Installation issue on Mac OS

[noriko-hiroi]

Hi,
I got an error to install BPCells.
My environment is macOS 12.6, intel 64-bit, R 4.2.3 on RStudio-2023.03.0-386.

I installed in advance hdf5 with;
% conda install -c anaconda hdf5

Then restarted RStudio and;
>remotes::install_github("bnprks/BPCells")

.
.

• installing source package ‘BPCells’ ...
  ** using staged installation
  Testing hdf5 by compiling example program...

Retrying with pkg-config flags...
Error running 'pkg-config hdf5 --cflags --libs'

Searching for hdf5 in a conda env...
no conda environment found in '$CONDA_PREFIX'

Unable to locate libhdf5. Please install manually or edit compiler flags.
ERROR: configuration failed for package ‘BPCells’

• removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BPCells’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/63/ngc0xtk17p5cbbs6762b48d80000gn/T//RtmpAUI64J/filec47557cbe71/BPCells_0.1.0.tar.gz’ had non-zero exit status

The error messages seems saying R cannot find hdf5.
I wonder what exactly I should do to overcome this error.
Any help I will be deeply grateful.

[bnprks]

Hi, thanks for your interest in BPCells. I think your problem is that you need to have the conda environment activated at install time. So assuming the conda environment is called base, you would do:

1. conda activate base
2. run R from the command line, then run remotes::install_github("bnprks/BPCells") within the R session

Once you have installed BPCells successfully, it won't matter if the conda environment is active (though if you delete the conda environment it will probably mess up your BPCells installation)

[noriko-hiroi]

Thank you for the kind instruction!
I will try and report the result at here.

I tried as follows and got an error to use R from terminal;

% conda activate base
% R
dyld[7375]: Library not loaded: '@rpath/libreadline.6.2.dylib'
dyld[7375]: Library not loaded: '@rpath/libreadline.6.2.dylib'
  Referenced from: '/Users/nf/opt/anaconda3/lib/R/lib/libR.dylib'
  Reason: tried: '/Users/nf/opt/anaconda3/lib/R/lib/libreadline.6.2.dylib' (no such file), '/Users/nf/opt/anaconda3/lib/libreadline.6.2.dylib' (no such file), '/Users/nf/opt/anaconda3/libreadline.6.2.dylib' (no such file)
zsh: abort      R

I thought I need to install libreadline.6.2.dylib, so tried;

% conda install libreadline.6.2.dylib
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - libreadline.6.2.dylib

Current channels:

  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Then, I followed the error message and visit https://anaconda.org, searched libreadline.6.2.dylib, and got a "There were no items found for this search".

I tried this before updating and after updated mac OS 12.6 to 12.6.5, and Xcode Command Line Tools for Xcode 14.2 (my Xcode is 14.2 because the OS is before 13.0), XQuartz 2.8.4 to 2.8.5, R 4.2.3 to R 4.3.0.

I have tried to find solutions appeared in conda/conda#6183, until now I haven't yet found a solution for my case.
I tried;
conda update -c rdonnellyr -c main --all
it didn't work.
I also tried to edit /Users/nf/opt/anaconda3/lib/R/lib/libR.dylib, the line @rpath/libreadline.6.2.dylib to @rpath/libreadline.8.2.dylib, because my enviroment has libreadline.8.2.dylib instead of libreadline.6.2.dylib, but this neither dosen't work (so I just wrote back into libreadline.6.2.dylib).

[bnprks]

Hi, sorry I lost track of your issue -- I didn't get a notification when you edited your response to include your new updates.

I've been getting several reports that installing clang via conda is not working for people with older Macs. I've updated the instructions in that original issue here, to a recommendation that I tested successfully on a 2015 iMac. Basically, I installed everything via homebrew and didn't use conda for hdf5 or clang. Could you try this approach to see if it fixes your problems?

Otherwise, I'm not very familiar with the errors you are running into, so it might be hard for me to provide much more help with your system configuration. If you still have problems after doing the homebred-based installation I suggested above, could you let me know:

• the compiler versions you're using (or have unsuccessfully tried installing with)
• the contents of your ~/.R/Makevars file
• the Mac model and year you are running on (from apple menu in top left -> About this Mac)
  It may or may not help me provide better advice, but it might surface something where I can give another suggestion

[noriko-hiroi]

Dear Bnprks/Bpcells team, Thank you for your response, I will try uninstall and install with homebrew and follow further instructions in the link, and will report the update! Sincerely, Noriko

…

On Sun, 30 Apr 2023 at 04:22, bnprks ***@***.***> wrote: Hi, sorry I lost track of your issue -- I didn't get a notification when you edited your response to include your new updates. I've been getting several reports that installing clang via conda is not working for people with older Macs. I've updated the instructions in that original issue here <#3 (comment)>, to a recommendation that I tested successfully on a 2015 iMac. Basically, I installed everything via homebrew and didn't use conda for hdf5 or clang. Could you try this approach to see if it fixes your problems? Otherwise, I'm not very familiar with the errors you are running into, so it might be hard for me to provide much more help with your system configuration. If you still have problems after doing the homebred-based installation I suggested above, could you let me know: - the compiler versions you're using (or have unsuccessfully tried installing with) - the contents of your ~/.R/Makevars file - the Mac model and year you are running on (from apple menu in top left -> About this Mac) It may or may not help me provide better advice, but it might surface something where I can give another suggestion — Reply to this email directly, view it on GitHub <#18 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJDQYK65YOJNYWWLAQ7XHCDXDVTAXANCNFSM6AAAAAAWYJMFUE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- ----------------------------------------------------------------------------------------------- Noriko F. Hiroi PhD, Professor, Kanagawa Institute of Technology ***@***.*** ***@***.*** ***@***.***> Bld. C2, Room 601/608 1030 Shimoogino, Atsugi, Kanagawa 243-0292 +81-46-291-3115 (ex 3496)

[noriko-hiroi]

Hi,

I finally could install BPCells.
Following Compilation issues on macOS #3, edited ~/.R/Makevars file was effective.

More detailed, after once more I cleaned R and reinstalled Xcode(14.2), Command Line Tools, XQuartz, R(4.3.0) and RStudio(2023.03.0+386), the error message for trying > remotes::install_github("bnprks/BPCells") got simplified just
"Unable to locate libhdf5. Please install manually or edit compiler flags.
ERROR: configuration failed for package ‘BPCells’".

Under this condition, I ran

% brew install hdf5 llvm
% brew info llvm

It gave me the information of CC and CXX location to me, and I also confirmed
% ls -l /usr/local/include/hdf5.h
and added the description

CFLAGS=-I/usr/local/include
CXXFLAGS=-I/usr/local/include

in the last lines of ~/.R/Makevars file.

After edited ~/.R/Makevars file, I ran > remotes::install_github("bnprks/BPCells") and got "* DONE (BPCells)"!

Thank you for all the kind instructions.
Just in case for the other persons who got a similar trouble, I note a bit additional information about my case.
First I used
% conda install -c anaconda hdf5
both gcc(13.1.0) and clang(14.0.0) have installed in my enviroment, and got the first fail.
Next, I tried % conda activate base in terminal and used % R in the environment to run > remotes::install_github("bnprks/BPCells"). This again didn't work in my case.
Third, I tried to use % brew install hdf5, this didn't change the situation, neither.
And finally I found the answer, and it was already explained in Compilation issues on macOS #3 from January!
I should find it by reading through.

Thank you for taking your time.
Really really helpful, thanks.

[bnprks]

Great! I'm glad we finally got a solution for you :)

Thanks for giving the details of what other options you tried, hopefully this will make installation easier for other Mac users