What versions of R/gcc does epactsR work with?

[ljmills]

While I can't directly get EPACTS installed there is a conda package that will install part of the program but doesn't install R or the epactsR package. I tried to install epactsR v3.3.3 using the available.tar.gz using R v 4.4.0 and get the following error:

(base) ljmills@ahl03 [~/miniconda3/share/EPACTS] % R CMD INSTALL epactsR_3.3.3.tar.gz

• installing to library ‘/users/2/ljmills/R/x86_64-pc-linux-gnu-library/4.4’
• installing source package ‘epactsR’ ...
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 11.3.0’
  using C++ compiler: ‘g++ (GCC) 11.3.0’
  /common/software/install/migrated/gcc/11.3.0/bin/g++ -std=gnu++17 -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c Error.cpp -o Error.o
  /common/software/install/migrated/gcc/11.3.0/bin/g++ -std=gnu++17 -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c PhredHelper.cpp -o PhredHelper.o
  /common/software/install/migrated/gcc/11.3.0/bin/gcc -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c adler32.c -o adler32.o
  /common/software/install/migrated/gcc/11.3.0/bin/gcc -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c bedidx.c -o bedidx.o
  /common/software/install/migrated/gcc/11.3.0/bin/gcc -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c bgzf.c -o bgzf.o
  /common/software/install/migrated/gcc/11.3.0/bin/gcc -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c compress.c -o compress.o
  /common/software/install/migrated/gcc/11.3.0/bin/gcc -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c crc32.c -o crc32.o
  /common/software/install/migrated/gcc/11.3.0/bin/gcc -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c deflate.c -o deflate.o
  /common/software/install/migrated/gcc/11.3.0/bin/g++ -std=gnu++17 -I"/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/include" -DNDEBUG -I/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/include/ -L/common/software/install/manual/bzip2/1.0.8-gcc11.3.0-fpic/lib -fpic -g -O2 -c epacts.cpp -o epacts.o
  In file included from fVcf.h:13,
  from epacts.cpp:4:
  pFile.h: In member function ‘const char* pFile::getLine()’:
  pFile.h:204:44: error: ordered comparison of pointer with integer zero (‘char*’ and ‘int’)
  204 | if ( gzgets(gf, line, MAX_LINE_SIZE) > 0 ) {
  | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
  In file included from epacts.cpp:4:
  fVcf.h: In member function ‘int fVcf::HOMMINC(int)’:
  fVcf.h:310:15: error: ‘isnan’ was not declared in this scope; did you mean ‘std::isnan’?
  310 | if ( !isnan(g) ) { // do not count missing at any place
  | ^~~~~
  | std::isnan
  In file included from fVcf.h:11,
  from epacts.cpp:4:
  /common/software/install/migrated/gcc/11.3.0/include/c++/11.3.0/cmath:632:5: note: ‘std::isnan’ declared here
  632 | isnan(_Tp __x)
  | ^~~~~
  In file included from epacts.cpp:4:
  fVcf.h: In member function ‘void fVcf::GENOCNT(int, int*)’:
  fVcf.h:339:15: error: ‘isnan’ was not declared in this scope; did you mean ‘std::isnan’?
  339 | if ( !isnan(g) ) { // do not count missing at any place
  | ^~~~~
  | std::isnan
  In file included from fVcf.h:11,
  from epacts.cpp:4:
  /common/software/install/migrated/gcc/11.3.0/include/c++/11.3.0/cmath:632:5: note: ‘std::isnan’ declared here
  632 | isnan(_Tp __x)
  | ^~~~~
  In file included from epacts.cpp:4:
  fVcf.h: In member function ‘void fVcf::CASECTRLCNT(int, int*, std::vector&)’:
  fVcf.h:353:13: error: ‘isnan’ was not declared in this scope; did you mean ‘std::isnan’?
  353 | if ( !isnan(g) ) { // do not count missing at any place
  | ^~~~~
  | std::isnan
  In file included from fVcf.h:11,
  from epacts.cpp:4:
  /common/software/install/migrated/gcc/11.3.0/include/c++/11.3.0/cmath:632:5: note: ‘std::isnan’ declared here
  632 | isnan(_Tp __x)
  | ^~~~~
  In file included from epacts.cpp:4:
  fVcf.h: In member function ‘void fVcf::print(FILE*)’:
  fVcf.h:398:14: error: ‘isnan’ was not declared in this scope; did you mean ‘std::isnan’?
  398 | if ( isnan(v) ) {
  | ^~~~~
  | std::isnan
  In file included from fVcf.h:11,
  from epacts.cpp:4:
  /common/software/install/migrated/gcc/11.3.0/include/c++/11.3.0/cmath:632:5: note: ‘std::isnan’ declared here
  632 | isnan(_Tp __x)
  | ^~~~~
  In file included from epacts.cpp:4:
  fVcf.h: In member function ‘int fVcf::fullParseMarkers(char*, int)’:
  fVcf.h:828:17: error: ‘isnan’ was not declared in this scope; did you mean ‘std::isnan’?
  828 | if ( !isnan(gt) ) {
  | ^~~~~
  | std::isnan
  In file included from fVcf.h:11,
  from epacts.cpp:4:
  /common/software/install/migrated/gcc/11.3.0/include/c++/11.3.0/cmath:632:5: note: ‘std::isnan’ declared here
  632 | isnan(_Tp __x)
  | ^~~~~
  epacts.cpp: In function ‘SEXPREC* writeMatrix(SEXP, SEXP)’:
  epacts.cpp:62:14: error: ‘isnan’ was not declared in this scope; did you mean ‘std::isnan’?
  62 | if ( isnan(e) ) {
  | ^~~~~
  | std::isnan
  In file included from fVcf.h:11,
  from epacts.cpp:4:
  /common/software/install/migrated/gcc/11.3.0/include/c++/11.3.0/cmath:632:5: note: ‘std::isnan’ declared here
  632 | isnan(_Tp __x)
  | ^~~~~
  epacts.cpp: In function ‘SEXPREC* writeNamedMatrix(SEXP, SEXP, SEXP)’:
  epacts.cpp:127:14: error: ‘isnan’ was not declared in this scope; did you mean ‘std::isnan’?
  127 | if ( isnan(e) ) {
  | ^~~~~
  | std::isnan
  In file included from fVcf.h:11,
  from epacts.cpp:4:
  /common/software/install/migrated/gcc/11.3.0/include/c++/11.3.0/cmath:632:5: note: ‘std::isnan’ declared here
  632 | isnan(_Tp __x)
  | ^~~~~
  make: *** [/common/software/install/manual/R/4.4.0-openblas-rocky8-fix/lib64/R/etc/Makeconf:202: epacts.o] Error 1
  ERROR: compilation failed for package ‘epactsR’
• removing ‘/users/2/ljmills/R/x86_64-pc-linux-gnu-library/4.4/epactsR’

Is there a specific version of something I need to get this to compile? Is there an updated version of this R package somewhere?

-L