Installation of package ‘HurdleNormal’ had non-zero exit status

[faizraza]

I have tried to install the package HurdleNormal using the command BiocManager::install('amcdavid/HurdleNormal') on Windows 10 (64-bit) using RStudio 2023.06.1+524. However, I always get an error: installation of package ‘HurdleNormal’ had non-zero exit status. I tried different things including removing and re-installing packages including Matrix, survival, nlme, and sfsmisc; updating R and RStudio, and trying to install using devtools but nothing worked. I always get the following output:

BiocManager::install('amcdavid/HurdleNormal')
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16 ucrt)
Installing github package(s) 'amcdavid/HurdleNormal'
Downloading GitHub repo amcdavid/HurdleNormal@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\faizr\AppData\Local\Temp\RtmpA1AcUL\remotes15481fb8668e\amcdavid-HurdleNormal-425d485/DESCRIPTION' (379ms)
─ preparing 'HurdleNormal': (815ms)
✔ 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
Removed empty directory 'HurdleNormal/inst/aoas_simulations'
Removed empty directory 'HurdleNormal/inst'
─ building 'HurdleNormal_0.98.8.tar.gz'

• installing source package 'HurdleNormal' ...
  ** using staged installation
  ** libs
  using C++ compiler: 'G__1.EXE (GCC) 12.2.0'
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/faizr/AppData/Local/R/win-library/4.3/RcppArmadillo/include' -I'C:/Users/faizr/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/faizr/AppData/Local/R/win-library/4.3/RcppArmadillo/include' -I'C:/Users/faizr/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hurdle_distributions.cpp -o hurdle_distributions.o
  g++ -std=gnu++17 -I"C:/PROGRA1/R/R-431.1/include" -DNDEBUG -I'C:/Users/faizr/AppData/Local/R/win-library/4.3/RcppArmadillo/include' -I'C:/Users/faizr/AppData/Local/R/win-library/4.3/Rcpp/include' -I"C:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hurdle_likelihood.cpp -o hurdle_likelihood.o
  g++ -std=gnu++17 -shared -s -static-libgcc -o HurdleNormal.dll tmp.def RcppExports.o hurdle_distributions.o hurdle_likelihood.o -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/RBuildTools/4.3/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA1/R/R-43~1.1/bin/x64 -lR
  C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: hurdle_likelihood.o:hurdle_likelihood.cpp:(.text+0x10e8): undefined reference to dgemv_' C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: hurdle_likelihood.o:hurdle_likelihood.cpp:(.text.hot+0x1b6): undefined reference to dgemm_'
  C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: hurdle_likelihood.o:hurdle_likelihood.cpp:(.text.hot+0x4e7): undefined reference to dsyrk_' C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: hurdle_likelihood.o:hurdle_likelihood.cpp:(.text.hot+0x79b): undefined reference to dgemv_'
  C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: hurdle_likelihood.o:hurdle_likelihood.cpp:(.text.hot+0xb2b): undefined reference to `dgemv_'
  collect2.exe: error: ld returned 1 exit status
  no DLL was created
  ERROR: compilation failed for package 'HurdleNormal'
• removing 'C:/Users/faizr/AppData/Local/R/win-library/4.3/HurdleNormal'
  Warning message:
  In i.p(...) :
  installation of package ‘C:/Users/faizr/AppData/Local/Temp/RtmpA1AcUL/file15486f481355/HurdleNormal_0.98.8.tar.gz’ had non-zero exit status

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: Asia/Karachi
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] processx_3.8.2 BiocManager_1.30.22 compiler_4.3.1 R6_2.5.1
[5] rprojroot_2.0.3 cli_3.6.1 prettyunits_1.1.1 tools_4.3.1
[9] rstudioapi_0.15.0 curl_5.0.2 crayon_1.5.2 remotes_2.4.2.1
[13] desc_1.4.2 callr_3.7.3 ps_1.7.5 pkgbuild_1.4.2

[amcdavid]

Hi @faizraza,

I checked and I was able to compile the package on linux using R 4.3.1 and the most recent packages on cran. So I suspect there's something amiss with the development setup on your machine. Can you install other packages that link to RcppArmadillo? Does BiocManager::install("ade4", type = "source") work?