Problem downloading Monocle3 dependencies (terra) on M1 Pro MacBook

[garrett-lam]

Describe the bug

• I am unable to download the Monocle3 dependencies ('terra') from Biocmanager

To Reproduce

library(BiocManager) Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',

• 'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',
• 'SummarizedExperiment', 'batchelor', 'Matrix.utils',
• 'HDF5Array', 'terra', 'ggrastr')) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) Installing package(s) 'terra'

There is a binary version available but the source version is later: binary source needs_compilation terra 1.5-21 1.6-3 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes installing the source package ‘terra’

trying URL 'https://cran.rstudio.com/src/contrib/terra_1.6-3.tar.gz' Content type 'application/x-gzip' length 686866 bytes (670 KB)

downloaded 670 KB

• installing source package ‘terra’ ... package ‘terra’ successfully unpacked and MD5 sums checked using staged installation configure: CC: clang -mmacosx-version-min=10.13 configure: CXX: clang++ -mmacosx-version-min=10.13 -std=gnu++11 checking for gdal-config... /opt/homebrew/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.5.1 checking GDAL version >= 2.0.1... yes checking for gcc... clang -mmacosx-version-min=10.13 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 we are using the GNU C compiler... yes checking whether clang -mmacosx-version-min=10.13 accepts -g... yes checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking gdal.h usability... yes checking gdal.h presence... yes checking for gdal.h... yes checking GDAL: linking with --libs only... no checking GDAL: linking with --libs and --dep-libs... no ld: warning: ignoring file /opt/homebrew/Cellar/gdal/3.5.1_1/lib/libgdal.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64 Undefined symbols for architecture x86_64: "_GDALAllRegister", referenced from: _main in gdal_test-8aeace.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) ld: warning: directory not found for option '-L/opt/homebrew/Cellar/poppler/22.06.0_1/lib' ld: library not found for -lcrypto clang: error: linker command failed with exit code 1 (use -v to see invocation) configure: Install failure: compilation and/or linkage problems. configure: error: GDALAllRegister not found in libgdal. ERROR: configuration failed for package ‘terra’
• removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/terra’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/terra’

The downloaded source packages are in ‘/private/var/folders/89/g3h_xtg92b725qqgg7b883sr0000gn/T/Rtmpl092so/downloaded_packages’ Old packages: 'edgeR', 'globals', 'MASS', 'RCurl', 'sf', 'terra' Update all/some/none? [a/s/n]: n Warning messages: 1: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'BiocGenerics' 'DelayedArray' 'DelayedMatrixStats' 'limma' 'lme4' 'S4Vectors' 'SingleCellExperiment' 'SummarizedExperiment' 'batchelor' 'Matrix.utils' 'HDF5Array' 'ggrastr' 2: In install.packages(...) : installation of package ‘terra’ had non-zero exit status

traceback()

traceback() No traceback available

sessionInfo():

sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.0.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages: [1] BiocManager_1.30.18

loaded via a namespace (and not attached): [1] compiler_4.2.1 tools_4.2.1

[techgirl2022]

Hi Garrett, I also noticed this issue while trying to install monocle3 dependencies on my macbook pro and am still troubleshooting this step. Did you run into any issues while installing 'sf'?

[garrett-lam]

Yes, I have problems installing 'sf' too. I posted on their github as well.

[brookeabrown]

Hello, I am having this issue as well. Have you had any success fixing the issue? Thanks!

[techgirl2022]

Mac OS X was giving me issues so I tried to install monocle3 on my Windows desktop computer and that worked (the difference is only needing to install Rtools while running R version 4.1.0.