`isoband` package installation fails, `testthat.h` not found - r

Question

I have R (version 3.6.3 (2020-02-29), Holding the Windsock) installed on Ubuntu 18.04.4 LTS. When I try to install ggplot2 from source, the installation of dependency package isoband fails with testthat.h not found. The full output:
> install.packages("ggplot2")
Installing package into ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependency ‘isoband’
trying URL 'https://cloud.r-project.org/src/contrib/isoband_0.2.1.tar.gz'
Content type 'application/x-gzip' length 2293333 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.0.tar.gz'
Content type 'application/x-gzip' length 3031461 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
* installing *source* package ‘isoband’ ...
** package ‘isoband’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c clip-lines.cpp -o clip-lines.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c isoband.cpp -o isoband.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c polygon.cpp -o polygon.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
-I"/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"
-I"/usr/local/lib/R/site-library/testthat/include" -fpic -g -O2
-fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c separate-polygons.cpp -o separate-polygons.o
separate-polygons.cpp:4:10: fatal error: testthat.h: No such file or directory
#include <testthat.h>
^~~~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:177: recipe for target 'separate-polygons.o' failed
make: *** [separate-polygons.o] Error 1
ERROR: compilation failed for package ‘isoband’
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/isoband’
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status
ERROR: dependency ‘isoband’ is not available for package ‘ggplot2’
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp5aYRcO/downloaded_packages’
I have already tried to install testthat manually, but it seems not to be available for R 3.6.3:
> install.packages("testthat")
...
Error: package or namespace load failed for ‘pkgload’:
.onLoad failed in loadNamespace() for 'pkgload', details:
call: NULL
error: package ‘testthat’ was installed by an R version with different internals;
it needs to be reinstalled for use with this R version
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependency ‘pkgload’ is not available for package ‘testthat’
* removing ‘/home/oszkar/R/x86_64-pc-linux-gnu-library/3.6/testthat’
Warning in install.packages :
installation of package ‘testthat’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp5aYRcO/downloaded_packages’
Any idea would be appreciated.

Answer 1

Solved. The cause of the problem was that after a series of Ubuntu and R upgrades there were some outdated packages installed from source remained on my system.
First I opened up an R console and looking for the paths for R packages built with pre 3.6 version:
> unique(subset(as.data.frame(installed.packages()),
grepl("^3\\.[^6]", Built))[, "LibPath"])
[1] /usr/local/lib/R/site-library /usr/lib/R/library
As it is not possible to apply remove.packages() on these outdated packages, I switched to bash, and listed all the package paths:
>grep 'Built: R 3.[0-5]' /usr/local/lib/R/site-library/*/DESCRIPTION /usr/lib/R/library/*/
DESCRIPTION
I have removed (simply deleted from /usr/local/lib/R/site-library/ and /usr/lib/R/library/) the packages on the previous commands output, and now everything works.