Re: [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
On Mon, 21 Nov 2022 13:19:22 -0500 Rob Kudyba wrote: > What would the ./configure options look like? ./configure LDFLAGS="-L/path/to/gcc -L/path/to/pcre" Here's where LDFLAGS is interpreted and appended to LD_LIBRARY_PATH: https://github.com/r-devel/r-svn/blob/d6fc5e0a983eaa61439d67cfff4dc4097698c831/configure.ac#L821-L828 -- Best regards, Ivan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [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
> В Mon, 21 Nov 2022 10:19:36 -0500 > Rob Kudyba пишет: > > > I edited the last line to be: > > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64 then > > make install errored with: > > /path/to/R-4.2.2/bin/exec/R: error while loading shared libraries: > > libpcre2-8.so.0: cannot open shared object file: No such file or > > directory > > > > So it appears that the same issue happens for PCRE! I then edited the > > line to be: > > export > > > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64:/path/to/pcre2-10.35/lib > > > > Then make install finished with: > > Successfully remade target file `install'. > > Does the installed copy of R work? > Yes Are you running make install as root? Programs starting as root are wary > of environment variables such as LD_LIBRARY_PATH and may ignore or > unset them while starting up (otherwise it would be trivial to load user > code into setuid root binaries and take over the system). You may have > to load the module again after you obtain the superuser privileges. > Ah I should've mentioned this. I did use sudo to install as the program modules are shared and installed by root. That has to be the reason. > "R Installation and Administration" [1] says that the R build process > remembers the library paths to put into LD_LIBRARY_PATH, but only if > they are specified in the LDFLAGS parameter, so if there's a set of > library paths that's not expected to be normally present in > LD_LIBRARY_PATH, perhaps it's best to mention them explicitly in the > ./configure call. > > -- > Best regards, > Ivan > > [1] https://cran.r-project.org/doc/manuals/R-admin.html What would the ./configure options look like? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [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
On Sun, Nov 20, 2022 at 2:26 PM Ivan Krylov wrote:
> On Sun, 20 Nov 2022 14:03:34 -0500
> Rob Kudyba wrote:
>
> > /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 automatically.
>
> Interesting that bin/R works but calling bin/R from what amounts to
> `make -C src/library install` doesn't. I think that the failing step is
> the following command:
>
> @$(ECHO) " building HTML index ..."
> @$(ECHO) "utils:::make.packages.html(.Library, verbose=FALSE,
> docdir=\"$(DESTDIR)${rdocdir}\")" | \
> R_DEFAULT_PACKAGES=NULL LC_ALL=C ${R_EXE} >/dev/null
>
> I don't see a reason for Make to lose the LD_LIBRARY_PATH when
> launching R like this.
>
> Can you see the failing step in the `make -d install` output? There
> will be a lot of text, most of it unrelated, unfortunately.
>
I've uploaded the output to https://easyupload.io/scuujn
The gcc-related part has this:
Considering target file `install-main'.
File `install-main' does not exist.
Considering target file `install-Rscript'.
File `install-Rscript' does not exist.
Finished prerequisites of target file `install-Rscript'.
Must remake target `install-Rscript'.
Invoking recipe from Makefile:71 to update target `install-Rscript'.
make[2]: Entering directory `/path/to/me/R-4.2.2/src/unix'
gcc -I. -I../../src/include -I../../src/include -I/usr/local/include
-DHAVE_CONFIG_H-g -O2 -L/usr/local/lib64
-DR_HOME='"/path/to/R-4.2/lib64/R"' \
-o Rscript ./Rscript.c
Putting child 0x65bc00 (install-Rscript) PID 240122 on the chain.
Live child 0x65bc00 (install-Rscript) PID 240122
If something loses the LD_LIBRARY_PATH environment variable on the way
> from Make to R, hard-coding it in etc/ldpaths should work around the
> problem, but it may be hard to find out what went wrong.
>
I edited the last line to be:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64 then make
install errored with:
/path/to/R-4.2.2/bin/exec/R: error while loading shared libraries:
libpcre2-8.so.0: cannot open shared object file: No such file or directory
So it appears that the same issue happens for PCRE! I then edited the line
to be:
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64:/path/to/pcre2-10.35/lib
Then make install finished with:
Successfully remade target file `install'.
