[R] make install libgfortran.so.5: cannot open shared object file: No such file or directory; conftest.c:1:10: fatal error: jni.h: No such file or directory

Rob Kudyba rk3199 @end|ng |rom co|umb|@@edu
Sun Nov 20 20:03:34 CET 2022

> It should be possible to run R without installing it, as
> /path/to/R-4.2.2/bin/R (strictly speaking, as bin/R under the build
> directory, if you're building R separately from the source tree). Does
> it work?

So far R does seem to be working and I've tested installing some packages.
Is there any sample R program I can run to test against this error?

> Does /path/to/R-4.2.2/bin/R -d ldd give you any useful information?

R -d ldd
linux-vdso.so.1 =>  (0x00002aaaaaacd000)
libRblas.so => /path/to/R-4.2/lib64/R/lib/libRblas.so (0x00002aaaaaccf000)
libgfortran.so.5 => /path/to/gcc-11.2/lib64/libgfortran.so.5
libm.so.6 => /lib64/libm.so.6 (0x00002aaaab3a0000)
libquadmath.so.0 => /path/to/gcc-11.2/lib64/libquadmath.so.0
libreadline.so.6 => /lib64/libreadline.so.6 (0x00002aaaab8e9000)
libpcre2-8.so.0 => /path/to/pcre2-10.35/lib/libpcre2-8.so.0
liblzma.so.5 => /lib64/liblzma.so.5 (0x00002aaaabd88000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00002aaaabfae000)
libz.so.1 => /lib64/libz.so.1 (0x00002aaaac1be000)
librt.so.1 => /lib64/librt.so.1 (0x00002aaaac3d4000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaac5dc000)
libgomp.so.1 => /path/to/gcc-11.2/lib64/libgomp.so.1 (0x00002aaaac7e0000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaaca21000)
libc.so.6 => /lib64/libc.so.6 (0x00002aaaacc3d000)
/lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)
libgcc_s.so.1 => /path/to/gcc-11.2/lib64/libgcc_s.so.1 (0x00002aaaad00a000)
libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00002aaaad222000)

> Can
> you use strace -f -e openat /path/to/R-4.2.2/bin/R to confirm that the
> dynamic library loader is looking in /path/to/gcc-11.2/lib64 for the
> shared objects?

[pid 241836] +++ exited with 0 +++
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=241836,
si_uid=547289, si_status=0, si_utime=0, si_stime=0} ---
openat(AT_FDCWD, "/sys/devices/system/cpu",

R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

strace: Process 241837 attached
strace: Process 241838 attached
[pid 241838] +++ exited with 0 +++
[pid 241837] --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED,
si_pid=241838, si_uid=547289, si_status=0, si_utime=0, si_stime=0} ---
[pid 241837] +++ exited with 0 +++
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=241837,
si_uid=547289, si_status=0, si_utime=0, si_stime=0} ---
strace: Process 241839 attached
[pid 241839] +++ exited with 0 +++
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=241839,
si_uid=547289, si_status=0, si_utime=0, si_stime=0} ---

If /path/to/gcc-11.2/lib64 is missing from both /etc/ld.so.conf and the
> environment variable LD_LIBRARY_PATH and you don't want to set it
> manually every time, you can either edit /path/to/R-4.2.2/etc/ldpaths
> or pass the -Wl,-rpath=/path/to/gcc-11.2/lib64 flag to the linker.

/path/to/gcc-11.2/lib is definitely in LD_LIBRARY_PATH when loading the GCC
11.2 module.

If using the /path/to/R-4.2.2/etc/ldpaths where would I put the correct
path? I would've hoped the configure/make process would've found this

if test -n "/usr/local/lib64"; then
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:/usr/local/lib64}
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
## This is DYLD_FALLBACK_LIBRARY_PATH on Darwin (macOS) and
## LD_LIBRARY_PATH elsewhere.
## However, on macOS >=10.11 (if SIP is enabled, the default), the
## environment value will not be passed to a script such as R.sh, so
## would not seen here.
if test -z "${LD_LIBRARY_PATH}"; then

> During make I see this error with Java:
> This error is not fatal. rJava won't work, but the rest of R should be
> fine.

On RHEL from what I see openjdk-devel provides jni.h.

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