Task #2174
closed
Dataminer and Statistical Manager packages
100%
Description
This ticket reports the packages and the software to be installed on the Dataminer and the Statistical Manager machines. Updates to this ticket will report new packages/software.
##General##
Mono:
https://support.d4science.org/issues/1368#change-5873
GDAL:
wget http://download.osgeo.org/gdal/1.11.0/gdal1110.zip
unzip gdal1110.zip -d gdal1110
./configure --with-gdal-config=/usr/local/bin/gdal-config
JAGS:
http://mcmc-jags.sourceforge.net/
R Packages:
data.table
doBy
multcomp
mvtnorm
survival
splines
TH.data
MASS
Matrix
lattice
abind
bayesmix
coda
R2jags
R2WinBUGS
rjags
runjags
abind
coda
maptools
rjags
sp
base
boot
class
cluster
codetools
compiler
datasets
foreign
graphics
grDevices
grid
KernSmooth
lattice
MASS
Matrix
methods
mgcv
nlme
nnet
parallel
rpart
spatial
splines
stats
stats4
survival
tcltk
tools
utils
withr
##ICES processes##
install.packages("/root/download/Rcpp_0.9.10.tar.gz", repos = NULL, type="source")
install.packages("/root/download/plyr_1.8.tar.gz", repos = NULL, type="source")
install.packages("stringr")
install.packages("/root/download/reshape2_1.2.tar.gz", repos = NULL, type="source")
install.packages("/root/download/data.table_1.9.2.tar.gz", repos = NULL, type="source")
install.packages("R2HTML")
install.packages("multcomp")
install.packages("Matrix")
install.packages("lattice")
install.packages("snow")
install.packages("/root/download/RcppEigen_0.3.2.0.tar.gz", repos = NULL, type="source")
install.packages("minqa")
install.packages("/root/download/lme4_1.0-5.tar.gz", repos = NULL, type="source")
install.packages("/root/download/doBy_4.5-3.tar.gz", repos = NULL, type="source")
install.packages("mvtnorm")
install.packages("survival")
install.packages("data.table")
help(package=splines)
help(package=TH.data)
help(package=MASS)
##FAO processes##
install.packages("RCurl")
install.packages("digest")
install.packages("/root/download/httr_0.2.tar.gz", repos = NULL, type="source")
install.packages("memoise")
install.packages("whisker")
install.packages("evaluate")
install.packages("/root/download/devtools_1.4.1.tar.gz", repos = NULL, type="source")
require(devtools)
install_github("rsdmx", "opensdmx")
apt-get update
apt-get install libgdal1-dev
apt-get install libgeos-dev
apt-get install libspatialite-dev
install.packages("rgdal")
install.packages("rgeos")
require(devtools)
install_github("RFigisGeo", "openfigis")
##Knitr##
install.packages('knitr', repos = c('http://yihui.name/xran', 'http://cran.rstudio.org'))
devtools::install_github('HenrikBengtsson/R.methodsS3')
devtools::install_github('HenrikBengtsson/R.oo')
devtools::install_github('eddelbuettel/digest')
devtools::install_github('HenrikBengtsson/R.utils')
devtools::install_github('HenrikBengtsson/R.cache')
devtools::install_github('christophergandrud/repmis')
->Install utf8x latex packages
install.packages("rworldmap", repos="http://R-Forge.R-project.org")
wget https://cran.r-project.org/src/contrib/spam_1.3-0.tar.gz
install.packages('./spam_1.3-0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/maps_3.0.1.tar.gz
install.packages('./maps_3.0.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/fields_8.3-5.tar.gz
install.packages('./fields_8.3-5.tar.gz', repos = NULL, type="source")
wget http://download.r-forge.r-project.org/src/contrib/rworldmap_1.3-4.tar.gz
install.packages('./rworldmap_1.3-4.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/highlight_0.4.7.tar.gz
install.packages('./highlight_0.4.7.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/Rcpp_0.12.2.tar.gz
install.packages('./Rcpp_0.12.2.tar.gz', repos = NULL, type="source")
devtools::install_github('hadley/pryr')
devtools::install_github('cran/RColorBrewer')
wget http://cran.jellyfish.lol/src/contrib/dichromat_2.0-0.tar.gz
install.packages('./dichromat_2.0-0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz
install.packages('./colorspace_1.2-6.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/munsell_0.4.2.tar.gz
install.packages('./munsell_0.4.2.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz
install.packages('./labeling_0.3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/scales_0.3.0.tar.gz
install.packages('./scales_0.3.0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/gtable_0.1.2.tar.gz
install.packages('./gtable_0.1.2.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/ggplot2_2.0.0.tar.gz
install.packages('./ggplot2_2.0.0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/jsonlite_0.9.19.tar.gz
