Installation fails on R4.3.0 under Ubuntu

[SMBaylis]

I've had an installation failure when installing from CRAN, with the following error message:

install.packages("cli")
Installing package into ‘/home/myname/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/cli_3.6.1.tar.gz'
Content type 'application/x-gzip' length 567293 bytes (553 KB)
==================================================
downloaded 553 KB

• installing source package ‘cli’ ...
  ** package ‘cli’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
  gcc -I"/usr/share/R/include" -DNDEBUG -ggdb -O0 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ansi.c -o ansi.o
  gcc -I"/usr/share/R/include" -DNDEBUG -ggdb -O0 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cleancall.c -o cleancall.o
  gcc -I"/usr/share/R/include" -DNDEBUG -ggdb -O0 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c diff.c -o diff.o
  gcc -I"/usr/share/R/include" -DNDEBUG -ggdb -O0 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c errors.c -o errors.o
  gcc -I"/usr/share/R/include" -DNDEBUG -ggdb -O0 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glue.c -o glue.o
  gcc -I"/usr/share/R/include" -DNDEBUG -ggdb -O0 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
  gcc -I"/usr/share/R/include" -DNDEBUG -ggdb -O0 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inst.c -o inst.o
  inst.c:2:10: fatal error: cli/progress.h: No such file or directory
  2 | #include <cli/progress.h>
  | ^~~~~~~~~~~~~~~~
  compilation terminated.
  make: *** [/usr/lib/R/etc/Makeconf:191: inst.o] Error 1
  ERROR: compilation failed for package ‘cli’
• removing ‘/home/bay043/R/x86_64-pc-linux-gnu-library/4.3/cli’

The downloaded source packages are in
‘/tmp/RtmpgJZxId/downloaded_packages’
Warning message:
In install.packages("cli") :
installation of package ‘cli’ had non-zero exit status

I get the same error message for both the latest CRAN version (3.6.1, at the time of writing), and the latest cli-main (3.6.1.9000).

workaround:
The issue does not affect cli version 3.5.0, which I have successfully installed via R CMD build and R CMD INSTALL

[gaborcsardi]

I don't think this is a cli issue, but possibly you are overwriting CFLAGS or PKG_CFLAGS in your ~/.R/Makevars file?

[SMBaylis]

Right you are. Thanks!

[gaborcsardi]

Btw. if you want to add additional compiler flags, use the += form, e.g.

CFLAGS+= -Wall

That keeps the original flags as well.