Error: PopGenome unable to install

[oninlaurel]

Hi @pievos101, I am trying to install PopGenome package in my R but I am unable to do so and I'm getting this error. I am using R v.4.4.2 and RStudio v.2024.09.0+375. I would appreciate if you could help me with the installation. Thank you!

>install.packages("PopGenome")
Warning in install.packages :
  package ‘PopGenome’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

[drew-olson-tmru]

Hi @oninlaurel,

Try using:

install.packages("devtools")
library(devtools)

devtools::install_github("pievos101/PopGenome")
library(PopGenome)

If you have an issue installing the package, then the likely factor is the installation of the "devtools" package. My local machine (Mac - UNIX) had an issue with the initial "devtools" installation, which prevented me from installing "PopGenome". This probably was just a me thing and not a Unix thing, but I was able to circumvent this by using an available HPC through my organization using a Linux system. I would recommend using an HPC from your institution/organization and access R from there.

[xxxicyixxx]

Hi @drew-olson-tmru,

I’m currently working with R version 4.3.3 on the HPC system, but I encountered an error when trying to install the "PopGenome" package.

The error message reads:
In file included from whopgenome/../tabix/tabix.h:33,
from whopgenome/whop_tabix.h:33,
from whopgenome/whopgen_common.h:272,
from whopgenome/whopgen_codemat.cpp:24:
whopgenome/../tabix/bgzf.h:29:10: fatal error: zlib.h: No such file or directory
29 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
ERROR: compilation failed for package ‘PopGenome’

Could you please let me know which version of R you are using? I’ve verified that the "devtools" package is not the issue, but I’m unsure if the R version might be causing this problem.

[drew-olson-tmru]

Hi @xxxicyixxx,

It looks like you may be missing a specific Linux package for zlib, which is leading to compilation issues. Here's a stackoverflow solution that may work: https://stackoverflow.com/questions/36374267/how-to-fix-fatal-error-zlib-h-no-such-file-or-directory

However, this may be an issue with developer tools available on the HPC itself. You can try some of the solutions associated with zlib.h, but you may need assistance via your HPC management group. Best of luck!

[Chatchamew]

I'm also having a problem of installing PopGenome. Last time I use the previous version of RStudio and I could download it manually without problem. However, when I update RStudio to the latest version. I got this error.

make: *** [whopgenome/readdnapp.o] Error 1
ERROR: compilation failed for package ‘PopGenome’

My computer is MacBook Pro with Apple M3 Pro chip and macOS Sequoia 15.3.1.
My version for R is 4.5.0 and my version for RStudio is 2024.12.1+563.

[Chatchamew]

The full error.

devtools::install_github("pievos101/PopGenome")
Downloading GitHub repo pievos101/PopGenome@HEAD
── R CMD build ─────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/8f/f796rj315876tvkpmhk_hw980000gn/T/RtmpSqSe4q/remotesa20c2229cff6/pievos101-PopGenome-ab39ee8/DESCRIPTION’ ...
─ preparing ‘PopGenome’:
✔ 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
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘PopGenome_2.7.7.tar.gz’

