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jbwhit/rjava-irkernel-problem.ipynb

Created May 31, 2017 22:52
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Weird problem with setting LD_LIBRARY_PATH for R Kernel in JupyterHub.
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rjava-irkernel-problem.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"CONDA_ROOT /opt/Anaconda3-4.2.0-Linux-x86_64\n",
"EDITOR vi\n",
"HOME /export/users/pho10\n",
"JPY_PARENT_PID 59624\n",
"LANG en_US.UTF-8\n",
"LN_S ln -s\n",
"MAKE make\n",
"PAGER /usr/bin/less\n",
"PATH /opt/jdk/bin:/opt/anaconda/bin:/sbin:/bin:/usr/sbin:/usr/bin\n",
"PWD /export/users/pho10\n",
"R_ARCH \n",
"R_BROWSER /usr/bin/firefox\n",
"R_BZIPCMD /usr/bin/bzip2\n",
"R_DOC_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/doc\n",
"R_GZIPCMD /bin/gzip\n",
"R_HOME /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R\n",
"R_INCLUDE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/include\n",
"R_LIBS_SITE \n",
"R_LIBS_USER ~/R/x86_64-pc-linux-gnu-library/3.3\n",
"R_PAPERSIZE a4\n",
"R_PDFVIEWER /usr/bin/evince\n",
"R_PLATFORM x86_64-pc-linux-gnu\n",
"R_PRINTCMD lpr\n",
"R_RD4PDF times,inconsolata,hyper\n",
"R_SESSION_TMPDIR /tmp/RtmpEL9LYU\n",
"R_SHARE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/share\n",
"R_SYSTEM_ABI linux,gcc,gxx,gfortran,?\n",
"R_TEXI2DVICMD /usr/local/bin/texi2dvi\n",
"R_UNZIPCMD /usr/bin/unzip\n",
"R_ZIPCMD /usr/bin/zip\n",
"SED /bin/sed\n",
"SHELL /bin/bash\n",
"SHLVL 0\n",
"TAR /bin/gtar\n",
"USER pho10"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"Sys.getenv()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error: package or namespace load failed for ‘rJava’\n",
"output_type": "error",
"traceback": [
"Error: package or namespace load failed for ‘rJava’\nTraceback:\n",
"1. library(rJava)",
"2. stop(gettextf(\"package or namespace load failed for %s\", sQuote(package)), \n . call. = FALSE, domain = NA)"
]
}
],
"source": [
"library(rJava)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"CONDA_ROOT /opt/Anaconda3-4.2.0-Linux-x86_64\n",
"EDITOR vi\n",
"HOME /export/users/pho10\n",
"JPY_PARENT_PID 59624\n",
"LANG en_US.UTF-8\n",
"LD_LIBRARY_PATH :@JAVA_LD@\n",
"LN_S ln -s\n",
"MAKE make\n",
"PAGER /usr/bin/less\n",
"PATH /opt/jdk/bin:/opt/anaconda/bin:/sbin:/bin:/usr/sbin:/usr/bin\n",
"PWD /export/users/pho10\n",
"R_ARCH \n",
"R_BROWSER /usr/bin/firefox\n",
"R_BZIPCMD /usr/bin/bzip2\n",
"R_DOC_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/doc\n",
"R_GZIPCMD /bin/gzip\n",
"R_HOME /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R\n",
"R_INCLUDE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/include\n",
"R_LIBS_SITE \n",
"R_LIBS_USER ~/R/x86_64-pc-linux-gnu-library/3.3\n",
"R_PAPERSIZE a4\n",
"R_PDFVIEWER /usr/bin/evince\n",
"R_PLATFORM x86_64-pc-linux-gnu\n",
"R_PRINTCMD lpr\n",
"R_RD4PDF times,inconsolata,hyper\n",
"R_SESSION_TMPDIR /tmp/RtmpEL9LYU\n",
"R_SHARE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/share\n",
"R_SYSTEM_ABI linux,gcc,gxx,gfortran,?\n",
"R_TEXI2DVICMD /usr/local/bin/texi2dvi\n",
"R_UNZIPCMD /usr/bin/unzip\n",
"R_ZIPCMD /usr/bin/zip\n",
"SED /bin/sed\n",
"SHELL /bin/bash\n",
"SHLVL 0\n",
"TAR /bin/gtar\n",
"USER pho10"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"Sys.getenv()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"Sys.setenv(LD_LIBRARY_PATH = \"/opt/jdk/jre/lib/amd64:/opt/jdk/jre/lib/amd64/server\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"CONDA_ROOT /opt/Anaconda3-4.2.0-Linux-x86_64\n",
