Update failed for stars... same error for leafem, leafgl, and rgee installation.

[YinOsu]

Update failed for stars

install.packages("stars") Installing package into ‘/usr/local/lib/R/4.4/site-library’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/stars_0.6-6.tar.gz' Content type 'application/x-gzip' length 3741200 bytes (3.6 MB)

downloaded 3.6 MB

• installing source package ‘stars’ ... package ‘stars’ successfully unpacked and MD5 sums checked using staged installation R data * moving datasets to lazyload DB demo inst byte-compile and prepare package for lazy loading

  Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/4.4/site-library/sf/libs/sf.so': dlopen(/usr/local/lib/R/4.4/site-library/sf/libs/sf.so, 0x0006): Library not loaded: /usr/local/opt/gdal/lib/libgdal.34.dylib Referenced from: <3FE68D79-51B5-3CC6-A059-6294E70939DF> /usr/local/lib/R/4.4/site-library/sf/libs/sf.so Reason: tried: '/usr/local/opt/gdal/lib/libgdal.34.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/opt/gdal/lib/libgdal.34.dylib' (no such file), '/usr/local/opt/gdal/lib/libgdal.34.dylib' (no such file), '/usr/local/Cellar/r/4.4.1/lib/R/lib/libgdal.34.dylib' (no such file), '/usr/local/Cellar/gdal/3.9.1_1/lib/libgdal.34.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/Cellar/gdal/3.9.1_1/lib/libgdal.34.dylib' (no such file), '/usr/local/Cellar/gdal/3.9.1_1/lib/libgdal.34.dylib' (no such file), '/usr/local/Cellar/r/4.4.1/lib/R/lib/libgd Execution halted ERROR: lazy loading failed for package ‘stars’

• removing ‘/usr/local/lib/R/4.4/site-library/stars’
• restoring previous ‘/usr/local/lib/R/4.4/site-library/stars’ Warning in install.packages : installation of package ‘stars’ had non-zero exit status

[edzer]

reinstall sf.

[YinOsu]

reinstall sf.

I have, and when I did, I got error.

remove.packages("sf") Removing package from ‘/usr/local/lib/R/4.4/site-library’ (as ‘lib’ is unspecified) install.packages("sf") Installing package into ‘/usr/local/lib/R/4.4/site-library’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/sf_1.0-16.tar.gz' Content type 'application/x-gzip' length 3493756 bytes (3.3 MB)

downloaded 3.3 MB

• installing source package ‘sf’ ... package ‘sf’ successfully unpacked and MD5 sums checked using staged installation configure: CC: clang configure: CXX: clang++ -std=gnu++17 checking for gdal-config... /usr/local/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.9.1 checking GDAL version >= 2.0.1... yes checking for gcc... clang 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 accepts -g... yes checking for clang option to enable C11 features... unsupported checking for clang option to enable C99 features... none needed 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 gdal.h... yes checking GDAL: linking with --libs only... yes checking GDAL: /usr/local/Cellar/gdal/3.9.1_1/share/gdal/pcs.csv readable... no checking GDAL: checking whether PROJ is available for linking:... yes checking GDAL: checking whether PROJ is available for running:... ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db ERROR 1: PROJ: proj_create: unrecognized format / unknown name ERROR 1: PROJ: proj_create: unrecognized format / unknown name no configure: error: OGRCoordinateTransformation() does not return a coord.trans: PROJ not available? ERROR: configuration failed for package ‘sf’
• removing ‘/usr/local/lib/R/4.4/site-library/sf’ Warning in install.packages : installation of package ‘sf’ had non-zero exit status

[edzer]

Looks like you're on MacOS (you didn't specify) - if this is the case, please install sf as a binary package.

[YinOsu]

Looks like you're on MacOS (you didn't specify) - if this is the case, please install sf as a binary package.

Sorry about that. is this the same as installing from the binary package.. ? which I have tried and still not successful.

install_github("r-spatial/sf", configure.args = "--with-proj-lib=$(brew --prefix)/lib/")

[edzer]

No, you'd use

install.packages("sf", type = "binary")

[YinOsu]

No, you'd use

install.packages("sf", type = "binary")

I get this error:

install.packages("sf", type = "binary") Error in install.packages : type 'binary' is not supported on this platform

@edzer

[edzer]

sorry, please try

install.packages("sf", type = "mac.binary")

[YinOsu]

sorry, please try

install.packages("sf", type = "mac.binary")

Here is the output @edzer

install.packages("sf", type = "mac.binary") Installing package into ‘/usr/local/lib/R/4.4/site-library’ (as ‘lib’ is unspecified) Warning in install.packages : unable to access index for repository https://cran.rstudio.com/bin/macosx/contrib/4.4: cannot open URL 'https://cran.rstudio.com/bin/macosx/contrib/4.4/PACKAGES'

package ‘sf’ is available as a source package but not as a binary

Warning in install.packages : package ‘sf’ is not available as a binary package for this version of R

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

[edzer]

This is not a stars issue, but an issue with your R installation; as I don't use a mac, I'm giving up, pls find help elsewhere.