[R-SIG-Mac] install.libs error

Sun Mar 23 15:44:06 CET 2025

You'd need to change the "-C /" in the tar command. I trust Simon enough to just run the script as root, though... 

-pd

> On 23 Mar 2025, at 14.37, Naresh Gurbuxani <naresh_gurbuxani using hotmail.com> wrote:
> 
> Peter,
> 
> In install.libs(), there is no argument for setting location where boost or other packages are installed.  How can I select a different directory to install boost using install.libs()?
> 
> Thanks,
> Naresh
> 
>> On Mar 23, 2025, at 7:55 AM, 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]]
>>>> 
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>>> 
>>> -- 
>>> 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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> 

-- 
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