"EDITOR vi\n",
"HOME /export/users/pho10\n",
"JPY_PARENT_PID 59624\n",
"LANG en_US.UTF-8\n",
"LD_LIBRARY_PATH /opt/jdk/jre/lib/amd64:/opt/jdk/jre/lib/amd64/server\n",
"LN_S ln -s\n",
"MAKE make\n",
"PAGER /usr/bin/less\n",
"PATH /opt/jdk/bin:/opt/anaconda/bin:/sbin:/bin:/usr/sbin:/usr/bin\n",
"PWD /export/users/pho10\n",
"R_ARCH \n",
"R_BROWSER /usr/bin/firefox\n",
"R_BZIPCMD /usr/bin/bzip2\n",
"R_DOC_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/doc\n",
"R_GZIPCMD /bin/gzip\n",
"R_HOME /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R\n",
"R_INCLUDE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/include\n",
"R_LIBS_SITE \n",
"R_LIBS_USER ~/R/x86_64-pc-linux-gnu-library/3.3\n",
"R_PAPERSIZE a4\n",
"R_PDFVIEWER /usr/bin/evince\n",
"R_PLATFORM x86_64-pc-linux-gnu\n",
"R_PRINTCMD lpr\n",
"R_RD4PDF times,inconsolata,hyper\n",
"R_SESSION_TMPDIR /tmp/RtmpEL9LYU\n",
"R_SHARE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/share\n",
"R_SYSTEM_ABI linux,gcc,gxx,gfortran,?\n",
"R_TEXI2DVICMD /usr/local/bin/texi2dvi\n",
"R_UNZIPCMD /usr/bin/unzip\n",
"R_ZIPCMD /usr/bin/zip\n",
"SED /bin/sed\n",
"SHELL /bin/bash\n",
"SHLVL 0\n",
"TAR /bin/gtar\n",
"USER pho10"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"Sys.getenv()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error: package or namespace load failed for ‘rJava’\n",
"output_type": "error",
"traceback": [
"Error: package or namespace load failed for ‘rJava’\nTraceback:\n",
"1. library(rJava)",
"2. stop(gettextf(\"package or namespace load failed for %s\", sQuote(package)), \n . call. = FALSE, domain = NA)"
]
}
],
"source": [
"library(rJava)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"CONDA_ROOT /opt/Anaconda3-4.2.0-Linux-x86_64\n",
"EDITOR vi\n",
"HOME /export/users/pho10\n",
"JPY_PARENT_PID 59624\n",
"LANG en_US.UTF-8\n",
"LD_LIBRARY_PATH /opt/jdk/jre/lib/amd64:/opt/jdk/jre/lib/amd64/server:@JAVA_LD@\n",
"LN_S ln -s\n",
"MAKE make\n",
"PAGER /usr/bin/less\n",
"PATH /opt/jdk/bin:/opt/anaconda/bin:/sbin:/bin:/usr/sbin:/usr/bin\n",
"PWD /export/users/pho10\n",
"R_ARCH \n",
"R_BROWSER /usr/bin/firefox\n",
"R_BZIPCMD /usr/bin/bzip2\n",
"R_DOC_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/doc\n",
"R_GZIPCMD /bin/gzip\n",
"R_HOME /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R\n",
"R_INCLUDE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/include\n",
"R_LIBS_SITE \n",
"R_LIBS_USER ~/R/x86_64-pc-linux-gnu-library/3.3\n",
"R_PAPERSIZE a4\n",
"R_PDFVIEWER /usr/bin/evince\n",
"R_PLATFORM x86_64-pc-linux-gnu\n",
"R_PRINTCMD lpr\n",
"R_RD4PDF times,inconsolata,hyper\n",
"R_SESSION_TMPDIR /tmp/RtmpEL9LYU\n",
"R_SHARE_DIR /opt/Anaconda3-4.2.0-Linux-x86_64/envs/gpma-gold/lib/R/share\n",
"R_SYSTEM_ABI linux,gcc,gxx,gfortran,?\n",
"R_TEXI2DVICMD /usr/local/bin/texi2dvi\n",
"R_UNZIPCMD /usr/bin/unzip\n",
"R_ZIPCMD /usr/bin/zip\n",
"SED /bin/sed\n",
"SHELL /bin/bash\n",
"SHLVL 0\n",
"TAR /bin/gtar\n",
"USER pho10"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"Sys.getenv()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "R [conda env:gpma-gold]",
"language": "R",
"name": "conda-env-gpma-gold-r"
},
"language_info": {
"codemirror_mode": "r",
"file_extension": ".r",
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.3.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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