##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
mkdir -p ../inst
(cd	adapterremoval && (/usr/bin/make -f"E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:295: warning: ignoring old recipe for target '.cc.o'
g++ -std=gnu++17  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++17  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++17  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c argparse.cc 
argparse.cc: In member function 'virtual size_t ar::argparse::knob::consume(ar::string_vec_citer, const ar::string_vec_citer&)':
argparse.cc:481:9: error: 'int64_t' was not declared in this scope
  481 |         int64_t temp = 0;
      |         ^~~~~~~
argparse.cc:39:1: note: 'int64_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
   38 | #include "strutils.h"
  +++ |+#include <cstdint>
   39 | 
argparse.cc:483:25: error: 'temp' was not declared in this scope; did you mean 'tm'?
  483 |         if (!(stream >> temp)) {
      |                         ^~~~
      |                         tm
argparse.cc:493:13: error: 'temp' was not declared in this scope; did you mean 'tm'?
  493 |         if (temp >= 0 && temp <= std::numeric_limits<unsigned>::max()) {
      |             ^~~~
      |             tm
make[1]: *** [Makefile.win:46: argparse.o] Error 1
make: *** [Makefile.win:12: all] Error 2
ERROR: compilation failed for package 'Rbowtie2'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/Rbowtie2'