Error at installing

[marioleivahidalgo]

Hi there,

I have some troubles to install de package. Next you will find the error:

Install cytoinstaller

remotes::install_github("RGLab/cytoinstaller") Downloading GitHub repo RGLab/cytoinstaller@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL 'https://api.github.com/repos/RGLab/cytoinstaller/tarball/HEAD'

[DillonHammill]

Please use BiocManager::install(c("cytolib", "flowCore", "flowWorkspace", "openCyto")) instead.

[jingliu-ut]

I have the same problem. I tried BiocManager::install(c("cytolib", "flowCore", "flowWorkspace", "openCyto")) and I can't install flowWorkspace and openCyto.

Warning message in i.p(...):
“installation of package ‘flowWorkspace’ had non-zero exit status”
Warning message in i.p(...):
“installation of package ‘openCyto’ had non-zero exit status”

[kim619]

I also have the same issue as above, please help :<

[jcantoralrebordinos]

Hello all,

Thank you very much for the package, I've been able to install and use it in the past and I'm really pleased with it.

Further to the above, I am getting the following error when attempting to install the packages you mentioned @DillonHammill on macOS Sonoma. If I run BiocManager::install(c("cytolib", "flowCore", "flowWorkspace", "openCyto")) or devtools::install_github("DillonHammill/CytoExploreR") I get the following error:

using C++ compiler: ‘Homebrew clang version 18.1.8’
using C++17
using SDK: ‘MacOSX14.4.sdk’
[...] (I've removed several lines here)
In file included from /Users/username/Library/R/arm64/4.4/library/cytolib/include/cytolib/compensation.hpp:15:
/Users/username/Library/R/arm64/4.4/library/cytolib/include/cytolib/transformation.hpp:38:27: fatal error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
struct ciLessBoost : std::binary_function<std::string, std::string, bool>
                     ~~~~~^~~~~~~~~~~~~~~
                          __binary_function
/opt/local/libexec/llvm-16/bin/../include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
^
1 error generated.
make: *** [R_API.o] Error 1
ERROR: compilation failed for package ‘flowWorkspace’
* removing ‘/Users/username/Library/R/arm64/4.4/library/flowWorkspace’
ERROR: dependency ‘flowWorkspace’ is not available for package ‘openCyto’
* removing ‘/Users/username/Library/R/arm64/4.4/library/openCyto’

I don't think I'm able to accurately pinpoint the origin of the error, but my concern is that whether the package needs an older version of C++ to compile. Would the source code need to be updated in order to run with C++17? If so, would there be a workaround at least that can be used in the meantime?

Thank you very much in advance.