[R-SIG-Mac] install.libs error

Peter Dalgaard pd@|gd @end|ng |rom gm@||@com
Sun Mar 23 14:18:08 CET 2025 

OK, so not the system tar; that settles that. Simon (cc'ed) might still want to fix J vs  j, though.

Re. permissions, I suspect you want to either

- run R as root for the installation
- change permissions on /opt/R & subdirectories
or
- install to a different directory

Re. MacPorts vs Simon's tools I really have no clue, except that it very often doesn't work to mix and match different toolchains. 

-pd


> On 23 Mar 2025, at 12.55, Naresh Gurbuxani <naresh_gurbuxani using hotmail.com> wrote:
> 
> 
> notes $ which tar
> /opt/local/libexec/gnubin/tar
> notes $ tar --version
> tar (GNU tar) 1.35
> Copyright (C) 2023 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.
> 
> Written by John Gilmore and Jay Fenlason.
> notes $ 
> 
> I use MacPorts package manager to install most software.  For R, I switched to manual install because, with MacPorts data.table could not pick up openmp support.  
> 
> Using uppercase J as suggested by Rodney successfully downloaded boost on my computer.  But it cannot install.  Below are first few lines of messages:
> 
>> install.libs("boost")
> Downloading https://mac.R-project.org/bin/REPOS ...
> Using repository  https://mac.R-project.org/bin/darwin20/x86_64 ...
> Downloading index  https://mac.R-project.org/bin/darwin20/x86_64/PACKAGES ...
> Downloading + installing  https://mac.R-project.org/bin/darwin20/x86_64/boost-1.86.0-darwin.20-x86_64.tar.xz ...
> tar: opt/R/x86_64/include: Cannot utime: Permission denied
> tar: opt/R/x86_64/lib: Cannot utime: Permission denied
> tar: opt/R/x86_64/pkg/boost-1.86.0-darwin.20-x86_64.list: Cannot open: Permission denied
> (Many more lines with Permission denied message)
> 
> I have another question.  I need boost to install RQuantLib.  My computer already has MacPorts-installed boost and MacPorts installed QuantLib.  But RQuantLib installation is not picking up boost.  Is there a way to get that working?
> 
>> install.packages("RQuantLib", lib = .libPaths()[2], repos = "https://cran.r-project.org", type = "source", configure.args = c("--with-boost-include=/opt/local/libexec/boost/1.76/include/"), configure.vars = c("CPPFLAGS='-DQL_HIGH_RESOLUTION_DATE'"))
> trying URL 'https://cran.r-project.org/src/contrib/RQuantLib_0.4.24.tar.gz'
> Content type 'application/x-gzip' length 195836 bytes (191 KB)
> ==================================================
> downloaded 191 KB
> 
> * installing *source* package ‘RQuantLib’ ...
> ** package ‘RQuantLib’ successfully unpacked and MD5 sums checked
> ** using staged installation
> checking whether the C++ compiler works... yes
> checking for C++ compiler default output file name... a.out
> checking for suffix of executables... 
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether the compiler supports GNU C++... yes
> checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
> checking for clang++ -arch x86_64 -std=gnu++17 option to enable C++11 features... none needed
> checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++17 -E
> checking whether the compiler supports GNU C++... (cached) yes
> checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... (cached) yes
> checking for clang++ -arch x86_64 -std=gnu++17 option to enable C++11 features... (cached) none needed
> checking for R... yes
> checking for quantlib-config... yes
> checking for suitable QuantLib version... yes (1.36)
> checking for Boost development files... no
> configure: error: Boost development files not found
> ERROR: configuration failed for package ‘RQuantLib’
> * removing ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RQuantLib’
> 
> The downloaded source packages are in
> ‘/private/var/folders/nb/2vppcjgd19l_h9brvzgdjcm40000gn/T/RtmpKL66sI/downloaded_packages’
> Warning message:
> In install.packages("RQuantLib", lib = .libPaths()[2], repos = "https://cran.r-project.org",  :
>  installation of package ‘RQuantLib’ had non-zero exit status
>   In terminal
> notes $ ls /opt/local/libexec/boost/1.76/include/
> boost
> 
>> On Mar 23, 2025, at 6:21 AM, peter dalgaard <pdalgd using gmail.com> wrote:
>> 
>> Oddly, this doesn't happen here, even though I also tar xj instead of xJ ot the .xz file.
>> 
>> Any chance you two could be picking up a different tar? I am seeing
>> 
>> PeterDaardsiMac:ISwR pd$ which tar
>> /usr/bin/tar
>> PeterDaardsiMac:ISwR pd$ tar --version
>> bsdtar 3.5.3 - libarchive 3.5.3 zlib/1.2.12 liblzma/5.4.3 bz2lib/1.0.8 
>> 
>> and "man tar" claims that j and J options are "c mode only" so presumably ignored and tar gets the compression type from the input itself.
>> 
>> -pd
>> 
>>> On 22 Mar 2025, at 15.53, Sparapani, Rodney via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
>>> 
>>> Hi Naresh:
>>> 
>>> I’m seeing the same error message.  And it makes sense
>>> because the boost tar-ball is compressed with xz and
>>> not bzip2.  On line 87 of install.R, we have the following…
>>> if (system(paste("curl", "-sSL", shQuote(u), "|", "tar fxj - -C /")) < 0)
>>> Little j means bzip2 while big J is xz.  So try substituting…
>>> if (system(paste("curl", "-sSL", shQuote(u), "|", "tar fxJ - -C /")) < 0)
>>> 
>>> --
>>> Rodney Sparapani, Associate Professor of Biostatistics
>>> President, Wisconsin Chapter of the American Statistical Association
>>> Division of Biostatistics, Data Science Institute
>>> Medical College of Wisconsin, Milwaukee Campus
>>> 
>>> 
>>> From: R-SIG-Mac <r-sig-mac-bounces using r-project.org> on behalf of Naresh Gurbuxani <naresh_gurbuxani using hotmail.com>
>>> Date: Saturday, March 22, 2025 at 8:02 AM
>>> To: r-sig-mac using r-project.org <r-sig-mac using r-project.org>
>>> Subject: [R-SIG-Mac] install.libs error
>>> Downloading + installing  https://mac.R-project.org/bin/darwin20/x86_64/boost-1.86.0-darwin.20-x86_64.tar.xz$<https://mac.R-project.org/bin/darwin20/x86_64/boost-1.86.0-darwin.20-x86_64.tar.xz%20$>  ...
>>> bzip2: (stdin) is not a bzip2 file.
>>> tar: Child died with signal 13
>>> tar: Error is not recoverable: exiting now
>>> curl: (23) Failure writing output to destination, passed 8192 returned 0
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> -- 
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business SchoolSolbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
> 
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business SchoolSolbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com

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