Error in installation

Question

Error in installation

JuliViglino opened this issue 6 months ago · comments

Hi, I'm facing some issues in sodium installation in Ubuntu 22.04.
I have already installedlibsodium-devthrough apt-get.

>iinstall.packages('sodium')

Installing package into ‘/home/julieta/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sodium_1.3.1.tar.gz'
Content type 'application/x-gzip' length 468383 bytes (457 KB)
==================================================
downloaded 457 KB

* installing *source* package ‘sodium’ ...
** package ‘sodium’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lsodium
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c diffie.c -o diffie.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c hashing.c -o hashing.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c helpers.c -o helpers.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c keygen.c -o keygen.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c messaging.c -o messaging.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c password.c -o password.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c seal.c -o seal.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c secret.c -o secret.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c signing.c -o signing.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c stream.c -o stream.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H0vbME/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c xor.c -o xor.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sodium.so diffie.o hashing.o helpers.o init.o keygen.o messaging.o password.o seal.o secret.o signing.o stream.o xor.o -lsodium -L/usr/lib/R/lib -lR
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/libsodium.a(libsodium_la-randombytes.o): warning: relocation against `randombytes_sysrandom_implementation' in read-only section `.text'
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/libsodium.a(libsodium_la-randombytes.o): relocation R_X86_64_PC32 against symbol `randombytes_sysrandom_implementation' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: sodium.so] Error 1
ERROR: compilation failed for package ‘sodium’
* removing ‘/home/julieta/R/x86_64-pc-linux-gnu-library/4.3/sodium’

The downloaded source packages are in
	‘/tmp/RtmpoaCSRZ/downloaded_packages’
Warning message:
In install.packages("sodium") :
  installation of package ‘sodium’ had non-zero exit status

System I'm using:

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS