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jpeg R package instalation does not find jpeglib.h in non standard location – CentOS

I’m trying to install jpeg package in R in a Linux server (in which I don’t have sudo access) and jpeg installation does not find jpeglib.h I installed locally. How do I tell R where to look for it when configure.args='--with-libjpeg-include=/path failed?

Sever OS version is CentOS Linux 7 (Core)

In R I ran:

>install.packages('jpeg', lib="/shared/mybossusr/R3.5.0/lib", repos="https://mirrors.nic.cz/R/", destdir="/shared/mybossusr/usr/tmp")

And I got this error:

rjcommon.h:11:21: fatal error: jpeglib.h: No such file or directory
#include

So I installed jpeg-turbo

wget https://downloads.sourceforge.net/libjpeg-turbo/libjpeg-turbo-2.0.2.tar.gz
mkdir libjpeg-turbo-2
cd libjpeg-turbo-2
cmake -G"Unix Makefiles" -DCMAKE_INSTALL_PREFIX:PATH=/shared/mybossusr/bin/libjpeg-turbo-2 /shared/mybossusr/download/libjpeg-turbo-2.0.2
make
make install

I checked and jpeglib.h is at /shared/mybossusr/bin/libjpeg-turbo-2/include

I added this at the end of my ~/.bashrc :

export CFLAGS="-I/usr/include -I=/shared/mybossusr/bin/libjpeg-turbo-2"

I logged out and in, and I got the same error when trying to install jpeg in R.
I also added the location of the library to my path at ~/.barsh:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/shared/mybossusr/bin/libjpeg-turbo-2/include
export PATH=$PATH:/shared/mybossusr/bin/libjpeg-turbo-2/include

just in case, because I don’t fully understand when a software looks where. Did source ~/.bashrc, logged out and in, but nothing changed.

So, I tried afterwards in R some arguments I came up with:

install.packages('jpeg', lib="/shared/mybossusr/R3.5.0/lib", repos="https://mirrors.nic.cz/R/", destdir="/shared/mybossusr/R3.5.0/tmp", configure.args='--with-libjpeg-include=/shared/mybossuser/bin/jpeg/include')

and:

install.packages('jpeg', lib="/shared/mybossusr/R3.5.0/lib", repos="https://mirrors.nic.cz/R/", destdir="/shared/mybossusr/R3.5.0/tmp", configure.args='--with-libjpeg=/shared/mybossuser/bin/jpeg')

or:

install.packages('jpeg', lib="/shared/mybossusr/R3.5.0/lib", repos="https://mirrors.nic.cz/R/", destdir="/shared/mybossusr/R3.5.0/tmp", configure.args='--with-libjpeg-lib=/shared/mybossuser/bin/jpeg/include')

to try to tell R where libjpeg was installed, but nothing worked.

Is there any configure.args that will do the trick? So far with other packages it was quite straight forward to use a --with-package_name-lib, but I’m clueless with this one…

Thanks in advance!

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3

Answers


  1. 0

    Try installing the libjpeg-turbo-devel package. That’s what did it for me on RHEL 7. According to this page, on CentOS 7 the package name is the same.

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  2. 0

    For me this is what did the trick:

    Install jpeg-turbo in a non-standard location, say $HOME/local, from:

    https://github.com/libjpeg-turbo/libjpeg-turbo/releases

    cmake -G"Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$HOME/local
make
make install

    Then point these globals to the install location in your .bashrc:

    export LIBRARY_PATH=$HOME/local/lib64:$HOME/local/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=$HOME/local/lib64:$HOME/local/lib:$LD_LIBRARY_PATH
export C_INCLUDE_PATH=$HOME/local/include:$C_INCLUDE_PATH

    Then try the R package again

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  3. 0

    I had the same issue with the config.args in the install.packages() command in R – for some reason --with-libjpeg-include doesn’t point the compiler to the non-standard location I speficied. So here’s how I worked around it.

    First, I installed libjpeg (link) in a non-standard location.

    # in bash: 
cd 
mkdir /home/tpytsui/libjpeg
cd /home/tpytsui/libjpeg
# download libjpeg.zip into cd
unzip libjpeg.zip
cd /home/tpytsui/libjpeg/libjpeg-master
./configure --prefix=/home/tpytsui/libjpeg/local
make
# make test # run make test to ensure no complaints
make install

    Then, I added the path to my libjpeg to LD_LIBRARY_PATH.

    # in bash
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/tpytsui/libjpeg/local/lib

    Then, in R, I told the c compiler (in my case gcc) where to look when compiling files. Normally, we shouldn’t do this, but we are only doing this because configure.args doesn’t work.

    # in R
Sys.setenv(C_INCLUDE_PATH = "/home/tpytsui/libjpeg/local/include")
Sys.setenv(LIBRARY_PATH = "/home/tpytsui/libjpeg/local/lib")

    Finally, I installed the r package jpeg. There is no need to add config.args because they didn’t work anyway.

    # in R
install.packages('jpeg', type='source', repos = "http://cran.rstudio.com")
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