[R-SIG-Mac] install.libs error

[Naresh Gurbuxani]

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