Installing new version fails on linux system

[GabrielHoffman]

I tried installing the latest GitHub version. It works find on my Mac, but fails on Linux likely do to an issue with zstd:

I played around with the makefile, but I couldn't figure it out.

configure: zstd 1.5.1 library detected but is too old (<1.5.2) -- compiling from source

Install from GitHub fails

> devtools::install_github("chrchang/plink-ng/2.0/pgenlibr")

Downloading GitHub repo chrchang/plink-ng@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
   checking for file ‘/tmp/RtmpdbIyM8/remotes4813b3cfed1bd/chrchang-plink-ng-5ea✔  checking for file ‘/tmp/RtmpdbIyM8/remotes4813b3cfed1bd/chrchang-plink-ng-5eab376/2.0/pgenlibr/DESCRIPTION’ (545ms)
─  preparing ‘pgenlibr’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (654ms)
─  checking for empty or unneeded directories (615ms)
─  building ‘pgenlibr_0.3.7.tar.gz’
   Warning: file 'pgenlibr/cleanup' did not have execute permissions: corrected
   Warning: file 'pgenlibr/configure' did not have execute permissions: corrected
   
Installing package into ‘/hpc/users/hoffmg01/.Rlib/R_441_bioc320’
(as ‘lib’ is unspecified)
* installing *source* package ‘pgenlibr’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
configure: C++ compiler: g++ -std=gnu++17
configure: zstd 1.5.1 library detected but is too old (<1.5.2) -- compiling from source
configure: libdeflate not detected by pkg-config; falling back on system header file check
no
configure: simde not detected by pkg-config; falling back on system header file check
no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 14.2.0’
g++ -std=gnu++17 -I"/hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DZSTD_DISABLE_ASM   -Izstd/lib -Izstd/lib/common -Ilibdeflate  -I../inst/include -I'/hpc/users/hoffmg01/.Rlib/R_441_bioc320/Rcpp/include' -I/usr/local/include    -fpic  -O3 -fopenmp   -c ../inst/include/pvar_ffi_support.cpp -o ../inst/include/pvar_ffi_support.o
g++ -std=gnu++17 -I"/hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DZSTD_DISABLE_ASM   -Izstd/lib -Izstd/lib/common -Ilibdeflate  -I../inst/include -I'/hpc/users/hoffmg01/.Rlib/R_441_bioc320/Rcpp/include' -I/usr/local/include    -fpic  -O3 -fopenmp   -c ../inst/include/pgenlib_ffi_support.cpp -o ../inst/include/pgenlib_ffi_support.o
g++ -std=gnu++17 -I"/hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DZSTD_DISABLE_ASM   -Izstd/lib -Izstd/lib/common -Ilibdeflate  -I../inst/include -I'/hpc/users/hoffmg01/.Rlib/R_441_bioc320/Rcpp/include' -I/usr/local/include    -fpic  -O3 -fopenmp   -c pvar.cpp -o pvar.o
g++ -std=gnu++17 -I"/hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DZSTD_DISABLE_ASM   -Izstd/lib -Izstd/lib/common -Ilibdeflate  -I../inst/include -I'/hpc/users/hoffmg01/.Rlib/R_441_bioc320/Rcpp/include' -I/usr/local/include    -fpic  -O3 -fopenmp   -c pgenlibr.cpp -o pgenlibr.o
g++ -std=gnu++17 -I"/hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DZSTD_DISABLE_ASM   -Izstd/lib -Izstd/lib/common -Ilibdeflate  -I../inst/include -I'/hpc/users/hoffmg01/.Rlib/R_441_bioc320/Rcpp/include' -I/usr/local/include    -fpic  -O3 -fopenmp   -c RcppExports.cpp -o RcppExports.o
make: *** No rule to make target 'zstd/lib/compress/zstdmt_compress.o', needed by 'libPGZSTD.a'.  Stop.
ERROR: compilation failed for package ‘pgenlibr’
* removing ‘/hpc/users/hoffmg01/.Rlib/R_441_bioc320/pgenlibr’
* restoring previous ‘/hpc/users/hoffmg01/.Rlib/R_441_bioc320/pgenlibr’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpdbIyM8/file4813b4a1e924/pgenlibr_0.3.7.tar.gz’ had non-zero exit status

