Error installing BoomSpikeSlab

[akshat3492]

Hi Everyone,

I am trying to install bsts package for that I need to install its dependencies Boom and BoomSpikeSlab. I was successfully able to install Boom after trying Mac Binaries from its CRAN page but I am not able to install BoomSpikeSlab. I am having Linus-gnu operating system and working on Rstudio.

Below is the error that I am getting......

Installing package into ‘/libs/workspace’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/BoomSpikeSlab_1.2.5.tar.gz'
Content type 'application/x-gzip' length 129209 bytes (126 KB)

downloaded 126 KB

• installing source package ‘BoomSpikeSlab’ ...
  ** package ‘BoomSpikeSlab’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/opt/R/3.6.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I"/libs/workspace/Boom/include" -I/usr/local/include -fpic -g -O2 -c boom_spike_slab_init.cc -o boom_spike_slab_init.o
  g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/opt/R/3.6.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I"/libs/workspace/Boom/include" -I/usr/local/include -fpic -g -O2 -c logit_spike_slab_wrapper.cc -o logit_spike_slab_wrapper.o
  In file included from /libs/workspace/Boom/include/LinAlg/VectorView.hpp:28:0,
  from /libs/workspace/Boom/include/LinAlg/Matrix.hpp:24,
  from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:25,
  from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22,
  from logit_spike_slab_wrapper.cc:10:
  /libs/workspace/Boom/include/LinAlg/VectorViewIterator.hpp:183:24: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive]
  template<> struct std::iterator_traitsBOOM::VectorViewIterator {
  ^
  In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0,
  from /usr/include/c++/4.8.2/bits/char_traits.h:39,
  from /usr/include/c++/4.8.2/string:40,
  from logit_spike_slab_wrapper.cc:5:
  /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive]
  struct iterator_traits
  ^
  In file included from /libs/workspace/Boom/include/LinAlg/VectorView.hpp:28:0,
  from /libs/workspace/Boom/include/LinAlg/Matrix.hpp:24,
  from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:25,
  from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22,
  from logit_spike_slab_wrapper.cc:10:
  /libs/workspace/Boom/include/LinAlg/VectorViewIterator.hpp:191:25: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive]
  template <> struct std::iterator_traitsBOOM::VectorViewConstIterator {
  ^
  In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0,
  from /usr/include/c++/4.8.2/bits/char_traits.h:39,
  from /usr/include/c++/4.8.2/string:40,
  from logit_spike_slab_wrapper.cc:5:
  /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive]
  struct iterator_traits
  ^
  In file included from /libs/workspace/Boom/include/LinAlg/Array.hpp:23:0,
  from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:28,
  from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22,
  from logit_spike_slab_wrapper.cc:10:
  /libs/workspace/Boom/include/LinAlg/ArrayIterator.hpp:135:25: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive]
  template <> struct std::iterator_traitsBOOM::ArrayIterator {
  ^
  In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0,
  from /usr/include/c++/4.8.2/bits/char_traits.h:39,
  from /usr/include/c++/4.8.2/string:40,
  from logit_spike_slab_wrapper.cc:5:
  /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive]
  struct iterator_traits
  ^
  In file included from /libs/workspace/Boom/include/LinAlg/Array.hpp:23:0,
  from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:28,
  from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22,
  from logit_spike_slab_wrapper.cc:10:
  /libs/workspace/Boom/include/LinAlg/ArrayIterator.hpp:144:24: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive]
  template<> struct std::iterator_traitsBOOM::ConstArrayIterator {
  ^
  In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0,
  from /usr/include/c++/4.8.2/bits/char_traits.h:39,
  from /usr/include/c++/4.8.2/string:40,
  from logit_spike_slab_wrapper.cc:5:
  /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive]
  struct iterator_traits
  ^
  make: *** [logit_spike_slab_wrapper.o] Error 1
  ERROR: compilation failed for package ‘BoomSpikeSlab’
• removing ‘/libs/workspace/BoomSpikeSlab’
  Warning in install.packages :
  installation of package ‘BoomSpikeSlab’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmprDP2RP/downloaded_packages’

Could any one please help me out how to install BoomSpikeSlab on R-Studio?

[steve-the-bayesian]

The compiler error says that std::iterator_traits is being specialized in the wrong namespace. It looks like your C++ toolchain calls that an error, while other toolchains on CRAN and my own setup don't make an issue of it. I'll make a note of this for the next release of Boom, etc. If you don't want to wait that long, go find .../LinAlg/ArrayIterator.hpp and at the bottom of that file replace the following lines... template <> struct std::iterator_traits<BOOM::ArrayIterator> { using iterator_category = std::forward_iterator_tag; // using difference_type = std::ptrdiff_t; using difference_type = void; using value_type = double; using pointer = double*; using reference = double&; }; template<> struct std::iterator_traits<BOOM::ConstArrayIterator> { using iterator_category = std::forward_iterator_tag; // using difference_type = std::ptrdiff_t; using difference_type = void; using value_type = double; using pointer = double*; using reference = double&; }; with namespace std { template <> struct iterator_traits<BOOM::ArrayIterator> { using iterator_category = std::forward_iterator_tag; // using difference_type = std::ptrdiff_t; using difference_type = void; using value_type = double; using pointer = double*; using reference = double&; }; template<> struct iterator_traits<BOOM::ConstArrayIterator> { using iterator_category = std::forward_iterator_tag; // using difference_type = std::ptrdiff_t; using difference_type = void; using value_type = double; using pointer = double*; using reference = double&; }; } // namespace std You might need to make a similar replacement for other iterators. Notably VectorViewIterator.

