[R-SIG-Mac] install.libs error

Naresh Gurbuxani n@re@h_gurbux@n| @end|ng |rom hotm@||@com
Sun Mar 23 17:36:39 CET 2025 

To give credit to Simon, at https://mac.r-project.org/bin instructions include a note that “If you do not have write permission, you may need to make it writeable or run sudo R.”

I ran sudo R and was able to install and download boost.  

~ $ ls /opt/R/x86_64/include/
boost      itclInt.h     tcl.h     tclTomMathDecls.h
fakemysql.h   itclIntDecls.h     tclDecls.h      tdbc.h
fakepq.h      itclMigrate2TclCore.h  tclOO.h     tdbcDecls.h
fakesql.h     itclTclIntStubsFcn.h   tclOODecls.h    tdbcInt.h
itcl.h      mysqlStubs.h     tclPlatDecls.h  tk.h
itcl2TclOO.h  odbcStubs.h     tclThread.h     tkDecls.h
itclDecls.h   pqStubs.h     tclTomMath.h    tkPlatDecls.h
~ $ 

However, I am still not able to install RQuantLib.  It does not find boost.
> install.packages("RQuantLib", type = "source", lib = .libPaths()[2], configure.args = c("--with-boost-include=/opt/R/x86_64/include/boost"), 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/Rtmp7YHJMO/downloaded_packages’
Warning message:
In install.packages("RQuantLib", type = "source", lib = .libPaths()[2],  :
  installation of package ‘RQuantLib’ had non-zero exit status
> 

> On Mar 23, 2025, at 10:44 AM, Peter Dalgaard <pdalgd using gmail.com> wrote:
> 
> 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]]
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> _______________________________________________
>>> 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
>

More information about the R-SIG-Mac mailing list