Couldn't install spdep on ubuntu

Fingernight1 commented 1 year ago

When I install.packages("spdep") via source or url or other ways. It didn't work and occurs this Error. Could someone help me with this issue? Thanks in advanced~! R data inst byte-compile and prepare package for lazy loading double free or corruption (out) Aborted (core dumped) ERROR: lazy loading failed for package ‘spdep’

removing ‘/home/jins/anaconda3/envs/R_new/lib/R/library/spdep’ Warning message: In install.packages("/home/jins/spdep_1.2-6.tar.gz", repos = NULL, : installation of package ‘/home/jins/spdep_1.2-6.tar.gz’ had non-zero exit status

rsbivand commented 1 year ago

Please always include full sessionInfo() output. Please do run update.packages(check.build=TRUE) before trying to install any package. Then install spData, sf, sp in turn before spdep. Report back on progress.

rsbivand commented 1 year ago

Also, anaconda is not checked or supported, so for non-standard installations, no help is available.

Fingernight1 commented 1 year ago

Thanks for your time~Here is all the output when I install.package("spdep")

installing source package ‘spdep’ ... using staged installation libs x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c card.c -o card.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c dfs_ncomp.c -o dfs_ncomp.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c dnn.c -o dnn.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c gabriel.c -o gabriel.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c gearyw.c -o gearyw.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c gsymtest.c -o gsymtest.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c init.c -o init.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c insiders.c -o insiders.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c jc.c -o jc.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c knn.c -o knn.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c lagw.c -o lagw.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c listw2sn.c -o listw2sn.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c nbdists.c -o nbdists.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c polypoly.c -o polypoly.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c relative.c -o relative.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c skater.c -o skater.o x86_64-conda-linux-gnu-cc -I"/home/jins/anaconda3/envs/R_new/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/jins/anaconda3/envs/R_new/include -I/home/jins/anaconda3/envs/R_new/include -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/jins/anaconda3/envs/R_new/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659993824316/work=/usr/local/src/conda/r-base-4.2.1 -fdebug-prefix-map=/home/jins/anaconda3/envs/R_new=/usr/local/src/conda-prefix -c symtest.c -o symtest.o x86_64-conda-linux-gnu-cc -shared -L/home/jins/anaconda3/envs/R_new/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/jins/anaconda3/envs/R_new/lib -Wl,-rpath-link,/home/jins/anaconda3/envs/R_new/lib -L/home/jins/anaconda3/envs/R_new/lib -o spdep.so card.o dfs_ncomp.o dnn.o gabriel.o gearyw.o gsymtest.o init.o insiders.o jc.o knn.o lagw.o listw2sn.o nbdists.o polypoly.o relative.o skater.o symtest.o -llapack -lblas -lgfortran -lm -lquadmath -L/home/jins/anaconda3/envs/R_new/lib/R/lib -lR installing to /home/jins/anaconda3/envs/R_new/lib/R/library/00LOCK-spdep/00new/spdep/libs R data inst byte-compile and prepare package for lazy loading double free or corruption (out) Aborted (core dumped) ERROR: lazy loading failed for package ‘spdep’
removing ‘/home/jins/anaconda3/envs/R_new/lib/R/library/spdep’ Warning message: In install.packages("/home/jins/spdep_1.2-6.tar.gz", repos = NULL, : installation of package ‘/home/jins/spdep_1.2-6.tar.gz’ had non-zero exit status

Because I couldn't install spData or sf, sp via install.packages, so I turn to conda to help me build the r-spdata r-sf and r-sp.

rsbivand commented 1 year ago

If you use anaconda, no support caan be given. Install sf, sp and spData simply, first installing sf's external dependencies https://github.com/r-spatial/sf/#ubuntu. Mixing compiler arguments is a clear potential cause of trouble.

r-spatial / spdep

Couldn't install spdep on ubuntu #88