toubleshooting easybuild_bootstrap.sh about easybuild-life-sciences HOT 4 CLOSED

== installing extension htmlwidgets 0.7 (261/519)...
== installing extension rgl 0.96.0 (262/519)...
== FAILED: Installation ended unsuccessfully (build directory: /easybuild/build/R/3.3.2/foss-2016b-fh1): build failed (first 300 chars): cmd "R CMD INSTALL /easybuild/sources/r/R/extensions/rgl_0.96.0.tar.gz --library=/easybuild/software/R/3.3.2-foss-2016b-fh1/lib/R/library --no-clean-on-error" exited with exitcode 1 and output:

• installing source package 'rgl' ...
  ** package 'rgl' successfully unpacked and MD5 sums checked
  chec
  == Results of the build can be found in the log file(s) /tmp/eb-21YUjL/easybuild-R-3.3.2-20161123.001424.yCuxx.log, /tmp/eb-21YUjL/easybuild-R-3.3.2-20161123.001424.yCuxx.log.1
  ERROR: Build of /easybuild/github/easybuild-life-sciences/easybuild/easyconfigs/R/R-3.3.2-foss-2016b-fh1.eb failed (err: 'build failed (first 300 chars): cmd "R CMD INSTALL /easybuild/sources/r/R/extensions/rgl_0.96.0.tar.gz --library=/easybuild/software/R/3.3.2-foss-2016b-fh1/lib/R/library --no-clean-on-error" exited with exitcode 1 and output:\n* installing source package 'rgl' ...\n** package 'rgl' successfully unpacked and MD5 sums checked\nchec')
  eb@eb25:$
  eb@eb25:$

from easybuild-life-sciences.

try installing X11 dev packages

eb@eb25:~$ sudo apt-get install xorg-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
libreadline6-dev libtinfo-dev
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
libboost-filesystem1.58.0 libboost-system1.58.0 libdmx-dev libdmx1 libdrm-dev libfontconfig1-dev libfontenc-dev libfreetype6-dev libfs-dev libfs6 libice-dev libmirclient-dev libmirclient9
libmircommon-dev libmircommon5 libmircookie-dev libmircookie2 libmirprotobuf3 libpciaccess-dev libpixman-1-dev libpng12-dev libprotobuf-dev libprotobuf-lite9v5 libprotobuf9v5 libsm-dev
libxaw7-dev libxcomposite-dev libxcursor-dev libxdamage-dev libxext-dev libxfixes-dev libxfont-dev libxfont1 libxft-dev libxi-dev libxinerama-dev libxkbcommon-dev libxkbcommon0 libxkbfile-dev
libxmu-dev libxmu-headers libxmuu-dev libxpm-dev libxrandr-dev libxrender-dev libxres-dev libxres1 libxss-dev libxss1 libxt-dev libxtst-dev libxv-dev libxvmc-dev libxvmc1 libxxf86dga-dev
libxxf86vm-dev mesa-common-dev mir-client-platform-mesa-dev x11proto-bigreqs-dev x11proto-composite-dev x11proto-damage-dev x11proto-dmx-dev x11proto-dri2-dev x11proto-dri3-dev
x11proto-fixes-dev x11proto-fonts-dev x11proto-gl-dev x11proto-present-dev x11proto-randr-dev x11proto-record-dev x11proto-render-dev x11proto-resource-dev x11proto-scrnsaver-dev
x11proto-video-dev x11proto-xcmisc-dev x11proto-xext-dev x11proto-xf86bigfont-dev x11proto-xf86dga-dev x11proto-xf86dri-dev x11proto-xf86vidmode-dev x11proto-xinerama-dev xserver-xorg-dev
Suggested packages:
libice-doc libsm-doc libxaw-doc libxext-doc libxt-doc
The following NEW packages will be installed:
libboost-filesystem1.58.0 libboost-system1.58.0 libdmx-dev libdmx1 libdrm-dev libfontconfig1-dev libfontenc-dev libfreetype6-dev libfs-dev libfs6 libice-dev libmirclient-dev libmirclient9
libmircommon-dev libmircommon5 libmircookie-dev libmircookie2 libmirprotobuf3 libpciaccess-dev libpixman-1-dev libpng12-dev libprotobuf-dev libprotobuf-lite9v5 libprotobuf9v5 libsm-dev
libxaw7-dev libxcomposite-dev libxcursor-dev libxdamage-dev libxext-dev libxfixes-dev libxfont-dev libxfont1 libxft-dev libxi-dev libxinerama-dev libxkbcommon-dev libxkbcommon0 libxkbfile-dev
libxmu-dev libxmu-headers libxmuu-dev libxpm-dev libxrandr-dev libxrender-dev libxres-dev libxres1 libxss-dev libxss1 libxt-dev libxtst-dev libxv-dev libxvmc-dev libxvmc1 libxxf86dga-dev
libxxf86vm-dev mesa-common-dev mir-client-platform-mesa-dev x11proto-bigreqs-dev x11proto-composite-dev x11proto-damage-dev x11proto-dmx-dev x11proto-dri2-dev x11proto-dri3-dev
x11proto-fixes-dev x11proto-fonts-dev x11proto-gl-dev x11proto-present-dev x11proto-randr-dev x11proto-record-dev x11proto-render-dev x11proto-resource-dev x11proto-scrnsaver-dev
x11proto-video-dev x11proto-xcmisc-dev x11proto-xext-dev x11proto-xf86bigfont-dev x11proto-xf86dga-dev x11proto-xf86dri-dev x11proto-xf86vidmode-dev x11proto-xinerama-dev xorg-dev
xserver-xorg-dev
0 upgraded, 83 newly installed, 0 to remove and 15 not upgraded.

from easybuild-life-sciences.

this did the trick

checking for GL/glu.h... no
configure: error: missing required header GL/glu.h
ERROR: configuration failed for package 'rgl'
eb@eb25:~$

eb@eb25:~$ sudo apt-get install libglu1-mesa-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
libreadline6-dev libtinfo-dev
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
libgl1-mesa-dev libglu1-mesa libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render0-dev libxcb-shape0-dev
libxcb-sync-dev libxcb-xfixes0 libxcb-xfixes0-dev libxshmfence-dev
The following NEW packages will be installed:
libgl1-mesa-dev libglu1-mesa libglu1-mesa-dev libx11-xcb-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-present-dev libxcb-randr0 libxcb-randr0-dev libxcb-render0-dev
libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0 libxcb-xfixes0-dev libxshmfence-dev
0 upgraded, 16 newly installed, 0 to remove and 15 not upgraded.
Need to get 520 kB of archives.
After this operation, 3063 kB of additional disk space will be used.
Do you want to continue? [Y/n] y

from easybuild-life-sciences.

The easybuild bootstrap is the best way for new sites to install EasyBuild.
Hutch easybuild work has moved to containers. https://github.com/FredHutch/EBcb

from easybuild-life-sciences.