Instalation issues.

[jmgs7]

Hi, I am getting this error installing BPcells in Fedora 40 using R 4.4.0:

g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I/usr/local/include   -march=native -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas  -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -c fragmentIterators/MergeFragments.cpp -o fragmentIterators/MergeFragments.o
fragmentIterators/MergeFragments.cpp: In member function ‘virtual const char* BPCells::MergeFragments::cellNames(uint32_t)’:
fragmentIterators/MergeFragments.cpp:186:20: error: ‘upper_bound’ is not a member of ‘std’; did you mean ‘lower_bound’?
  186 |     auto it = std::upper_bound(cell_id_offset.begin(), cell_id_offset.end(), cell_id);
      |                    ^~~~~~~~~~~
      |                    lower_bound
fragmentIterators/MergeFragments.cpp: In member function ‘virtual bool BPCells::MergeFragments::load()’:
fragmentIterators/MergeFragments.cpp:258:26: error: ‘upper_bound’ is not a member of ‘std’; did you mean ‘lower_bound’?
  258 |         available = std::upper_bound(start.begin(), start.begin() + loaded, max_sorted_start) -
      |                          ^~~~~~~~~~~
      |                          lower_bound
make: *** [/usr/lib64/R/etc/Makeconf:204: fragmentIterators/MergeFragments.o] Error 1
ERROR: compilation failed for package ‘BPCells’
* removing ‘/home/user/R/x86_64-redhat-linux-gnu-library/4.4/BPCells’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpjJ0lYt/file12213ee0e631/BPCells_0.1.0.tar.gz’ had non-zero exit status

Any hint of how could I solve it? Thank you very much, best regards.

[bnprks]

Hi José, thanks for your question. I'm not fully sure of the cause of your problems, but have two things you can try:

1. Could you try re-installing BPCells after this update I just made (commit 0e23af2bc)? I might have had a forgotten #include statement which could have caused your problems. (If you reinstall but the error message changes, I'd also like to know about that, since that would indicate additional things I should fix)

2. Could you run g++ --version on the command line to let me know what compiler version you're running with? I'm using g++ version 11.3.0 right now, so if you have or can upgrade to a newer version than that it also might solve your problem.

Let me know if either of those work for you

-Ben

[jmgs7]

Hi,

Thank you very much for such quick answer.

The changes uploaded in your new commit solved the issue, thank you very much!

[bnprks]

Glad to hear it, feel free to reach out again if you have any other issues :)