I am installing a package from github in R (link here: https://github.com/aliceyiwang/mvabund), using devtools. I have installed Rtools, using the instructions for another package (here: https://cran.r-project.org/web/packages/dynr/vignettes/InstallationForUsers.pdf) and all the checks there indicate that GSL and RTools are installed properly.
I've set the Windows system environment variables LIB_GSL (as "C:/R/local323"
) and PATHS (as "C:/RTools/bin/", "C:/RTools/mingw_64/bin", "C:/R/R-3.5.1/bin"
)
I also run the following code in R before installing the package:
Sys.setenv("LIB_GSL" = "C:/R/local323")
Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")
Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:/RTools/bin/",
"C:/RTools/mingw_64/bin", "C:/R/R-3.5.1/bin", sep = ";"))
Question:
When I run:
devtools::install_github("aliceyiwang/mvabund")
The code initiates well and starts installing the package. There comes a point, however, when this happens:
[...excluded very long list of undefined references like that below...]
summary.o:summary.cpp:(.text+0x194c): undefined reference to `gsl_vector_free'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'mvabund'
* removing 'C:/R/R-3.5.1/library/mvabund'
In R CMD INSTALL
Error in i.p(...) :
(converted from warning) installation of package ‘C:/Users/Joshua/AppData/Local/Temp/RtmpsPp5oY/file2154340c11f8/mvabund_4.0.tar.gz’ had non-zero exit status
My guess is that somewhere, some path to those functions has not been defined properly. What am I doing wrong?
My session info is
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] usethis_1.4.0 devtools_2.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 rstudioapi_0.8 magrittr_1.5 pkgload_1.0.2 R6_2.3.0 rlang_0.3.0.1
[7] tools_3.5.1 pkgbuild_1.0.2 sessioninfo_1.1.1 cli_1.0.1 withr_2.1.2 remotes_2.0.2
[13] yaml_2.2.0 assertthat_0.2.0 digest_0.6.18 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.1
[19] callr_3.1.0 fs_1.2.6 ps_1.2.1 curl_3.2 testthat_2.0.1 memoise_1.1.0
[25] glue_1.3.0 compiler_3.5.1 desc_1.2.0 backports_1.1.2 prettyunits_1.0.2
>