>
> If you run `mkfifo /tmp/1` and insert `read foo etc/ldpaths, it should hang until you write something into /tmp/1.
> Using this, it should be possible to inspect /proc/${pid}/environ for
> the whole process tree from the parent Make process to the shell that's
> about to launch R. Can you find the first process that lacks the proper
> LD_LIBRARY_PATH environment variable?
>
I ran the 1st command and then added the 'read' to the file. I'm not
following what should've happened? I didn't need to include the back
ticks,`, in the file, correct? Perhaps the debug from make install will
provide you more info?
Would this be considered a bug or enhancement?
Thanks for your help on this.
Rob
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Re: [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
В Mon, 21 Nov 2022 10:19:36 -0500 Rob Kudyba пишет: > I edited the last line to be: > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64 then > make install errored with: > /path/to/R-4.2.2/bin/exec/R: error while loading shared libraries: > libpcre2-8.so.0: cannot open shared object file: No such file or > directory > > So it appears that the same issue happens for PCRE! I then edited the > line to be: > export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/gcc-11.2/lib64:/path/to/pcre2-10.35/lib > > Then make install finished with: > Successfully remade target file `install'. Does the installed copy of R work? Are you running make install as root? Programs starting as root are wary of environment variables such as LD_LIBRARY_PATH and may ignore or unset them while starting up (otherwise it would be trivial to load user code into setuid root binaries and take over the system). You may have to load the module again after you obtain the superuser privileges. > I ran the 1st command and then added the 'read' to the file. I'm not > following what should've happened? I didn't need to include the back > ticks,`, in the file, correct? Yes, I meant to omit the backticks. What I'm suggesting to perform is Linux process debugging: 1) Make etc/ldpaths hang just before R is (unsuccessfully) launched by adding an I/O operation that you can control. 2) While make install -> (lots of child processes) -> bin/R is hung, run `top`, `htop`, or any other process manager to have a look at the process tree. There should be your shell process, the Make process, and a number of child shell processes. The grand-(grand-...)child should be sleeping in I/O. 3) Using either your process manager or the command https://cran.r-project.org/doc/manuals/R-admin.html __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [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
> 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 => (0x2aacd000)
libRblas.so => /path/to/R-4.2/lib64/R/lib/libRblas.so (0x2accf000)
libgfortran.so.5 => /path/to/gcc-11.2/lib64/libgfortran.so.5
(0x2aef9000)
libm.so.6 => /lib64/libm.so.6 (0x2b3a)
libquadmath.so.0 => /path/to/gcc-11.2/lib64/libquadmath.so.0
(0x2b6a2000)
libreadline.so.6 => /lib64/libreadline.so.6 (0x2b8e9000)
libpcre2-8.so.0 => /path/to/pcre2-10.35/lib/libpcre2-8.so.0
(0x2bb2f000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x2bd88000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x2bfae000)
libz.so.1 => /lib64/libz.so.1 (0x2c1be000)
librt.so.1 => /lib64/librt.so.1 (0x2c3d4000)
libdl.so.2 => /lib64/libdl.so.2 (0x2c5dc000)
libgomp.so.1 => /path/to/gcc-11.2/lib64/libgomp.so.1 (0x2c7e)
libpthread.so.0 => /lib64/libpthread.so.0 (0x2ca21000)
libc.so.6 => /lib64/libc.so.6 (0x2cc3d000)
/lib64/ld-linux-x86-64.so.2 (0x2aaab000)
libgcc_s.so.1 => /path/to/gcc-11.2/lib64/libgcc_s.so.1 (0x2d00a000)
libtinfo.so.5 => /lib64/libtinfo.so.5 (0x2d222000)
> 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",
O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 3
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
automatically.
if test -n "/usr/local/lib64"; then
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:/usr/local/lib64}
else
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib}
fi
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
fi
## This is DYLD_FALLBACK_LIBRARY_PATH on Darwin (macOS) and
## LD_LIBRARY_PATH elsewhere.
## However, on macOS >=10.11 (if SIP is enabled, the default), the
## environment value will not be passed to a script such as R.sh, so
## would not seen here.
if test -z "${LD_LIBRARY_PATH}"; then
LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
else
LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}"
fi
export LD_LIBRARY_PATH
> During make I see this error with Java:
>
> This error is not fatal. rJava won't work, but the rest of R should be
> fine.
