I am not able to install RStoolbox packages in Ubuntu

Jannatul · August 31, 2022, 7:32pm

The RStudio server is showing error in installing devtools, RStoolbox. Error messages are:

For install.packages("RStoolbox"):

ERROR: lazy loading failed for package ‘exactextractr’

removing ‘/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/exactextractr’
Warning in install.packages :
installation of package ‘exactextractr’ had non-zero exit status
ERROR: dependencies ‘rgdal’, ‘exactextractr’ are not available for package ‘RStoolbox’
removing ‘/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/RStoolbox’
Warning in install.packages :
installation of package ‘RStoolbox’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmpbz9sJx/downloaded_packages’

When I tried to install dependencies, it showed error:

Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libgdal1-dev

I tried the code below for installing dependencies, it installed

sudo apt -y install libgdal-dev

but still couldn't install RStoolbox packages. It showed the same error:

"ERROR: dependencies ‘rgdal’, ‘exactextractr’ are not available for package ‘RStoolbox’
installation of package ‘RStoolbox’ had non-zero exit status"

Any suggestions will be highly appreciated! Thank you so much.

andresrcs · August 31, 2022, 9:11pm

I can install rgdal on Ubuntu 22.04.1 for WSL2 without any issues. These are the system libraries I usually install for spatial packages, give them a try.

sudo apt install libgdal-dev gdal-bin libgeos-dev libproj-dev libudunits2-dev sqlite3

Do you get any error messages while doing this?

Jannatul · August 31, 2022, 9:43pm

No, I didn't get any error messages. It showed already the newest version (3.4.3+dfsg-1~focal0) were there, as I have installed them already. Thank you.

andresrcs · August 31, 2022, 9:45pm

Can you show the complete console output you get when you try to install rgdal?
Also, maybe you would have better luck by installing a binary from the public RStudio Package Manager

install.packages("rgdal", repos=c('https://packagemanager.rstudio.com/all/__linux__/jammy/latest', 'https://cran.rstudio.com/'))

Note: This repository is specific for Ubuntu 22.04.1, make sure you are using this Ubuntu version.

Jannatul · August 31, 2022, 10:02pm

I am using Ubuntu 20.04 LTS. Shall I still try that code?

##The R console output is:

Thank you!

andresrcs · August 31, 2022, 10:18pm

Please do not post screenshots, it is considered a bad practice here, post the console output as formatted code instead, here is how to do it:

Now about your issue, you are showing a very different error message now

#> free() invalid pointer 
#> Aborted
#> ERROR: loading failed

it seems your system has fallen into a bad state I would try restarting the whole thing (Just closing the console doesn't restart WSL2) and trying to install rgdal again.

For Ubuntu 20 the RSPM repository has a different link, you can try with this

install.packages("rgdal", repos=c('https://packagemanager.rstudio.com/all/__linux__/focal/latest', 'https://cran.rstudio.com/'))

Jannatul · August 31, 2022, 10:36pm

My apology for the screenshots. Thank you for the instructions.

Did you mean installing the WSL2 again?

andresrcs · August 31, 2022, 10:50pm

No, just restarting WSL2 (or your computer) is enough.

Jannatul · August 31, 2022, 11:20pm

I have tried this code. rgdal has been installed but the other dependency ‘exactextractr’has not been installed. And RStoolbox installation was aborted.

install.packages("rgdal", repos=c('https://packagemanager.rstudio.com/all/__linux__/focal/latest', 'https://cran.rstudio.com/'))


[Show in New Window]

Installing package into ‘/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
also installing the dependency ‘exactextractr’

trying URL 'https://cloud.r-project.org/src/contrib/exactextractr_0.9.0.tar.gz'
Content type 'application/x-gzip' length 629871 bytes (615 KB)
==================================================
downloaded 615 KB

trying URL 'https://cloud.r-project.org/src/contrib/RStoolbox_0.3.0.tar.gz'
Content type 'application/x-gzip' length 991987 bytes (968 KB)
==================================================
downloaded 968 KB

