Error with proj and glibc

[pgcudahy]

After a recent brew upgrade my installation of jupyter can no longer open notebooks with the irkernel R kernel. They all fail with the error

Error in dyn.load("/home/linuxbrew/.linuxbrew/lib/libproj.so.25") :
unable to load shared object '/home/linuxbrew/.linuxbrew/lib/libproj.so.25':
/lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.35' not found (required by /home/linuxbrew/.linuxbrew/lib/libproj.so.25)
Execution halted

This is on Ubuntu 20.04
I've tried reinstalling jupyter, proj and glibc but the same error keeps occurring. Anyone have an idea of where to start?

[carlocab]

What is the output of brew config and brew doctor?

[carlocab]

Also, what is the output of brew info proj, and how did you install the Jupyter and R?

[pgcudahy]

brew config

~$ brew config
HOMEBREW_VERSION: 3.5.10-112-ge689cc0
ORIGIN: https://github.com/Homebrew/brew
HEAD: e689cc07d92d3d06bc832ddbe1724dbb8ab8ae7c
Last commit: 3 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: a0d05eaccdc7b2fdb3ecb0f23836a5226540d341
Core tap last commit: 2 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: localhost:10.0
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 20
Homebrew Ruby: 2.6.8 => /home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.8_1/bin/ruby
CPU: 20-core 64-bit broadwell
Clang: 14.0.6
Git: 2.37.3 => /home/linuxbrew/.linuxbrew/bin/git
Curl: 7.68.0 => /usr/bin/curl
Kernel: Linux 5.4.0-125-generic x86_64 GNU/Linux
OS: Ubuntu 20.04.5 LTS (focal)
Host glibc: 2.31
/usr/bin/gcc: 9.4.0
/usr/bin/ruby: 2.7.0
glibc: 2.35
gcc@5: 5.5.0_8
xorg: N/A

Brew doctor

~$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
  /usr/local/include/htslib/bgzf.h
  /usr/local/include/htslib/cram.h
  /usr/local/include/htslib/faidx.h
  /usr/local/include/htslib/hfile.h
  /usr/local/include/htslib/hts.h
  /usr/local/include/htslib/hts_defs.h
  /usr/local/include/htslib/hts_endian.h
  /usr/local/include/htslib/hts_log.h
  /usr/local/include/htslib/hts_os.h
  /usr/local/include/htslib/kbitset.h
  /usr/local/include/htslib/kfunc.h
  /usr/local/include/htslib/khash.h
  /usr/local/include/htslib/khash_str2int.h
  /usr/local/include/htslib/klist.h
  /usr/local/include/htslib/knetfile.h
  /usr/local/include/htslib/kroundup.h
  /usr/local/include/htslib/kseq.h
  /usr/local/include/htslib/ksort.h
  /usr/local/include/htslib/kstring.h
  /usr/local/include/htslib/regidx.h
  /usr/local/include/htslib/sam.h
  /usr/local/include/htslib/synced_bcf_reader.h
  /usr/local/include/htslib/tbx.h
  /usr/local/include/htslib/thread_pool.h
  /usr/local/include/htslib/vcf.h
  /usr/local/include/htslib/vcf_sweep.h
  /usr/local/include/htslib/vcfutils.h
  /usr/local/include/snp-sites/alignment-file.h
  /usr/local/include/snp-sites/fasta-of-snp-sites.h
  /usr/local/include/snp-sites/kseq.h
  /usr/local/include/snp-sites/phylib-of-snp-sites.h
  /usr/local/include/snp-sites/snp-sites.h
  /usr/local/include/snp-sites/vcf.h

Warning: Unbrewed '.la' files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected '.la' files:
  /usr/local/lib/libsnp-sites.la

Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected '.pc' files:
  /usr/local/lib/pkgconfig/htslib.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected static libraries:
  /usr/local/lib/libhts.a
  /usr/local/lib/libsnp-sites.a
Warning: Use bioperl instead of deprecated brewsci/bio/bioperl
Warning: Use bioperl instead of deprecated brewsci/bio/bioperl

brew info proj

~$ brew info proj
==> proj: stable 9.1.0 (bottled), HEAD
Cartographic Projections Library
https://proj.org/
Conflicts with:
  blast (because both install a `libproj.a` library)
/home/linuxbrew/.linuxbrew/Cellar/proj/9.1.0 (438 files, 599.3MB) *
  Built from source on 2022-09-02 at 06:23:03
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/proj.rb
License: MIT
==> Dependencies
Build: cmake ✔, libtool ✔, pkg-config ✔
Required: libtiff ✔, curl ✔, sqlite ✔
==> Options
--HEAD
        Install HEAD version
==> Analytics
install: 13,482 (30 days), 47,315 (90 days), 124,834 (365 days)
install-on-request: 2,917 (30 days), 11,182 (90 days), 40,851 (365 days)
build-error: 4 (30 days)

Jupyter was installed through homebrew while R is a system install

[carlocab]

This is your problem:

  Built from source on 2022-09-02 at 06:23:03

It is built from source, which means that it's linked with the glibc formula, which is newer than your system's glibc.

