Problem installing Maaslin2

Downstream analysis and statistics
1 
if(!requireNamespace("BiocManager", quietly = TRUE))
	install.packages("BiocManager")
BiocManager::install("Maaslin2")


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

R version 4.4.2

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.

3

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’
4

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?