Problem installing Maaslin2

if(!requireNamespace("BiocManager", quietly = TRUE))

ERROR: dependency 'lpsymphony' is not available for package 'Maaslin2'

R version 4.4.2

That dependency should have been installed automatically by BiocManager. Maybe you told it to compile from source without having compilers installed? It’s hard to say without more information. Try BiocManager::install('lpsymphony') and see where that leads you.

That gave me the error below:

icpc -DHAVE_CONFIG_H -I. -I. -I/tmp/Rtmp48WLPH/Rbuild56dab4bdb9c69/lpsymphony/src/SYMPHONY/include/coin -w -g -O2 -DOSI_BUILD -c OsiAuxInfo.cpp -fPIC -DPIC -o OsiAuxInfo.o
OsiAuxInfo.cpp(10): catastrophic error: cannot open source file “CoinPragma.hpp”
#include “CoinPragma.hpp”

make[4]: *** [Makefile:535: OsiAuxInfo.lo] Error 1
make[4]: Leaving directory ‘/scratch/nm31/ta0341/tmp/Rtmp9H6wdk/R.INSTALL2a74b961a5f62f/lpsymphony/src/SYMPHONY/Osi/src/Osi’
make[3]: *** [Makefile:407: all] Error 2
make[3]: Leaving directory ‘/scratch/nm31/ta0341/tmp/Rtmp9H6wdk/R.INSTALL2a74b961a5f62f/lpsymphony/src/SYMPHONY/Osi/src/Osi’
make[2]: *** [Makefile:532: all-recursive] Error 1
make[2]: Leaving directory ‘/scratch/nm31/ta0341/tmp/Rtmp9H6wdk/R.INSTALL2a74b961a5f62f/lpsymphony/src/SYMPHONY/Osi’
make[1]: *** [Makefile:324: all-recursive] Error 1
make[1]: Leaving directory ‘/scratch/nm31/ta0341/tmp/Rtmp9H6wdk/R.INSTALL2a74b961a5f62f/lpsymphony/src/SYMPHONY’
make: *** [Makevars:13: SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’

  • removing ‘/home/554/ta0341/R/x86_64-pc-linux-gnu-library/4.2/lpsymphony’

You likely don’t have your system set up to compile packages correctly. An internet search lead me to this page where people were having a similar issue with lpsymphony that they solved by tweaking pkg-config. Maybe that’s the cause of your issue?