• installing source package ‘PopGenome’ ...
  ** this is package ‘PopGenome’ version ‘2.7.7’
  ** using staged installation
  ** libs
  using C compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
  using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
  using SDK: ‘MacOSX15.2.sdk’
  clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c whopgenome/readdnapp.cpp -o whopgenome/readdnapp.o
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:808:28: error: too many arguments provided to function-like macro invocation
  808 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:807:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  807 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:874:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  874 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:808:9: error: expected ';' at end of declaration list
  808 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:890:28: error: too many arguments provided to function-like macro invocation
  890 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:889:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  889 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:874:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  874 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:890:9: error: expected ';' at end of declaration list
  890 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:971:28: error: too many arguments provided to function-like macro invocation
  971 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:970:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  970 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:874:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  874 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:971:9: error: expected ';' at end of declaration list
  971 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1134:28: error: too many arguments provided to function-like macro invocation
  1134 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1133:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  1133 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:874:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  874 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1134:9: error: expected ';' at end of declaration list
  1134 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  whopgenome/readdnapp.cpp:438:76: warning: format specifies type 'long long' but the argument has type 'unsigned int' [-Wformat]
  438 | Rprintf("(!!) Failed to allocate %lld bytes to load file into memory!\n",filebytelength);
  | ~~~~ ^~~~~~~~~~~~~~
  | %u
  whopgenome/readdnapp.cpp:447:72: warning: format specifies type 'unsigned long long' but the argument has type 'unsigned int' [-Wformat]
  447 | Rprintf("(!!) Only %d bytes of %llu could be read!\n",numbytesloaded,filebytelength);
  | ~~~~ ^~~~~~~~~~~~~~
  | %u
  In file included from whopgenome/readdnapp.cpp:811:
  whopgenome/rdnapp_Fasta.h:127:46: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  127 | FDBG Rprintf("at end of file - numsamples= %d numsamples\n");
  | ~^
  whopgenome/rdnapp_Fasta.h:130:24: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  130 | FDBG Rprintf("blkidx %d blkidx\n");
  | ~^
  whopgenome/rdnapp_Fasta.h:131:25: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  131 | FDBG Rprintf("fileidx %d fileidx\n");
  | ~^
  In file included from whopgenome/readdnapp.cpp:817:
  whopgenome/rdnapp_Phylip.h:99:12: warning: variable 'samplenameidx' set but not used [-Wunused-but-set-variable]
  99 | for( int samplenameidx=0; c != ' ';samplenameidx++)
  | ^
  whopgenome/rdnapp_Phylip.h:122:60: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  122 | Rprintf("\tdistance in elements to end of matrix=%d\n",matend - matrowptr);
  | ~~ ^~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_Phylip.h:173:71: warning: format specifies type 'unsigned long long' but the argument has type 'long' [-Wformat]
  173 | Rprintf("\tdistance in elements to end of matrix=%" PRIu64 "\n", matend - matrowptr );
  | ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~
  In file included from whopgenome/readdnapp.cpp:823:
  whopgenome/rdnapp_MAF.h:164:79: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  164 | ONDBG Rprintf(" sequence name length exceeds available buffer size %d\n",sizeof(seqnamebuf));
  | ~~ ^~~~~~~~~~~~~~~~~~
  | %lu
  whopgenome/rdnapp_MAF.h:401:89: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  401 | Rprintf("(!!) MAF error : Sequence name length exceeds available buffer size %d\n",sizeof(seqnamebuf));
  | ~~ ^~~~~~~~~~~~~~~~~~
  | %lu
  whopgenome/rdnapp_MAF.h:462:38: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  462 | Rprintf("*********>>>>>> %d\n",(mat - debug_mat_offs_begin)/numsamples );
  | ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:495:30: warning: array subscript is of type 'char' [-Wchar-subscripts]
  495 | c = (int)nucleotide_mapping['-'];
  | ^~~~
  whopgenome/rdnapp_MAF.h:502:39: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  502 | ONDBG Rprintf("matoffsstart=%d\n",mat-debug_mat_offs_begin);
  | ~~ ^~~~~~~~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:506:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  506 | ONDBG Rprintf("jj=%d: %d\n",jj,((mat-matbegin)-ii)/numsamples);
  | ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:509:92: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  509 | Rprintf("(!!) MAF error : fill-unused-positions would write %d beyond matrix end!\n",matend-mat);
  | ~~ ^~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:280:6: warning: variable 'currentalignmentoffset' set but not used [-Wunused-but-set-variable]
  280 | currentalignmentoffset=0 //where the current alignment-block begins
  | ^
  whopgenome/readdnapp.cpp:980:57: warning: format specifies type 'unsigned long long' but the argument has type 'unsigned int' [-Wformat]
  980 | ONDBG { Rprintf("File='%s'\nFilesize=%llu\n",filename,filebytelength); }
  | ~~~~ ^~~~~~~~~~~~~~
  | %u
  17 warnings and 12 errors generated.
  make: *** [whopgenome/readdnapp.o] Error 1
  ERROR: compilation failed for package ‘PopGenome’
• removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PopGenome’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/8f/f796rj315876tvkpmhk_hw980000gn/T//RtmpSqSe4q/filea20c200b3546/PopGenome_2.7.7.tar.gz’ had non-zero exit status

[CarolinaA09]

I have the a similar problem. Does anybody know how to solve it?

devtools::install_github("pievos101/PopGenome")
Downloading GitHub repo pievos101/PopGenome@HEAD
── R CMD build ───────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/f_/b2jp6m_s38v6zwc_v49jbz5r0000gn/T/Rtmp6Xaxkc/remotes18c767d49716/pievos101-PopGenome-ab39ee8/DESCRIPTION’ ...
─ preparing ‘PopGenome’:
✔ 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
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘PopGenome_2.7.7.tar.gz’

