.4.5   2020-03-01 [1] CRAN (R 3.6.0) rprojroot     1.3-2   2018-01-03 [2] CRAN (R 3.6.0) rstudioapi    0.11    2020-02-07 [2] CRAN (R 3.6.0) sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.0) testthat      2.3.2   2020-03-02 [1] CRAN (R 3.6.0) usethis     * 1.5.1   2019-07-04 [1] CRAN (R 3.6.0) withr         2.1.2   2018-03-15 [2] CRAN (R 3.6.0)[1] /home/rstudio/R/x86_64-pc-linux-gnu-library/3.6[2] /usr/local/lib/R/site-library[3] /usr/lib/R/site-library[4] /usr/lib/R/library

Viewing all articles
Browse latest Browse all 29421

Trending Articles



<script src="https://jsc.adskeeper.com/r/s/rssing.com.1596347.js" async> </script>