Comments (4)
eitsupi
commented on August 24, 2024
Why not use rig for R installation and pak for R package installation? If you use pak on a Linux distribution like RHEL, the dependent system packages will be installed automatically and you will not need to install them manually.
from httpgd.
nx10
commented on August 24, 2024
I second that pak might be worth a try but in general there seems something wrong with the R c++ build setup. Is httpgd/unigd the only source package you have trouble with? Updating all the build tools (GCC, make, ...) might be worth a try. I think the rocker (Ubuntu based) images build R from source.
Edit: it might also be worth to ask over at lambdr
from httpgd.
jimgar
commented on August 24, 2024
Hi both, thanks for the replies!
Why not use rig for R installation and pak for R package installation? If you use pak on a Linux distribution like RHEL, the dependent system packages will be installed automatically and you will not need to install them manually.
@eitsupi, this is a good question. Honestly, it didn't cross my mind. I've never had a need to use either of these before because we haven't had lambdas running R processes - we just do our thing on macbooks. System dependencies are ours to resolve individually.
I've looked into it though and the answer is that pak doesn't resolve system requirements for the AL2023 distro, which is not a standard Linux distro but rather a bespoke one that AWS has made. I installed pak in the container and ran pak::sysreqs_is_supported(), which returned FALSE. Also, pak doesn't seem to support installing specific versions of packages from what I can tell, and I want that to be able to pin versions for production. But please correct me if I'm wrong on that.
I second that pak might be worth a try but in general there seems something wrong with the R c++ build setup. Is httpgd/unigd the only source package you have trouble with? Updating all the build tools (GCC, make, ...) might be worth a try. I think the rocker (Ubuntu based) images build R from source.
Edit: it might also be worth to ask over at lambdr
@nx10 unigd seems to install fine, and so did pak and its dependencies which all installed from source (see below).
I've only observed the issue with httpgd. I added gcc and make-devel to the container but it didn't make a difference.
Any other ideas about the tool chain?
pak compiling from source
> install.packages("pak")
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/pak_0.7.2.tar.gz'
Content type 'application/x-gzip' length 2027490 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘pak’ ...
** package ‘pak’ successfully unpacked and MD5 sums checked
** using staged installation
** Running ./configure
** libs
Current platform: x86_64-pc-linux-gnu
Build platform:
Target platform:
Compiling R6
Compiling cli
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/cli/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c ansi.c -o ansi.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c cleancall.c -o cleancall.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c diff.c -o diff.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c errors.c -o errors.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c glue.c -o glue.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c inst.c -o inst.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c keypress-unix.c -o keypress-unix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c keypress-win.c -o keypress-win.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c keypress.c -o keypress.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c md5.c -o md5.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c progress-altrep.c -o progress-altrep.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c progress.c -o progress.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c sha1.c -o sha1.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c sha256.c -o sha256.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c thread.c -o thread.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c tty.c -o tty.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c utf8.c -o utf8.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c utils.c -o utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c vt.c -o vt.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c vtparse.c -o vtparse.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c vtparse_table.c -o vtparse_table.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c win-utf8.c -o win-utf8.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -I../inst/include -fpic -g -O2 -c winfiles.c -o winfiles.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/cli/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/cli/libs
Compiling curl
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/curl/src'
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c callbacks.c -o callbacks.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c curl.c -o curl.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c download.c -o download.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c escape.c -o escape.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fetch.c -o fetch.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c findport.c -o findport.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c form.c -o form.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c getdate.c -o getdate.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c handle.c -o handle.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ieproxy.c -o ieproxy.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c interrupt.c -o interrupt.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c multi.c -o multi.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c nslookup.c -o nslookup.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c options.c -o options.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c reflist.c -o reflist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c split.c -o split.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ssl.c -o ssl.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c typechecking.c -o typechecking.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils.c -o utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c winidn.c -o winidn.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c writer.c -o writer.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/curl/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/curl/libs
