R @4.0.2: configuration fails (error: bzip2 library and headers are required)

[jfb007]

Dear All

I tried to install R on my MBP (15", 2017) running Catalina (macOS 10.15.6). After completely removing macports I made a fresh install of Xcode 11.6 (11E708) and the command line tools (Command_Line_Tools_for_Xcode_12_beta_4.dmg). I installed around 500 ports without any problems (texlive, pandoc, octave, gimp2, ImageMagick, etc.).

Unfortunately I was unable to install R. Here the relevant output in the terminal:

$ sudo port -v install R
--->  Computing dependencies for R.
--->  Fetching archive for R
--->  R-4.0.2_1+builtin_lapack+cairo+gcc10+recommended+x11.darwin_19.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
--->  Attempting to fetch R-4.0.2_1+builtin_lapack+cairo+gcc10+recommended+x11.darwin_19.x86_64.tbz2 from https://packages.macports.org/R
...
...
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... no
checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required
Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_R/R/work/R-4.0.2" && ./configure --prefix=/opt/local/Library/Frameworks --enable-R-framework --enable-memory-profiling --enable-R-shlib --enable-BLAS-shlib --without-tcltk --with-cairo --disable-java --with-included-gettext --without-blas --without-lapack --with-recommended-packages --with-x --x-include=/opt/local/include/X11 --x-lib=/opt/local/lib 
Exit code: 1
Error: Failed to configure R, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_R/R/work/R-4.0.2/config.log
Error: Failed to configure R: configure failure: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_R/R/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port R failed

I have installed bzip2, the libraries and the header files, as the following should show:

$ which bzip2
/opt/local/bin/bzip2

$ bzip2 --version
bzip2, a block-sorting file compressor.  Version 1.0.8, 13-Jul-2019.
   
   Copyright (C) 1996-2019 by Julian Seward.
   
   This program is free software; you can redistribute it and/or modify
   it under the terms set out in the LICENSE file, which is included
   in the bzip2 source distribution.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   LICENSE file for more details.
   
bzip2: I won't write compressed data to a terminal.
bzip2: For help, type: `bzip2 --help'.

$ port content bzip2
Port bzip2 contains:
  /opt/local/bin/bunzip2
  /opt/local/bin/bzcat
  /opt/local/bin/bzcmp
  /opt/local/bin/bzdiff
  /opt/local/bin/bzegrep
  /opt/local/bin/bzfgrep
  /opt/local/bin/bzgrep
  /opt/local/bin/bzip2
  /opt/local/bin/bzip2recover
  /opt/local/bin/bzless
  /opt/local/bin/bzmore
  /opt/local/include/bzlib.h
  /opt/local/lib/libbz2.1.0.8.dylib
  /opt/local/lib/libbz2.1.0.dylib
  /opt/local/lib/libbz2.1.dylib
  /opt/local/lib/libbz2.a
  /opt/local/lib/libbz2.dylib
  /opt/local/share/man/man1/bzcmp.1.gz
  /opt/local/share/man/man1/bzdiff.1.gz
  /opt/local/share/man/man1/bzegrep.1.gz
  /opt/local/share/man/man1/bzfgrep.1.gz
  /opt/local/share/man/man1/bzgrep.1.gz
  /opt/local/share/man/man1/bzip2.1.gz
  /opt/local/share/man/man1/bzless.1.gz
  /opt/local/share/man/man1/bzmore.1.gz

Thanks for any help and best Regards

Josef

[mf2k (Frank Schima)]

In the future, please fill in the Port field and add the port maintainer(s) to Cc (port info --maintainers R), if any.

[jmroot (Joshua Root)]

#60976

[jfb007]

This is the correct config.log (the former was indeed generated using "./configure" directly)

[jfb007]

My initial "config.log" was indeed from a run of "configure" in the build directory! I added now the correct "config.log".

Here is part of the output of "sudo port -vv install R"

checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking mmap support for zlib... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... no
checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required
Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_R/R/work/R-4.0.2" && ./configure --prefix=/opt/local/Library/Frameworks --enable-R-framework --enable-memory-profiling --enable-R-shlib --enable-BLAS-shlib --without-tcltk --with-cairo --disable-java --with-included-gettext --without-blas --without-lapack --with-recommended-packages --with-x --x-include=/opt/local/include/X11 --x-lib=/opt/local/lib 
Exit code: 1
Error: Failed to configure R, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_R/R/work/R-4.0.2/config.log
Error: Failed to configure R: configure failure: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_math_R/R/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port R failed

The output suggests, that bzip2 is not version >= 1.0.6, whereas the following commands say, it is version 1.0.8 and it is installed!

$ which bzip2
/opt/local/bin/bzip2
$ ls -l /opt/local/bin/bzip2
-rwxr-xr-x  1 root  admin  44352 28 Okt  2019 /opt/local/bin/bzip2
$ /opt/local/bin/bzip2 --version
bzip2, a block-sorting file compressor.  Version 1.0.8, 13-Jul-2019.
   
   Copyright (C) 1996-2019 by Julian Seward.
   
   This program is free software; you can redistribute it and/or modify
   it under the terms set out in the LICENSE file, which is included
   in the bzip2 source distribution.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   LICENSE file for more details.
   
bzip2: I won't write compressed data to a terminal.
bzip2: For help, type: `bzip2 --help'.

Please forgive my mistakes and I would very, very welcome any help to be able to compile R (or is there an alternative?)

Thanks a lot in advance and Regards

Josef

[jmroot (Joshua Root)]

This is still a duplicate; please follow up in the original ticket #60976 so we don't have discussion split between two tickets for the same issue.