Is there any reason why you built proj from source? Installing it from a bottle will fix your issue.

[pgcudahy]

I tried installing from source after the problem started to see if I could get it to work. Going back to a bottled install still leaves me with the same issue

~$ brew info proj
==> proj: stable 9.1.0 (bottled), HEAD
Cartographic Projections Library
https://proj.org/
Conflicts with:
  blast (because both install a `libproj.a` library)
/home/linuxbrew/.linuxbrew/Cellar/proj/9.1.0 (438 files, 599.3MB) *
  Poured from bottle on 2022-09-02 at 08:05:08
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/proj.rb
License: MIT
==> Dependencies
Build: cmake ✔, libtool ✔, pkg-config ✔
Required: libtiff ✔, curl ✔, sqlite ✔
==> Options
--HEAD
        Install HEAD version
==> Analytics
install: 13,482 (30 days), 47,315 (90 days), 124,834 (365 days)
install-on-request: 2,917 (30 days), 11,182 (90 days), 40,851 (365 days)
build-error: 4 (30 days)

Error in dyn.load("/home/linuxbrew/.linuxbrew/lib/libproj.so.25") :
unable to load shared object '/home/linuxbrew/.linuxbrew/lib/libproj.so.25':
/lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /home/linuxbrew/.linuxbrew/lib/libresolv.so.2)
Execution halted

[carlocab]

The error is similar, but not the same.

Still, I wonder why formulae aren't using the glibc you have installed.

What's the output of

realpath /home/linuxbrew/.linuxbrew/lib/libresolv.so.2

?

@danielnachun would probably know what's going on here. CC @Homebrew/linux

[pgcudahy]

~$ realpath /home/linuxbrew/.linuxbrew/lib/libresolv.so.2
/home/linuxbrew/.linuxbrew/Cellar/glibc/2.35/lib/libresolv.so.2

[danielnachun]

I’m not entirely sure what’s going here. One problem is that you cannot link a brewed library to a non-brewed R if you are using brewed glibc. If you try installing R with Homebrew and then installing the R package that uses proj, do you get the same error?

[pgcudahy]

It's been working for a while, but now with an upgrade to R 4.2.2 lots of package installs are failing with file: /lib/x86_64-linux-gnu/libc.so.6: version 'GLIBC_2.32' not found (required by /home/linuxbrew/.linuxbrew/opt/xz/lib/liblzma.so.5). I tried making ~/.R/Makevars as you suggested but get errors like

> install.packages("Rcpp", verbose=TRUE)
Installing package into ‘/home/pgcudahy/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
system (cmd0): /home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/bin/R CMD INSTALL
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.9.tar.gz'
Content type 'application/x-gzip' length 2957812 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

