update configure.ac to use C++

[mtmorgan]

• test for sys/mman.h
• use AC_SEARCH_LIBS() to add -lrt if necessary, instead of AC_CHECK_LIB(), as recommended by https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Libraries.html
• updates Need to link to -lrt for shm_open #93, updates add configure.ac, src/Makevars.in to check librt for shm_open and… #94

[mtmorgan]

@spotrh Not sure if you still have a configuration where you can test this update? It uses C++ as configured by R when performing the test. It also tests for the availability (in C++) of the appropriate header file. This is from a comment from a CRAN member.

[mmokrejs]

I am hitting this with R-3.4.4 on Ubuntu-20.04 on which I am trying to install Bioconductor-3.6. I do not see configure.ac to be patched in the BiocParallel_1.12.0.tar.gz file.

But magic happened:

$ R CMD INSTALL BiocParallel_1.16.6.tar.gz 
* installing to library ‘/home/biomex/lib64/R/library’
* installing *source* package ‘BiocParallel’ ...
checking for gcc... gcc
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for shm_open in -lrt... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I/home/biomex/lib64/R/include -DNDEBUG  -I"/home/biomex/lib64/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2 -c ipcmutex.cpp -o ipcmutex.o
g++ -std=gnu++11 -shared -L/home/biomex/lib64/R/lib -L/usr/local/lib64 -o BiocParallel.so ipcmutex.o -lrt -L/home/biomex/lib64/R/lib -lR
installing to /home/biomex/lib64/R/library/BiocParallel/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocParallel)
$

So the -lrt got into its place.

[mtmorgan]

@mmokrejs thanks for the report of success with BiocParallel_1.16.6.

Bioconductor-3.6 is from 2017 and is very old. Changes are introduced into the 'devel' or sometimes current release branch, but cannot be ported to earlier releases (Bioconductor does not allow commits to older releases, and does not build & propagate older packages).