* installing *source* package ‘exactextractr’ ...
** package ‘exactextractr’ successfully unpacked and MD5 sums checked
** using staged installation
configure: exactextractr: 0.9.0
checking for geos-config... /bin/geos-config
checking geos-config usability... yes
configure: GEOS version: 3.10.2
checking geos version at least 3.5.0... yes
checking compiling and building against geos_c... yes
configure: PKG_CXX: g++
configure: PKG_CXXFLAGS: -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include
configure: PKG_LIBS: -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu -lgeos_c
configure: creating ./config.status

config.status: creating src/Makevars
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exact_extract.cpp -o exact_extract.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c raster_utils.cpp -o raster_utils.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c coverage_fraction.cpp -o coverage_fraction.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c rasterize.cpp -o rasterize.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c resample.cpp -o resample.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/area.cpp -o exactextract/src/area.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/box.cpp -o exactextract/src/box.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/cell.cpp -o exactextract/src/cell.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/coordinate.cpp -o exactextract/src/coordinate.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/floodfill.cpp -o exactextract/src/floodfill.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/geos_utils.cpp -o exactextract/src/geos_utils.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/grid.cpp -o exactextract/src/grid.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/perimeter_distance.cpp -o exactextract/src/perimeter_distance.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/raster_cell_intersection.cpp -o exactextract/src/raster_cell_intersection.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/side.cpp -o exactextract/src/side.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/traversal.cpp -o exactextract/src/traversal.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/traversal_areas.cpp -o exactextract/src/traversal_areas.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c exactextract/src/weighted_quantiles.cpp -o exactextract/src/weighted_quantiles.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o exactextractr.so RcppExports.o exact_extract.o raster_utils.o coverage_fraction.o rasterize.o resample.o exactextract/src/area.o exactextract/src/box.o exactextract/src/cell.o exactextract/src/coordinate.o exactextract/src/floodfill.o exactextract/src/geos_utils.o exactextract/src/grid.o exactextract/src/perimeter_distance.o exactextract/src/raster_cell_intersection.o exactextract/src/side.o exactextract/src/traversal.o exactextract/src/traversal_areas.o exactextract/src/weighted_quantiles.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/x86_64-linux-gnu -lgeos_c -L/usr/lib/R/lib -lR
installing to /home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-exactextractr/00new/exactextractr/libs

** R
** inst
** byte-compile and prepare package for lazy loading
double free or corruption (out)
Aborted
ERROR: lazy loading failed for package ‘exactextractr’
* removing ‘/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/exactextractr’
Warning in install.packages :
  installation of package ‘exactextractr’ had non-zero exit status
ERROR: dependency ‘exactextractr’ is not available for package ‘RStoolbox’
* removing ‘/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/RStoolbox’
Warning in install.packages :
  installation of package ‘RStoolbox’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpZI5NSw/downloaded_packages’

I couldn't install devtools package also. Thank you very much for helping me. I appreciated it.

andresrcs · September 1, 2022, 12:23am

This is a problem between your system and the compiler, I have never seen this sort of low-level memory corruption issue so I have no idea what the cause might be.
The only workaround solution I can think off is to install exactextractr and RStoolbox also from the RSPM

install.packages("exactextractr", repos=c('https://packagemanager.rstudio.com/all/__linux__/focal/latest', 'https://cran.rstudio.com/'))
install.packages("RStoolbox", repos=c('https://packagemanager.rstudio.com/all/__linux__/focal/latest', 'https://cran.rstudio.com/'))

Jannatul · September 1, 2022, 1:14pm

Thank you. Now I have received another error for installing RStoolbox about boot system. It says host is down. The error message is

** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
System has not been booted with systemd as init system (PID 1). Can't operate.
Failed to create bus connection: Host is down
Warning in system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
double free or corruption (out)
Aborted
ERROR: lazy loading failed for package ‘RStoolbox’
* removing ‘/home/jannatul/R/x86_64-pc-linux-gnu-library/4.2/RStoolbox’
Warning in install.packages :
  installation of package ‘RStoolbox’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmpgs1b05/downloaded_packages’

Do you know what can be the reason for it? Thank you so much.

andresrcs · September 1, 2022, 1:42pm

Sorry but I'm out of ideas, there is something weird going on with your setup since I can't replicate your issues on WSL2.

Jannatul · September 1, 2022, 8:16pm

It's okay. Thank you for helping me tough.
Do you know any other way instead of windows subsystem that will allow me to boot two system together?

andresrcs · September 1, 2022, 8:58pm

You can use full virtual machines with VirtualBox or VMware or you can also install a Linux distribution natively in a different drive or partition in your computer but that is outside of this forum's scope.

Jannatul · September 1, 2022, 9:27pm

Sounds good! Thank you for the suggestions. I appreciated it!

system · October 15, 2022, 7:33pm

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