Opened 4 years ago
Closed 4 years ago
#61013 closed defect (duplicate)
R @4.0.2: configuration fails (error: bzip2 library and headers are required)
Reported by: | jfb007 | Owned by: | kjellpk (Kjell Konis) |
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Priority: | Normal | Milestone: | |
Component: | ports | Version: | 2.6.3 |
Keywords: | Cc: | i0ntempest | |
Port: | R |
Description
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
Attachments (2)
Change History (7)
Changed 4 years ago by jfb007
Attachment: | config.log added |
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comment:1 Changed 4 years ago by mf2k (Frank Schima)
comment:2 Changed 4 years ago by mf2k (Frank Schima)
Cc: | i0ntempest added; kjell.konis@… removed |
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Keywords: | R bzip2 removed |
Owner: | set to kjellpk |
Port: | R added |
Status: | new → assigned |
comment:3 Changed 4 years ago by jmroot (Joshua Root)
Resolution: | → duplicate |
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Status: | assigned → closed |
Changed 4 years ago by jfb007
Attachment: | config.2.log added |
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This is the correct config.log (the former was indeed generated using "./configure" directly)
comment:4 Changed 4 years ago by jfb007
Resolution: | duplicate |
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Status: | closed → reopened |
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
comment:5 Changed 4 years ago by jmroot (Joshua Root)
Resolution: | → duplicate |
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Status: | reopened → closed |
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.
N/M