I am trying to load RSQLite in my R installation using Home-brew on a Mac OS Catalina with no success.
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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> library(RSQLite)
Error: package or namespace load failed for ‘RSQLite’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/3.6/site-library/RSQLite/libs/RSQLite.so':
dlopen(/usr/local/lib/R/3.6/site-library/RSQLite/libs/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /usr/local/lib/R/3.6/site-library/RSQLite/libs/RSQLite.so
Reason: image not found
The issue is, the RSQLite.so file seems to be there:
rll307@Rodrigos-iMac RSQLite % ls /usr/local/lib/R/3.6/site-library/RSQLite/libs/RSQLite.so
-rwxr-xr-x 1 2096184 Apr 4 08:52 /usr/local/lib/R/3.6/site-library/RSQLite/libs/RSQLite.so*
I downloaded RSQLite_2.2.0.tar binary from CRAN and installed manually
Update
I uninstalled RSQLite and encountered the following error as I tried to install it again:
> install.packages("RSQLite")
Installing package into ‘/usr/local/lib/R/3.6/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_2.2.0.tar.gz'
Content type 'application/x-gzip' length 2373785 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/3.6/site-library/BH/include" -I"/usr/local/lib/R/3.6/site-library/plogr/include" -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -fPIC -g -O2 -c DbColumn.cpp -o DbColumn.o
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/container/stable_vector.hpp:23:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config.hpp:57:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/detail/posix_features.hpp:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:655:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/gethostuuid.h:39:17: error: unknown type name 'uuid_t'
int gethostuuid(uuid_t, const struct timespec *) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_NA);
^
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/container/stable_vector.hpp:23:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config.hpp:57:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:662:27: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int getsgroups_np(int *, uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/container/stable_vector.hpp:23:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config.hpp:57:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:664:27: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int getwgroups_np(int *, uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/container/stable_vector.hpp:23:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config.hpp:57:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:727:31: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int setsgroups_np(int, const uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
In file included from DbColumn.cpp:1:
In file included from ./pch.h:1:
In file included from ./RSQLite.h:14:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/container/stable_vector.hpp:23:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config.hpp:57:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /usr/local/lib/R/3.6/site-library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:729:31: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int setwgroups_np(int, const uuid_t);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t uid_t;
^
5 errors generated.
make: *** [DbColumn.o] Error 1
ERROR: compilation failed for package ‘RSQLite’
* removing ‘/usr/local/lib/R/3.6/site-library/RSQLite’
Warning in install.packages :
installation of package ‘RSQLite’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/l3/g7br_rgx7m965vn322wtxky00000gn/T/RtmptnBNRO/downloaded_packages’
Thanks for the help
