Hi, I want to install the package phyloseq from bioconductor using Rstudio (Version 1.1.463 ) with this command:
source('http://bioconductor.org/biocLite.R')
biocLite('phyloseq')
But I get this error:
/usr/bin/x86_64-linux-gnu-ld: cannot find -lgfortran
/usr/bin/x86_64-linux-gnu-ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [vegan.so] Error 1
ERROR: compilation failed for package ‘vegan’
* removing ‘/usr/local/lib/R/site-library/vegan’
ERROR: dependencies ‘ade4’, ‘ape’, ‘igraph’, ‘vegan’ are not available for package ‘phyloseq’
* removing ‘/usr/local/lib/R/site-library/phyloseq’
The downloaded source packages are in
‘/tmp/Rtmp1Cty9l/downloaded_packages’
installation path not writeable, unable to update packages: mgcv
Warning messages:
1: 'biocLite' is deprecated.
Use 'BiocManager::install' instead.
See help("Deprecated")
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘ade4’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘ape’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘igraph’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘vegan’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘phyloseq’ had non-zero exit status
This is the information from sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=nb_NO.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=nb_NO.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=nb_NO.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.4 BiocInstaller_1.32.1 usethis_1.4.0 devtools_2.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 rstudioapi_0.9.0 magrittr_1.5 pkgload_1.0.2 R6_2.3.0 rlang_0.3.1 tools_3.5.2
[8] pkgbuild_1.0.2 sessioninfo_1.1.1 cli_1.0.1 withr_2.1.2 remotes_2.0.2 yaml_2.2.0 assertthat_0.2.0
[15] digest_0.6.18 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.1 callr_3.1.1 fs_1.2.6 ps_1.3.0
[22] curl_3.3 testthat_2.0.1 memoise_1.1.0 glue_1.3.0 compiler_3.5.2 desc_1.2.0 backports_1.1.3
[29] prettyunits_1.0.2
Thanks for the help