…

On Thu, Jul 7, 2022 at 10:07 AM akshat3492 ***@***.***> wrote: Hi Everyone, I am trying to install bsts package for that I need to install its dependencies Boom and BoomSpikeSlab. I was successfully able to install Boom after trying Mac Binaries from its CRAN page but I am not able to install BoomSpikeSlab. I am having Linus-gnu operating system and working on Rstudio. Below is the error that I am getting...... Installing package into ‘/libs/workspace’ (as ‘lib’ is unspecified) trying URL ' https://cloud.r-project.org/src/contrib/BoomSpikeSlab_1.2.5.tar.gz' Content type 'application/x-gzip' length 129209 bytes (126 KB) downloaded 126 KB - installing *source* package ‘BoomSpikeSlab’ ... ** package ‘BoomSpikeSlab’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/opt/R/3.6.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I"/libs/workspace/Boom/include" -I/usr/local/include -fpic -g -O2 -c boom_spike_slab_init.cc -o boom_spike_slab_init.o g++ -std=gnu++11 -I"/opt/R/3.6.1/lib/R/include" -DNDEBUG -I/opt/R/3.6.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I"/libs/workspace/Boom/include" -I/usr/local/include -fpic -g -O2 -c logit_spike_slab_wrapper.cc -o logit_spike_slab_wrapper.o In file included from /libs/workspace/Boom/include/LinAlg/VectorView.hpp:28:0, from /libs/workspace/Boom/include/LinAlg/Matrix.hpp:24, from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:25, from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22, from logit_spike_slab_wrapper.cc:10: /libs/workspace/Boom/include/LinAlg/VectorViewIterator.hpp:183:24: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive] template<> struct std::iterator_traitsBOOM::VectorViewIterator { ^ In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0, from /usr/include/c++/4.8.2/bits/char_traits.h:39, from /usr/include/c++/4.8.2/string:40, from logit_spike_slab_wrapper.cc:5: /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive] struct iterator_traits ^ In file included from /libs/workspace/Boom/include/LinAlg/VectorView.hpp:28:0, from /libs/workspace/Boom/include/LinAlg/Matrix.hpp:24, from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:25, from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22, from logit_spike_slab_wrapper.cc:10: /libs/workspace/Boom/include/LinAlg/VectorViewIterator.hpp:191:25: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive] template <> struct std::iterator_traitsBOOM::VectorViewConstIterator { ^ In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0, from /usr/include/c++/4.8.2/bits/char_traits.h:39, from /usr/include/c++/4.8.2/string:40, from logit_spike_slab_wrapper.cc:5: /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive] struct iterator_traits ^ In file included from /libs/workspace/Boom/include/LinAlg/Array.hpp:23:0, from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:28, from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22, from logit_spike_slab_wrapper.cc:10: /libs/workspace/Boom/include/LinAlg/ArrayIterator.hpp:135:25: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive] template <> struct std::iterator_traitsBOOM::ArrayIterator { ^ In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0, from /usr/include/c++/4.8.2/bits/char_traits.h:39, from /usr/include/c++/4.8.2/string:40, from logit_spike_slab_wrapper.cc:5: /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive] struct iterator_traits ^ In file included from /libs/workspace/Boom/include/LinAlg/Array.hpp:23:0, from /libs/workspace/Boom/include/r_interface/boom_r_tools.hpp:28, from /libs/workspace/Boom/include/r_interface/seed_rng_from_R.hpp:22, from logit_spike_slab_wrapper.cc:10: /libs/workspace/Boom/include/LinAlg/ArrayIterator.hpp:144:24: error: specialization of ‘template struct std::iterator_traits’ in different namespace [-fpermissive] template<> struct std::iterator_traitsBOOM::ConstArrayIterator { ^ In file included from /usr/include/c++/4.8.2/bits/stl_algobase.h:65:0, from /usr/include/c++/4.8.2/bits/char_traits.h:39, from /usr/include/c++/4.8.2/string:40, from logit_spike_slab_wrapper.cc:5: /usr/include/c++/4.8.2/bits/stl_iterator_base_types.h:159:12: error: from definition of ‘template struct std::iterator_traits’ [-fpermissive] struct iterator_traits ^ make: *** [logit_spike_slab_wrapper.o] Error 1 ERROR: compilation failed for package ‘BoomSpikeSlab’ - removing ‘/libs/workspace/BoomSpikeSlab’ Warning in install.packages : installation of package ‘BoomSpikeSlab’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmprDP2RP/downloaded_packages’ Could any one please help me out how to install BoomSpikeSlab on R-Studio? 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