Missing Boost files due to compiler dependent compilation

[Flamefire]

It seems the included Boost files are generated (as per the included instructions) by running strace -e open -f R CMD INSTALL .. 2>&1 | grep '"./boost/[^=]* = [0-9]' | cut -d \" -f 2 2>&1 | sort | uniq >/tmp/boost-includes.log

However this will miss out on compiler-dependent includes, for example on Arch it fails to find boost/smart_ptr/detail/sp_counted_base_sync.hpp, see

mzR/src/boost/boost/smart_ptr/detail/sp_counted_base.hpp

Lines 71 to 72 in 39380f5

	#elif defined( BOOST_SP_HAS_SYNC )
	# include <boost/smart_ptr/detail/sp_counted_base_sync.hpp>

I'd hence strongly recommend to not cut down on boost headers or at least do it on the library level, e.g. if anything from boost/foo is included, copy the whole folder, not parts of it. Being able to use a system installed Boost would be even better

[sneumann]

Hi Alexander, your observation is spot on, and we don't have a good solution yet. Any suggestions welcome, I am not a boost wizard. IIRC the BH package carries the headers only, so we can't take that alone. Currently I don't have an estimate how large we'd get if we include entire libraries used by pwiz. However, an upgrade in mzR to a new pwiz is overdue :-(
I have an abandoned branch that didn't work well enough to be merged. It would be great to get something rolling into the next devel release. Yours, Steffen

[sneumann]

Just as update, there is an updated branch with the new boost stuff in
https://github.com/sneumann/mzR/tree/feature/updatePwiz_3_0_20290
Which compiles but then fails somewhere when reading the mzML :-(
Yours, Steffen

[sneumann]

Hi, I can confirm that mzR-3.9.3 at http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/ at commit 458704d builds fine with a new pwiz version. There might be still / again missing header files. Please report back if things work on your platform now. Yours, Steffen

[Flamefire]

and we don't have a good solution yet. Any suggestions welcome, I am not a boost wizard.

A suggestion was already provided:

I'd hence strongly recommend to not cut down on boost headers or at least do it on the library level, e.g. if anything from boost/foo is included, copy the whole folder, not parts of it. Being able to use a system installed Boost would be even better

Haven't checked on the affected machine by now, so it might be solved already, but keep the above in mind

[sneumann]

Hi @Flamefire , does mzR >= 2.29.3 work now on your setup ? If yes, please report back so we can close this issue. Yours, Steffen