Compiling filelock
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/filelock/src'
rm -f filelock.so init.o filelock-unix.o locklist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c filelock-unix.c -o filelock-unix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c locklist.c -o locklist.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o filelock.so init.o filelock-unix.o locklist.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/filelock/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/filelock/libs
Compiling jsonlite
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/jsonlite/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c base64.c -o base64.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c collapse_array.c -o collapse_array.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c collapse_object.c -o collapse_object.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c escape_chars.c -o escape_chars.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c is_datelist.c -o is_datelist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c is_recordlist.c -o is_recordlist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c null_to_na.c -o null_to_na.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c num_to_char.c -o num_to_char.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c parse.c -o parse.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c prettify.c -o prettify.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c push_parser.c -o push_parser.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c r-base64.c -o r-base64.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c register.c -o register.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c row_collapse.c -o row_collapse.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c transpose_list.c -o transpose_list.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c validate.c -o validate.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/jsonlite/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/jsonlite/libs
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr”
Compiling lpSolve
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/lpSolve/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c colamd.c -o colamd.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c commonlib.c -o commonlib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c hbio.c -o hbio.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c ini.c -o ini.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c isfixedvar.c -o isfixedvar.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_Hash.c -o lp_Hash.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_LUSOL.c -o lp_LUSOL.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_MDO.c -o lp_MDO.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_MPS.c -o lp_MPS.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_SOS.c -o lp_SOS.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_crash.c -o lp_crash.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_lib.c -o lp_lib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_matrix.c -o lp_matrix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_mipbb.c -o lp_mipbb.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_params.c -o lp_params.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_presolve.c -o lp_presolve.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_price.c -o lp_price.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_pricePSE.c -o lp_pricePSE.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_report.c -o lp_report.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_rlp.c -o lp_rlp.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_scale.c -o lp_scale.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_simplex.c -o lp_simplex.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_utils.c -o lp_utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lp_wlp.c -o lp_wlp.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lpslink56.c -o lpslink56.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lusol.c -o lusol.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c lusolio.c -o lusolio.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c mmio.c -o mmio.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c myblas.c -o myblas.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c sparselib.c -o sparselib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include -fpic -g -O2 -c yacc_read.c -o yacc_read.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o lpSolve.so colamd.o commonlib.o hbio.o ini.o init.o isfixedvar.o lp_Hash.o lp_LUSOL.o lp_MDO.o lp_MPS.o lp_SOS.o lp_crash.o lp_lib.o lp_matrix.o lp_mipbb.o lp_params.o lp_presolve.o lp_price.o lp_pricePSE.o lp_report.o lp_rlp.o lp_scale.o lp_simplex.o lp_utils.o lp_wlp.o lpslink56.o lusol.o lusolio.o mmio.o myblas.o sparselib.o yacc_read.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/lpSolve/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/lpSolve/libs
Compiling ps
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/ps/src'
gcc -g -O2 -L/usr/local/lib -Wall px.c -o px
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-common.c -o api-common.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c common.c -o common.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c extra.c -o extra.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dummy.c -o dummy.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c error-codes.c -o error-codes.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c posix.c -o posix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-posix.c -o api-posix.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c linux.c -o linux.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-linux.c -o api-linux.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o posix.o api-posix.o linux.o api-linux.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/ps/src'
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/ps
Compiling zip
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/zip/src'
gcc -g -O2 miniz.c zip.c unixutils.c tools/cmdzip.c -o tools/cmdzip
gcc -g -O2 miniz.c zip.c unixutils.c tools/cmdunzip.c -o tools/cmdunzip
