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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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Fails to compile/install on Fedora 38 / R 4.3.0 #282

Closed c4chris closed 1 year ago

c4chris commented 1 year ago

Hello,

I tried and failed to get the mzR package to install through BioConductor in the latest release of Fedora (version 38), running R version 4.3

After applying the attached simple patch, I got it to compile and install

I do not know if it is the proper way to fix things, but here it is in case it is useful

Kind regards, Christian

mzR_diff.txt

sneumann commented 1 year ago

Hi, thanks for reporting and even sending a patch.

If you contributed that as a pull request, we'd even see results on the continuous integration testing, that would speed things up on our side. Oh, and you'd be listed as contributor on the GitHub stats :-) If not, I'll try to get to it in the coming days.

Yours, Steffen

c4chris commented 1 year ago

Ok, done in pull request #283

sneumann commented 1 year ago

This might also fix the following report by Prof. Ripley:

Files

pwiz/data/msdata/BinaryDataEncoder.hpp
pwiz/data/msdata/MSData.hpp
pwiz/utility/misc/BinaryData.cpp

are missing including <cstdint>, as they use std::int64_t.

It also fails to install with current LLVM clang 16.0.2 unless flag
-Wno-error=enum-constexpr-conversion is passed.

see also comments in https://www.stats.ox.ac.uk/pub/bdr/gcc13/README.txt

Yours, Steffen

sneumann commented 1 year ago

still trying to find an appropriate container for CI, r/rhub/fedora-gcc-devel has R-4.4 and only gcc-12, so 1) fails to install via BiocManager:install and 2) not reproducing the issue .