Installation problem

[coralzhang]

Hi, I keep. having issues with installing the package. Please see below for messages. Could you please help?

> BiocManager::install("BiocParallel")
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)
Installing package(s) 'BiocParallel'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocParallel_1.40.0.tar.gz'
Content type 'application/x-gzip' length 1000414 bytes (976 KB)
==================================================
downloaded 976 KB

* installing *source* package ‘BiocParallel’ ...
** package ‘BiocParallel’ 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++ -std=gnu++17 accepts -g... yes
checking for clang++ -std=gnu++17 option to enable C++11 features... none needed
checking for library containing shm_open... none required
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/mman.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Homebrew clang version 19.1.6’
using C++11
using SDK: ‘MacOSX15.2.sdk’
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.4.2_2/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.4/site-library/BH/include' -I'/usr/local/lib/R/4.4/site-library/cpp11/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include    -fPIC  -g -O2   -c cpp11.cpp -o cpp11.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.4.2_2/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.4/site-library/BH/include' -I'/usr/local/lib/R/4.4/site-library/cpp11/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include    -fPIC  -g -O2   -c ipcmutex.cpp -o ipcmutex.o
In file included from ipcmutex.cpp:14:
In file included from /usr/local/lib/R/4.4/site-library/BH/include/boost/interprocess/managed_shared_memory.hpp:25:
In file included from /usr/local/lib/R/4.4/site-library/BH/include/boost/interprocess/detail/managed_memory_impl.hpp:30:
/usr/local/lib/R/4.4/site-library/BH/include/boost/interprocess/segment_manager.hpp:1055:41: error: 
      a template argument list is expected after a name prefixed by the template
      keyword [-Wmissing-template-arg-list-after-template-kw]
 1055 |          hdr = block_header_t::template from_first_header(reinterpret_ca...
      |                                         ^
1 error generated.
make: *** [ipcmutex.o] Error 1
ERROR: compilation failed for package ‘BiocParallel’
* removing ‘/usr/local/lib/R/4.4/site-library/BiocParallel’

The downloaded source packages are in
	‘/private/var/folders/z_/z5x1_q9n5pv0ztcsd9r3wlch0000gp/T/RtmpXi3IFN/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘BiocParallel’ had non-zero exit status

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin23.6.0
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS:   /usr/local/Cellar/openblas/0.3.28/lib/libopenblasp-r0.3.28.dylib 
LAPACK: /usr/local/Cellar/r/4.4.2_2/lib/R/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.25 compiler_4.4.2      tools_4.4.2   

[mtmorgan]

The package should be available as a pre-built binary; do you have options(pkgType = "both") so that it does not need to be compiled on your machine? If you need to build from source, then you need to follow R's directions https://mac.r-project.org/tools/ , in particular not using homebrew's clang compiler.