Install from CRAN succeeds

> install.packages("pgenlibr")

trying URL 'https://cran.wustl.edu/src/contrib/pgenlibr_0.3.7.tar.gz'
Content type 'application/x-gzip' length 1603887 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

* installing *source* package ‘pgenlibr’ ...
** package ‘pgenlibr’ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
configure: C++ compiler: g++ -std=gnu++17
configure: zstd 1.5.1 library detected but is too old (<1.5.2) -- compiling from source
configure: libdeflate not detected by pkg-config; falling back on system header file check
no
configure: simde not detected by pkg-config; falling back on system header file check
no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 14.2.0’
g++ -std=gnu++17 -I"/hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DZSTD_DISABLE_ASM   -Izstd/lib -Izstd/lib/common -Ilibdeflate  -I'/hpc/users/hoffmg01/.Rlib/R_441_bioc320/Rcpp/include' -I/usr/local/include    -fpic  -O3 -fopenmp   -c pvar_ffi_support.cpp -o pvar_ffi_support.o
g++ -std=gnu++17 -I"/hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/include" -DNDEBUG -DNO_UNALIGNED -DPGENLIB_NOPRINT -DZSTD_DISABLE_ASM   -Izstd/lib -Izstd/lib/common -Ilibdeflate  -I'/hpc/users/hoffmg01/.Rlib/R_441_bioc320/Rcpp/include' -I/usr/local/include    -fpic  -O3 -fopenmp   -c pgenlib_ffi_support.cpp -o pgenlib_ffi_support.o

[cutoff here since everything works]

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 9.4 (Blue Onyx)

Matrix products: default
BLAS:   /hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/lib/libRblas.so 
LAPACK: /hpc/packages/minerva-rocky9/R/4.4.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.3         rlang_1.1.4       processx_3.8.4   
 [5] purrr_1.0.2       pkgload_1.4.0     promises_1.3.0    shiny_1.9.1      
 [9] xtable_1.8-4      glue_1.8.0        htmltools_0.5.8.1 httpuv_1.6.15    
[13] ps_1.8.1          pkgbuild_1.4.5    ellipsis_0.3.2    fastmap_1.2.0    
[17] lifecycle_1.0.4   memoise_2.0.1     compiler_4.4.1    miniUI_0.1.1.1   
[21] fs_1.6.5          sessioninfo_1.2.2 htmlwidgets_1.6.4 Rcpp_1.0.13-1    
[25] urlchecker_1.0.1  later_1.3.2       digest_0.6.37     R6_2.5.1         
[29] curl_6.0.1        usethis_3.0.0     callr_3.7.6       magrittr_2.0.3   
[33] tools_4.4.1       mime_0.12         devtools_2.4.5    profvis_0.4.0    
[37] desc_1.4.3        cachem_1.1.0      remotes_2.5.0

[GabrielHoffman]

I was able to fix this in my particular case, but it doesn't solve the underlying issue. And other users on that same machine still can't install that package

Adding -lzstd to PKG_LIBS here:

plink-ng/2.0/pgenlibr/src/Makevars.in

Line 5 in 5eab376

PKG_LIBS = -lPLINK2 -L. @ZSTD_LIBS@ @LIBDEFLATE_LIBS@ -lz -lpthread

Install forcing zstd version shipped with pgenlibr:

R CMD INSTALL --configure-args="--with-zstd-lib=../inst/include/zstd/lib/ --with-zstd-include=../inst/include/zstd/lib/" .

[chrchang]

Ok, I will try to address this in the upcoming CHROM/POS pgenlibr update.