foundpkgs: Rcpp, /tmp/RtmpXMNgOk/downloaded_packages/Rcpp_1.0.9.tar.gz
files: /tmp/RtmpXMNgOk/downloaded_packages/Rcpp_1.0.9.tar.gz
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++-12 -std=gnu++14 -I"/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/include" -DNDEBUG -I../inst/include/  -I/home/linuxbrew/.linuxbrew/opt/libtirpc/include/tirpc -I/home/linuxbrew/.linuxbrew/opt/gettext/include -I/home/linuxbrew/.linuxbrew/opt/readline/include -I/home/linuxbrew/.linuxbrew/opt/xz/include -I/home/linuxbrew/.linuxbrew/include   -fpic  -g -O2  -c api.cpp -o api.o
g++-12 -std=gnu++14 -I"/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/include" -DNDEBUG -I../inst/include/  -I/home/linuxbrew/.linuxbrew/opt/libtirpc/include/tirpc -I/home/linuxbrew/.linuxbrew/opt/gettext/include -I/home/linuxbrew/.linuxbrew/opt/readline/include -I/home/linuxbrew/.linuxbrew/opt/xz/include -I/home/linuxbrew/.linuxbrew/include   -fpic  -g -O2  -c attributes.cpp -o attributes.o
g++-12 -std=gnu++14 -I"/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/include" -DNDEBUG -I../inst/include/  -I/home/linuxbrew/.linuxbrew/opt/libtirpc/include/tirpc -I/home/linuxbrew/.linuxbrew/opt/gettext/include -I/home/linuxbrew/.linuxbrew/opt/readline/include -I/home/linuxbrew/.linuxbrew/opt/xz/include -I/home/linuxbrew/.linuxbrew/include   -fpic  -g -O2  -c barrier.cpp -o barrier.o
g++-12 -std=gnu++14 -I"/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/include" -DNDEBUG -I../inst/include/  -I/home/linuxbrew/.linuxbrew/opt/libtirpc/include/tirpc -I/home/linuxbrew/.linuxbrew/opt/gettext/include -I/home/linuxbrew/.linuxbrew/opt/readline/include -I/home/linuxbrew/.linuxbrew/opt/xz/include -I/home/linuxbrew/.linuxbrew/include   -fpic  -g -O2  -c date.cpp -o date.o
g++-12 -std=gnu++14 -I"/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/include" -DNDEBUG -I../inst/include/  -I/home/linuxbrew/.linuxbrew/opt/libtirpc/include/tirpc -I/home/linuxbrew/.linuxbrew/opt/gettext/include -I/home/linuxbrew/.linuxbrew/opt/readline/include -I/home/linuxbrew/.linuxbrew/opt/xz/include -I/home/linuxbrew/.linuxbrew/include   -fpic  -g -O2  -c module.cpp -o module.o
g++-12 -std=gnu++14 -I"/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/include" -DNDEBUG -I../inst/include/  -I/home/linuxbrew/.linuxbrew/opt/libtirpc/include/tirpc -I/home/linuxbrew/.linuxbrew/opt/gettext/include -I/home/linuxbrew/.linuxbrew/opt/readline/include -I/home/linuxbrew/.linuxbrew/opt/xz/include -I/home/linuxbrew/.linuxbrew/include   -fpic  -g -O2  -c rcpp_init.cpp -o rcpp_init.o
g++-12 -std=gnu++14 -shared -L/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/lib -nostdlib -L/home/linuxbrew/.linuxbrew/lib -Wl,-rpath,/home/linuxbrew/.linuxbrew/lib --dynamic-linker /home/linuxbrew/.linuxbrew/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/lib -lR
g++-12: error: unrecognized command-line option '--dynamic-linker'
make: *** [/home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/share/make/shlib.mk:10: Rcpp.so] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/pgcudahy/R/x86_64-pc-linux-gnu-library/4.2/Rcpp’
* restoring previous ‘/home/pgcudahy/R/x86_64-pc-linux-gnu-library/4.2/Rcpp’

The downloaded source packages are in
        ‘/tmp/RtmpXMNgOk/downloaded_packages’
Warning message:
In install.packages("Rcpp", verbose = TRUE) :
  installation of package ‘Rcpp’ had non-zero exit status

or

> install.packages("units", verbose=TRUE)
Installing package into ‘/home/pgcudahy/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
system (cmd0): /home/linuxbrew/.linuxbrew/Cellar/r/4.2.2/lib/R/bin/R CMD INSTALL
trying URL 'https://cloud.r-project.org/src/contrib/units_0.8-0.tar.gz'
Content type 'application/x-gzip' length 866695 bytes (846 KB)
==================================================
downloaded 846 KB

foundpkgs: units, /tmp/RtmpXMNgOk/downloaded_packages/units_0.8-0.tar.gz
files: /tmp/RtmpXMNgOk/downloaded_packages/units_0.8-0.tar.gz
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.8-0
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpBaewel/R.INSTALL19b3c583c6d2f/units':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/home/pgcudahy/R/x86_64-pc-linux-gnu-library/4.2/units’

The downloaded source packages are in
        ‘/tmp/RtmpXMNgOk/downloaded_packages’
Warning message:
In install.packages("units", verbose = TRUE) :
  installation of package ‘units’ had non-zero exit status

Is there an error in the formatting of the Makevar example you provided? (eg g++-12: error: unrecognized command-line option '--dynamic-linker' and configure: error: C++ compiler cannot create executables)

[danielnachun]

Yes, I think there is a mistake. It should probably be -Wl,--dynamic-linker instead of --dynamic-linker, as --dynamic-linker is linker command, not a compiler command.

[pgcudahy]

I've tried the fix, but most package installations are failing with file: /lib/x86_64-linux-gnu/libc.so.6: version GLIBC_2.32' not found (required by /home/linuxbrew/.linuxbrew/opt/xz/lib/liblzma.so.5)orawk: /lib/x86_64-linux-gnu/libc.so.6: version GLIBC_2.33' not found (required by /home/linuxbrew/.linuxbrew/opt/readline/lib/libreadline.so.8). I've reinstalled gcc, glibc, r, xz, and readline with no success. Any ideas?

[danielnachun]

Ah, that seems to be because your system file and awk binaries are also using the host libc and brewed xz/readline. I think the solution could be to do brew install gawk file-formula so that the brewed versions of those formulae are used instead of the host ones.

[pgcudahy]

That did it! Thanks very much.

[mgood7123]

seems like a lot of work just to correctly build a fully self contained brew o.o