install.packages('./jsonlite_0.9.19.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz
install.packages('./magrittr_1.5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/gridExtra_2.0.0.tar.gz
install.packages('./gridExtra_2.0.0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/viridis_0.3.1.tar.gz
install.packages('./viridis_0.3.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz
install.packages('./base64enc_0.1-3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/htmltools_0.2.6.tar.gz
install.packages('./htmltools_0.2.6.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/htmlwidgets_0.5.tar.gz
install.packages('./htmlwidgets_0.5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/plotly_2.0.16.tar.gz
install.packages('./plotly_2.0.16.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mapdata_2.2-5.tar.gz
install.packages('./mapdata_2.2-5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mapplots_1.5.tar.gz
install.packages('./mapplots_1.5.tar.gz', repos = NULL, type="source")
->install the netcdf-bin linux package
wget https://cran.r-project.org/src/contrib/ncdf_1.6.9.tar.gz
install.packages('./ncdf_1.6.9.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mnormt_1.5-3.tar.gz
install.packages('./mnormt_1.5-3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/numDeriv_2014.2-1.tar.gz
install.packages('./numDeriv_2014.2-1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/sn_1.3-0.tar.gz
install.packages('./sn_1.3-0.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/mclust_5.1.tar.gz
install.packages('./mclust_5.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/tclust_1.2-3.tar.gz
install.packages('./tclust_1.2-3.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/modeltools_0.2-21.tar.gz
install.packages('./modeltools_0.2-21.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/flexmix_2.3-13.tar.gz
install.packages('./flexmix_2.3-13.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/prabclus_2.2-6.tar.gz
install.packages('./prabclus_2.2-6.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/diptest_0.75-7.tar.gz
install.packages('./diptest_0.75-7.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/DEoptimR_1.0-4.tar.gz
install.packages('./DEoptimR_1.0-4.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/robustbase_0.92-5.tar.gz
install.packages('./robustbase_0.92-5.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/kernlab_0.9-22.tar.gz
install.packages('./kernlab_0.9-22.tar.gz', repos = NULL, type="source")
wget http://cran.jellyfish.lol/src/contrib/trimcluster_0.1-2.tar.gz
install.packages('./trimcluster_0.1-2.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/fpc_2.1-10.tar.gz
install.packages('./fpc_2.1-10.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz
install.packages('./RJSONIO_1.3-0.tar.gz', repos = NULL, type="source")
require(devtools)
install_github('rCharts', 'ramnathv')
wget https://cran.r-project.org/src/contrib/cowplot_0.6.0.tar.gz
install.packages('./cowplot_0.6.0.tar.gz', repos = NULL, type="source")
require(devtools)
install_github("IRDTunaAtlas", "juldebar")
Updated by Gianpaolo Coro over 9 years ago
Latest packages:
##Absence records##
wget https://cran.r-project.org/src/contrib/DBI_0.3.1.tar.gz
install.packages('./DBI_0.3.1.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/RPostgreSQL_0.4.tar.gz
install.packages('./RPostgreSQL_0.4.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/maptools_0.8-37.tar.gz
install.packages('./maptools_0.8-37.tar.gz', repos = NULL, type="source")
wget https://cran.r-project.org/src/contrib/sp_1.2-1.tar.gz
install.packages('./sp_1.2-1.tar.gz', repos = NULL, type="source")
install.packages("raster", repos="http://R-Forge.R-project.org")
#VPA Workflow
install.packages('xtable')
install.packages('reshape')
install_github("FLCore", "flr")
install_github("FLa4a", "flr")
install.packages('kobe')
install.packages('shiny')
Updated by Gianpaolo Coro over 9 years ago
- Status changed from New to In Progress
#MONO Installation (#2173)
on Ubuntu 12.04.5 LTS, the following two packages are required to run EwECmd.exe
mono-runtime libmono-microsoft-visualbasic10.0-cil They can be installed, as root, with: apt-get install mono-runtime libmono-microsoft-visualbasic10.0-cil
Updated by Andrea Dell'Amico over 9 years ago
The FLa4a R package needs the following debs:
- gsl-bin - libgsl0-dev
Updated by Andrea Dell'Amico over 9 years ago
- % Done changed from 0 to 80
- Infrastructure Production added
Those R packages and their dependencies are installed on all the dataminer (dev and prod) and all the statistical manager nodes.
