installing without sudo

[dm8000]

Hello. I have tried installing magick in a R terminal and got this

> install.packages("magick")
Installing package into ‘/data04/projects04/MarianaBoroni/adipocyte_int/lib/Gabiluizlib_2/Gabiluizlib2/Gabiluizlib’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/magick_2.7.3.tar.gz'
Content type 'application/x-gzip' length 4813163 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

* installing *source* package ‘magick’ ...
** package ‘magick’ successfully unpacked and MD5 sums checked
** using staged installation
Package Magick++ was not found in the pkg-config search path.
Perhaps you should add the directory containing `Magick++.pc'
to the PKG_CONFIG_PATH environment variable
No package 'Magick++' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lMagick++-6.Q16
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the Magick++ library. Try installing:
 - deb: libmagick++-dev (Debian, Ubuntu)
 - rpm: ImageMagick-c++-devel (Fedora, CentOS, RHEL)
 - csw: imagemagick_dev (Solaris)
 - brew imagemagick@6 (MacOS)
For Ubuntu versions Trusty (14.04) and Xenial (16.04) use our PPA:
   sudo add-apt-repository -y ppa:cran/imagemagick
   sudo apt-get update
   sudo apt-get install -y libmagick++-dev
If Magick++ is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a Magick++.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:22: fatal error: Magick++.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘magick’
* removing ‘/data04/projects04/MarianaBoroni/adipocyte_int/lib/Gabiluizlib_2/Gabiluizlib2/Gabiluizlib/magick’
Warning in install.packages :
  installation of package ‘magick’ had non-zero exit status

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

I am using R remotely and I have no root access. I have tried downloading the rpm binaries for installation instead, but there is an unending loop of dependencies that make this impossible. Is there any alternative for the installation?

[zhenglukai]

In this case you need to build magick from source. For example, to install magick in /cluster/soft/magick and let R find it, you may do like this:

tar xvzf ImageMagick.tar.gz
cd ImageMagick-7.1.0-51
./configure --prefix=/cluster/soft/magick
make
make install

export PKG_CONFIG_PATH=/cluster/soft/magick/lib/pkgconfig
export LD_LIBRARY_PATH=/cluster/soft/magick/lib

cd /temp/dir/to/build/r-magick
git clone https://github.com/ropensci/magick
R CMD INSTALL magick

[burnsal]

@zhenglukai I am trying this process to install magick for use on HPC system and am running into some issues. Due to allocation limits I am trying to install into an R library I specified in my project directory. I adjusted the first code chunk as follows:

tar xvzf ImageMagick.tar.gz  
cd ImageMagick-7.1.0-62  
./configure --prefix=/project/dir/R/lib/magick LDFLAGS='-L/project/dir/R/lib'  
make  
make install

At this point, I get the following warning:

cp -f Magick++/lib/Magick++.pc Magick++/lib/Magick++-7.Q16HDRI.pc
make[1]: warning:  Clock skew detected.  Your build may be incomplete.

When I run the R CMD at the end of the code chunk, I get the following error:

ERROR: cannot install to srcdir for package ‘magick’

I have already tried conventional package installation in R v4.2.0 and when running in console it outputs the following error:

Error: package or namespace load failed for ‘magick’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/project/dir/R/lib/magick/libs/magick.so':
libMagick++-6.Q16.so.8: cannot open shared object file: No such file or directory

Interestingly, this installation works if I'm using an interactive RStudio Server session. However, I need to be able to submit batch jobs that can run a long time so need to find a way to get a complete install.

[zhenglukai]

Hi @burnsal ,

Regarding the "Clock skew detected" warning, usually make clean and rebuilding the software could help.

libMagick++-6.Q16.so.8: cannot open shared object file: No such file or directory

Please take a look at the directory where you installed ImageMagick. You built ImageMagick from the source file of version 7.1.0, so I assume there is no libMagick++-6.Q16.so.8. See if making a soft link named libMagick++-6.Q16.so.8 to the actual file in your folder helps.

Good luck!

[burnsal]

Thanks @zhenglukai ! Still trying to find a workaround. Do you have any thoughts on the srcdir error?

ERROR: cannot install to srcdir for package ‘magick’

[zhenglukai]

Thanks @zhenglukai ! Still trying to find a workaround. Do you have any thoughts on the srcdir error?

ERROR: cannot install to srcdir for package ‘magick’

Did you download the source code of the R package to the location of your R library (R_LIBS_USER)? If that is the case, try to download the source in another place and R CMD INSTALL magick there.

[ywjin0707]

I was having a similar issue installing the package in RStudio server being managed by IT (so no sudo for me). I followed the steps posted by @zhenglukai but ended up with the following error message when calling library(magick): libMagick++-7.Q16HDRI.so.5: cannot open shared object file: No such file or directory The missing piece of information to solve this issue was to use: dyn.load("/path/to/libMagick++-7.Q16HDRI.so.5")

Now just gotta go figure out how to install popper for pdftools...