>
On RHEL from what I see openjdk-devel provides jni.h.
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Re: [R] make install libgfortran.so.5: cannot open shared object file: No such file or directory; conftest.c:1:10: fatal error: jni.h: No such file or directory
On Sun, 20 Nov 2022 14:03:34 -0500
Rob Kudyba wrote:
> /path/to/gcc-11.2/lib is definitely in LD_LIBRARY_PATH when loading
> the GCC 11.2 module.
>
> If using the /path/to/R-4.2.2/etc/ldpaths where would I put the
> correct path? I would've hoped the configure/make process would've
> found this automatically.
Interesting that bin/R works but calling bin/R from what amounts to
`make -C src/library install` doesn't. I think that the failing step is
the following command:
@$(ECHO) " building HTML index ..."
@$(ECHO) "utils:::make.packages.html(.Library, verbose=FALSE,
docdir=\"$(DESTDIR)${rdocdir}\")" | \
R_DEFAULT_PACKAGES=NULL LC_ALL=C ${R_EXE} >/dev/null
I don't see a reason for Make to lose the LD_LIBRARY_PATH when
launching R like this.
Can you see the failing step in the `make -d install` output? There
will be a lot of text, most of it unrelated, unfortunately.
If something loses the LD_LIBRARY_PATH environment variable on the way
from Make to R, hard-coding it in etc/ldpaths should work around the
problem, but it may be hard to find out what went wrong.
If you run `mkfifo /tmp/1` and insert `read foo https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [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
On Fri, 18 Nov 2022 16:45:14 -0500 Rob Kudyba wrote: > Here is where the error occurs in make install: > [...] > installing packages ... > building HTML index ... > /path/to/R-4.2.2/bin/exec/R: error while loading shared libraries: > libgfortran.so.5: cannot open shared object file: No such file or > directory make[2]: *** [install] Error 127 > make[2]: Leaving directory `/path/to/R-4.2.2/src/library' > make[1]: *** [install] Error 1 > make[1]: Leaving directory `/path/to/rk3199/R-4.2.2/src' > make: *** [install] Error 1 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? Does /path/to/R-4.2.2/bin/R -d ldd give you any useful information? 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? 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. > 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. -- Best regards, Ivan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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
On RHEL 8 with GCC 11.2.0 loaded as a module in a non-standard location I'm the below error with make install. libgfortran.so is definitely in $LD_LIBRARY_PATH, i.e., /path/to/gcc-11.2/lib64 ls -l /path/to/gcc-11.2/lib64/*fortran.so* lrwxrwxrwx 1 rk3199 user20 Mar 24 2022 libgfortran.so -> libgfortran.so.5.0.0 lrwxrwxrwx 1 rk3199 user20 Mar 24 2022 libgfortran.so.5 -> libgfortran.so.5.0.0 -rwxr-xr-x 1 rk3199 user 8595744 Mar 24 2022 libgfortran.so.5.0.0 Here is where the error occurs in make install: [...] installing packages ... building HTML index ... /path/to/R-4.2.2/bin/exec/R: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory make[2]: *** [install] Error 127 make[2]: Leaving directory `/path/to/R-4.2.2/src/library' make[1]: *** [install] Error 1 make[1]: Leaving directory `/path/to/rk3199/R-4.2.2/src' make: *** [install] Error 1 During make I see this error with Java: configuring Java ... Java interpreter : /usr/bin/java Java version : 1.8.0_161 Java home path : /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/jre Java compiler: not present Java headers gen.: Java archive tool: trying to compile and link a JNI program detected JNI cpp flags: detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm make[2]: Entering directory `/tmp/Rjavareconf.3sImDz' gcc -I"/path/to/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -O3 -march=native -c conftest.c -o conftest.o conftest.c:1:10: fatal error: jni.h: No such file or directory 1 | #include | ^~~ compilation terminated. make[2]: *** [conftest.o] Error 1 make[2]: Leaving directory `/tmp/Rjavareconf.3sImDz' Unable to compile a JNI program JAVA_HOME: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/jre Java library path: JNI cpp flags: JNI linker flags : Updating Java configuration in /path/to/R-4.2.2 Done. That seems a little more straight forward in that our Java 1.7.0 nor 1.8.0 have a jni.h file. Looks like we'd need the devel package installed. Thanks for any suggestions for the former. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
