I am try to install the hdp package by Nicola Robers using the following command in R:
devtools::install_github("nicolaroberts/hdp", build_vignettes = TRUE)This used to get compiled and installed fine when I had the R version 3.6.2 and gcc version 9.2.1 on an (Arch) Linux machine. After updating the system to R 4.0.0 and gcc 10.1.0, the installation fails with the following message:
* installing *source* package ‘hdp’ ...** using staged installation** libsgcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c R-base.c -o R-base.ogcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c R-conparam.c -o R-conparam.ogcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c R-dp.c -o R-dp.ogcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c R-hdp.c -o R-hdp.ogcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c R-hdpMultinomial_iterate.c -o R-hdpMultinomial_iterate.ogcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c R-multinomial.c -o R-multinomial.ogcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c R-utils.c -o R-utils.ogcc -I"/usr/include/R/" -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -c randutils.c -o randutils.ogcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o hdp.so R-base.o R-conparam.o R-dp.o R-hdp.o R-hdpMultinomial_iterate.o R-multinomial.o R-utils.o randutils.o -L/usr/lib64/R/lib -lR/usr/bin/ld: R-conparam.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here/usr/bin/ld: R-dp.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here/usr/bin/ld: R-hdp.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here/usr/bin/ld: R-hdpMultinomial_iterate.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here/usr/bin/ld: R-multinomial.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here/usr/bin/ld: R-utils.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here/usr/bin/ld: randutils.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined herecollect2: error: ld returned 1 exit statusmake: *** [/usr/share/R//make/shlib.mk:6: hdp.so] Error 1ERROR: compilation failed for package ‘hdp’
The individual files are compiling fine, but the linking seems to fail. Any idea on how to go about debugging what is missing?