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c miniz.c -o miniz.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rzip.c -o rzip.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c zip.c -o zip.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c unixutils.c -o unixutils.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o zip.so init.o miniz.o rzip.o zip.o unixutils.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/zip/src'
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/zip
Compiling processx
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/processx/src'
gcc -g -O2 -L/usr/local/lib -Wall tools/px.c -o tools/px
gcc -g -O2 -L/usr/local/lib -I../inst/include -Wall tools/sock.c -o tools/sock
gcc -g -O2 -L/usr/local/lib supervisor/supervisor.c \
supervisor/utils.c -o supervisor/supervisor
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c client.c -o client.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c errors.c -o errors.o
gcc -shared -L"/opt/R/4.3.2/lib/R/lib" -L/usr/local/lib -o client.so base64.o client.o errors.o \
-L"/opt/R/4.3.2/lib/R/lib" -lR
if [ -n "" ]; then \
echo Removing libR.so dependency from client.so; \
patchelf --remove-needed libR.so client.so; \
fi
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c poll.c -o poll.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-connection.c -o processx-connection.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-vector.c -o processx-vector.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c create-time.c -o create-time.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/childlist.c -o unix/childlist.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/connection.c -o unix/connection.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/processx.c -o unix/processx.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/sigchld.c -o unix/sigchld.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/utils.c -o unix/utils.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/named_pipe.c -o unix/named_pipe.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cleancall.c -o cleancall.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/processx/src'
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/processx
Compiling callr
Compiling desc
Compiling pkgbuild
Compiling pkgcache
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
make[1]: Entering directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/pkgcache/src'
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c errors.c -o errors.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lib.c -o lib.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c winfiles.c -o winfiles.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o pkgcache.so errors.o init.o lib.o winfiles.o -L/opt/R/4.3.2/lib/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpdUJBuy/R.INSTALLabd38db717d/pak/src/library/pkgcache/src'
installing to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak/library/pkgcache/libs
Compiling pkgsearch
Compiling pkgdepends
installing via 'install.libs.R' to /opt/R/4.3.2/lib/R/library/00LOCK-pak/00new/pak
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘pak’
finding HTML links ... done
cache html
faq html
features html
get-started html
handle_package_not_found html
install html
lib_status html
local_deps html
local_deps_explain html
local_install html
local_install_deps html
local_install_dev_deps html
local_package_trees html
local_system_requirements html
lockfile_create html
lockfile_install html
metadata html
package-dependency-types html
pak-config html
pak-package html
pak html
pak_cleanup html
pak_install_extra html
pak_package_sources html
pak_setup html
pak_sitrep html
pak_solver html
pak_update html
pkg_deps html
pkg_deps_explain html
pkg_deps_tree html
pkg_download html
pkg_history html
pkg_install html
pkg_name_check html
pkg_remove html
pkg_search html
pkg_status html
pkg_sysreqs html
ppm_has_binaries html
ppm_platforms html
ppm_r_versions html
ppm_repo_url html
ppm_snapshots html
repo_add html
repo_get html
repo_status html
sysreqs html
sysreqs_check_installed html
sysreqs_db_list html
sysreqs_db_match html
sysreqs_db_update html
sysreqs_is_supported html
sysreqs_list_system_packages html
sysreqs_platforms html
system_r_platform html
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pak)
Making 'packages.html' ... done
The downloaded source packages are in
‘/tmp/Rtmp2lvTI7/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
from httpgd.
jimgar
commented on August 24, 2024
Ok, I've got a solution.
I think the issue here, ultimately, is that AWS have their own lightweight distro of Linux. It's an RPM-based distro, but not directly comparable to any Fedora release, CentOS, or RHEL. From there, my lack of confidence and understanding caused the mess. I had the RHEL 9 version of R installing, but was then attempting to install R packages from the CentOS 7 Posit Package Manager repo. Total mismatch.
I changed the R package installation to look like the below, bringing it in line with the R version, and now it's all good.
RUN Rscript -e "install.packages(c( \
'httpgd', \
'jsonlite', \
'languageserver' \
), repos = 'https://packagemanager.posit.co/cran/__linux__/rhel9/2024-04-08')"
Not really sure if I should be using RHEL 9 or CentOS 7. But certainly using RHEL 9 has sorted out the httpgd install, so I'm going to go ahead and close this. Thanks again for the package and best wishes!
from httpgd.
Related Issues (20)
- Pdf option not available when exporting plot HOT 2
- Resize plot to any ratio and size HOT 1
- fonts not working on Linux HOT 7
- Open plots in external browser by default
- `par_old = par(no.readonly = TRUE)` triggers the plot window and makes the subsequent figure size incorrect
- Can't open Rplot window when running vscode-R HOT 1
- http no response when get plot HOT 2
- not respecting spacings in ggplot HOT 2
- Server don't response when used via RServe
- CRAN status HOT 31
- Server immediately crash HOT 28
- Use GH releases for CRAN releases HOT 1
- `hgd_browse()`: This site can’t be reached HOT 2
- httpgd crashing and live html site not loading in VScode HOT 1
- No fonts detected for basic plot
- rstudio server and rstudio desktop connection lost
- When I open the external browser, ggplot2 in vscode always encounters depth error. HOT 7
- CRAN packages showing warnings with GCC 14 HOT 1
- Problem creating a conda environment with R=4.4.1 and httpgd
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from httpgd.