Updated by Gianpaolo Coro over 9 years ago
- % Done changed from 80 to 0
#Additional Package for VPA Workflow
install.packages('ncdf4')
Updated by Andrea Dell'Amico over 9 years ago
Can I install it on all the servers? dataminer prod/dev, statistical prod/dev ?
Updated by Gianpaolo Coro over 9 years ago
They are meant for the next release/pre-release.
Updated by Pasquale Pagano over 9 years ago
- Tracker changed from Support to Task
Updated by Gianpaolo Coro over 9 years ago
#Packages for I2S processes
install.packages("readxl")
Updated by Andrea Dell'Amico over 9 years ago
New requests for packages on the statistical manager (and dataminer too?):
- lubridate - dplyr - tidyr - gam - rgl - readxl
Updated by Gianpaolo Coro over 9 years ago
Hi Andrea, the packages should be aligned between StatMan and Dataminer, because the latter is going to substitute the former in the next months.
Updated by Andrea Dell'Amico over 9 years ago
Gianpaolo Coro wrote:
Hi Andrea, the packages should be aligned between StatMan and Dataminer, because the latter is going to substitute the former in the next months.
Right, I forgot that all the statistical and dataminer playbooks share the same R packages list (there are two separate files actually, one for the production servers and one for the devel/preprod, but they are identical right now).
Updated by Andrea Dell'Amico over 9 years ago
I see that the rgl package needs the GL include files. All the other new packages have just been installed on the production statistical managers.
Updated by Andrea Dell'Amico over 9 years ago
The statistical manager nodes now have all the new modules installed.
Updated by Gianpaolo Coro over 9 years ago
Newly requested are:
install.packages("geosphere")
install.packages("shapefiles")
Updated by Andrea Dell'Amico over 9 years ago
Questions:
- Do they need to be installed on the rstudio servers too?
- Do you want them installed on the dataminer servers immediately? I just updated the statistical-manager to satisfy the request arrived by email.
Updated by Gianpaolo Coro over 9 years ago
Let me explain the approach I suggest: the packages listed here should be prepared for being installed on the StatMan and Dataminer services (not on RStudio, unless explicitly requested) in the production environments.
In other words, they should be only added to the installation scripts.
The scripts should be run only when requested by a release activity.
I add the packages inhere after having already installed and checked them on the development machines, that's why I report the exact command instead of the simple package names.
Updated by Gianpaolo Coro over 9 years ago
The pandoc package for Linux is required too.
Updated by Andrea Dell'Amico over 9 years ago
Added both rmarkdown and pandoc to the list of packages. They will be installed at the next upgrade, or the next playbook run.
Updated by Gianpaolo Coro over 9 years ago
The following python packages are required:
numpy, matplotlib, psycopg2, scipy, scikit-learn, networkx, pandas, igraph
Updated by Andrea Dell'Amico over 9 years ago
They are the same listed on #3970 but spark, for which I'm waiting for an answer.
Updated by Gianpaolo Coro over 9 years ago
I have just updated the Dataminer installation Wiki page with the following requirement for vessels data analysis algorithms:
download the file following file (http://thredds.research-infrastructures.eu/thredds/fileServer/public/netcdf/gebco_08_OCEANS_CLIMATOLOGY_METEOROLOGY_ATMOSPHERE_.nc) under the "ecocfg" folder and rename it as "gebco_08.nc"
This is needed to be added to the installation process, although the file is quite large.
Updated by Andrea Dell'Amico over 9 years ago
Gianpaolo Coro wrote:
The following python packages are required:
numpy, matplotlib, psycopg2, scipy, scikit-learn, networkx, pandas, igraph
Those have been installed on all the dataminer servers.
Updated by Gianpaolo Coro over 9 years ago
install.packages("curl")
install.packages("caret")
Updated by Gianpaolo Coro over 9 years ago
install.packages("httr")
install.packages("XML")
Updated by Gianpaolo Coro over 9 years ago
Postgres and PostGIS clients are required (have been already installed on dataminer1-d):
apt-get install postgresql-client apt-get install postgis
Updated by Gianpaolo Coro about 9 years ago
install_github("flr/FLCore")
install_github("flr/FLash")
install_github("flr/FLAssess")
install_github("flr/ggplotFL")
install.packages("GA")
Updated by Gianpaolo Coro over 8 years ago
install.packages("kobe")
install_github("flr/FLRDynState")
install_github("flr/FLBEIA")
Updated by Gianpaolo Coro over 8 years ago
- Status changed from In Progress to Closed
Since this update is going to become fully automatic, the list of packages will be maintained on SVN only:
https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/r_cran_pkgs.txt
https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/r_deb_pkgs.txt
https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/r_github_pkgs.txt