• installing source package ‘PopGenome’ ...
  ** this is package ‘PopGenome’ version ‘2.7.7’
  ** using staged installation
  ** libs
  using C compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
  using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
  using SDK: ‘MacOSX15.4.sdk’
  clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c whopgenome/readdnapp.cpp -o whopgenome/readdnapp.o
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:792:28: error: too many arguments provided to function-like macro invocation
  792 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:791:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  791 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:549:22: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  549 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:792:9: error: expected ';' at end of declaration list
  792 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:874:28: error: too many arguments provided to function-like macro invocation
  874 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:873:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  873 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:549:22: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  549 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:874:9: error: expected ';' at end of declaration list
  874 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:955:28: error: too many arguments provided to function-like macro invocation
  955 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:954:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  954 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:549:22: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  549 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:955:9: error: expected ';' at end of declaration list
  955 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1118:28: error: too many arguments provided to function-like macro invocation
  1118 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1009:9: note: macro 'length' defined here
  1009 | #define length(x) Rf_length(x)
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1117:3: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
  1117 | _LIBCPP_HIDE_FROM_ABI int
  | ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:549:22: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  549 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
  | ^
  In file included from whopgenome/readdnapp.cpp:43:
  In file included from whopgenome/whop_rsupport.h:33:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:325:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:19:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:35:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1118:9: error: expected ';' at end of declaration list
  1118 | length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
  | ^
  whopgenome/readdnapp.cpp:438:76: warning: format specifies type 'long long' but the argument has type 'unsigned int' [-Wformat]
  438 | Rprintf("(!!) Failed to allocate %lld bytes to load file into memory!\n",filebytelength);
  | ~~~~ ^~~~~~~~~~~~~~
  | %u
  whopgenome/readdnapp.cpp:447:72: warning: format specifies type 'unsigned long long' but the argument has type 'unsigned int' [-Wformat]
  447 | Rprintf("(!!) Only %d bytes of %llu could be read!\n",numbytesloaded,filebytelength);
  | ~~~~ ^~~~~~~~~~~~~~
  | %u
  In file included from whopgenome/readdnapp.cpp:811:
  whopgenome/rdnapp_Fasta.h:127:46: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  127 | FDBG Rprintf("at end of file - numsamples= %d numsamples\n");
  | ~^
  whopgenome/rdnapp_Fasta.h:130:24: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  130 | FDBG Rprintf("blkidx %d blkidx\n");
  | ~^
  whopgenome/rdnapp_Fasta.h:131:25: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
  131 | FDBG Rprintf("fileidx %d fileidx\n");
  | ~^
  In file included from whopgenome/readdnapp.cpp:817:
  whopgenome/rdnapp_Phylip.h:99:12: warning: variable 'samplenameidx' set but not used [-Wunused-but-set-variable]
  99 | for( int samplenameidx=0; c != ' ';samplenameidx++)
  | ^
  whopgenome/rdnapp_Phylip.h:122:60: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  122 | Rprintf("\tdistance in elements to end of matrix=%d\n",matend - matrowptr);
  | ~~ ^~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_Phylip.h:173:71: warning: format specifies type 'unsigned long long' but the argument has type 'long' [-Wformat]
  173 | Rprintf("\tdistance in elements to end of matrix=%" PRIu64 "\n", matend - matrowptr );
  | ~~~~~~~~~ ^~~~~~~~~~~~~~~~~~
  In file included from whopgenome/readdnapp.cpp:823:
  whopgenome/rdnapp_MAF.h:164:79: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  164 | ONDBG Rprintf(" sequence name length exceeds available buffer size %d\n",sizeof(seqnamebuf));
  | ~~ ^~~~~~~~~~~~~~~~~~
  | %lu
  whopgenome/rdnapp_MAF.h:401:89: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  401 | Rprintf("(!!) MAF error : Sequence name length exceeds available buffer size %d\n",sizeof(seqnamebuf));
  | ~~ ^~~~~~~~~~~~~~~~~~
  | %lu
  whopgenome/rdnapp_MAF.h:462:38: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  462 | Rprintf("*********>>>>>> %d\n",(mat - debug_mat_offs_begin)/numsamples );
  | ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:502:39: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  502 | ONDBG Rprintf("matoffsstart=%d\n",mat-debug_mat_offs_begin);
  | ~~ ^~~~~~~~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:506:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  506 | ONDBG Rprintf("jj=%d: %d\n",jj,((mat-matbegin)-ii)/numsamples);
  | ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:509:92: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  509 | Rprintf("(!!) MAF error : fill-unused-positions would write %d beyond matrix end!\n",matend-mat);
  | ~~ ^~~~~~~~~~
  | %ld
  whopgenome/rdnapp_MAF.h:280:6: warning: variable 'currentalignmentoffset' set but not used [-Wunused-but-set-variable]
  280 | currentalignmentoffset=0 //where the current alignment-block begins
  | ^
  whopgenome/readdnapp.cpp:980:57: warning: format specifies type 'unsigned long long' but the argument has type 'unsigned int' [-Wformat]
  980 | ONDBG { Rprintf("File='%s'\nFilesize=%llu\n",filename,filebytelength); }
  | ~~~~ ^~~~~~~~~~~~~~
  | %u
  16 warnings and 12 errors generated.
  make: *** [whopgenome/readdnapp.o] Error 1
  ERROR: compilation failed for package ‘PopGenome’
• removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/PopGenome’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/f_/b2jp6m_s38v6zwc_v49jbz5r0000gn/T//Rtmp6Xaxkc/file18c7360b5a9b/PopGenome_2.7.7.tar.gz’ had non-zero exit status

[mdondrup]

Hi I have tried the same approach on a MacBook M4 und Tahoe. However there are many errors due to legacy code. It is unlikely that the package can be compiled using a modern compiler like clang. I strongly suggest to use a different software.