Task #131
closed
Report the R Interpreter environment to reproduce on the Generic Worker nodes
100%
Description
In this ticket we will report the environment to install on a Generic Worker node to make it compliant with current algorithms requirements
Related issues
Updated by Gianpaolo Coro over 10 years ago
- Status changed from New to In Progress
- % Done changed from 0 to 80
The Worker nodes host a different R Environment with respect to the Statistical Managers. The latters are far more complicated and will require attention in the future.
As regards the Workers, here I report the information I have collected so far to reproduce the current running R environment.
The packages should be already available from the CRAN (i.e. they should be easy to install).
R version 2.14.1 (2011-12-22)
PackageName Licence Version
R2WinBUGS "GPL-2" "2.14.1"
R2jags "GPL (>= 2)" "2.14.1"
abind "LGPL (>= 2)" "2.14.1"
bayesmix "GPL (>= 2)" "2.14.1"
coda "GPL (>= 2)" "2.14.1"
rjags "GPL (== 2)" "2.14.1"
runjags "GPL-2" "2.14.1"
coda "GPL (>= 2)" "2.14.0"
maptools "GPL (>= 2)" "2.12.0"
rjags "GPL (== 2)" "2.13.1"
sp "GPL (>= 2)" "2.13.0"
KernSmooth "Unlimited" "2.14.0"
MASS "GPL-2 | GPL-3" "2.14.0"
Matrix "GPL (>= 2)" "2.14.0"
base "Part of R 2.14.1" "2.14.1"
boot "Unlimited" "2.14.0"
class "GPL-2 | GPL-3" "2.12.0"
cluster "GPL (>= 2)" "2.13.2"
codetools "GPL" "2.12.1"
compiler "Part of R 2.14.1" "2.14.1"
datasets "Part of R 2.14.1" "2.14.1"
foreign "GPL (>= 2)" "2.14.0"
grDevices "Part of R 2.14.1" "2.14.1"
graphics "Part of R 2.14.1" "2.14.1"
grid "Part of R 2.14.1" "2.14.1"
lattice "GPL (>= 2)" "2.14.0"
methods "Part of R 2.14.1" "2.14.1"
mgcv "GPL (>= 2)" "2.14.0"
nlme "GPL (>= 2)" "2.13.1"
nnet "GPL-2 | GPL-3" "2.13.2"
parallel "Part of R 2.14.1" "2.14.1"
rpart "GPL-2 | GPL-3" "2.13.0"
spatial "GPL-2 | GPL-3" "2.14.0"
splines "Part of R 2.14.1" "2.14.1"
stats "Part of R 2.14.1" "2.14.1"
stats4 "Part of R 2.14.1" "2.14.1"
survival "GPL (>= 2)" "2.13.2"
tcltk "Part of R 2.14.1" "2.14.1"
tools "Part of R 2.14.1" "2.14.1"
utils "Part of R 2.14.1" "2.14.1"
Operating System packages to install:
R 2.14.1 (of course)
JAGS: http://mcmc-jags.sourceforge.net/
Updated by Andrea Dell'Amico over 10 years ago
It seems that CRAN is also availabe as a Ubuntu repository: http://sites.psu.edu/theubunturblog/installing-r-in-ubuntu/
Updated by Andrea Dell'Amico over 10 years ago
Which jags version is needed? The one distributed with Ubuntu precise is 3.1.0, via CRAN the 3.2.0, 3.3.0, 3.4.0 are also available.
Updated by Andrea Dell'Amico over 10 years ago
- Category set to System Application
- Assignee set to Andrea Dell'Amico
- % Done changed from 80 to 30
Updated by Andrea Dell'Amico over 10 years ago
I've automated the packages installation but some versions differ from your list:
Package Version abind "abind" "1.4-3" bayesmix "bayesmix" "0.7-3" coda "coda" "0.17-1" R2jags "R2jags" "0.5-6" R2WinBUGS "R2WinBUGS" "2.1-19" rjags "rjags" "3-15" runjags "runjags" "2.0.1-4" abind "abind" "1.4-0" coda "coda" "0.14-5" maptools "maptools" "0.7-38" rjags "rjags" "3-3" sp "sp" "0.9-81" base "base" "2.14.1" boot "boot" "1.3-3" class "class" "7.3-3" cluster "cluster" "1.14.1" codetools "codetools" "0.2-8" compiler "compiler" "2.14.1" datasets "datasets" "2.14.1" foreign "foreign" "0.8-48" graphics "graphics" "2.14.1" grDevices "grDevices" "2.14.1" grid "grid" "2.14.1" KernSmooth "KernSmooth" "2.23-7" lattice "lattice" "0.20-0" MASS "MASS" "7.3-16" Matrix "Matrix" "1.0-2" methods "methods" "2.14.1" mgcv "mgcv" "1.7-12" nlme "nlme" "3.1-102" nnet "nnet" "7.3-1" parallel "parallel" "2.14.1" rpart "rpart" "3.1-50" spatial "spatial" "7.3-3" splines "splines" "2.14.1" stats "stats" "2.14.1" stats4 "stats4" "2.14.1" survival "survival" "2.36-10" tcltk "tcltk" "2.14.1" tools "tools" "2.14.1" utils "utils" "2.14.1"
Updated by Andrea Dell'Amico over 10 years ago
- Status changed from In Progress to Feedback
Updated by Andrea Dell'Amico over 10 years ago
- Status changed from Feedback to In Progress
- Assignee changed from Andrea Dell'Amico to Gianpaolo Coro
Updated by Gianpaolo Coro over 10 years ago
The required JAGS version is 3.1.0.
The packages compatible with the algorithms are the following:
R2jags_0.03-08
abind_1.4-0
rjags_3-10
R2WinBUGS_2.1-19
boot_1.3-3
coda_0.16-1
lattice_0.20-0
All the others should be with the version specified in my post.
Testing the compatibility of the packages is not straightforward, because requires long runs of models (8 hours) to check if learning algorithms converge.
We need to investigate why it is not possible to reproduce the environment I indicated or if the other packages are compatible.
Which is the output of the following commands on the newly installed machine?
R >installed.packages() >sessionInfo()
Updated by Andrea Dell'Amico over 10 years ago
Gianpaolo Coro wrote:
The required JAGS version is 3.1.0.
The packages compatible with the algorithms are the following:
R2jags_0.03-08
abind_1.4-0
rjags_3-10
R2WinBUGS_2.1-19
boot_1.3-3
coda_0.16-1
lattice_0.20-0
Those versions meet the output of my list but is different from yours.
All the others should be with the version specified in my post.
Testing the compatibility of the packages is not straightforward, because requires long runs of models (8 hours) to check if learning algorithms converge.
We need to investigate why it is not possible to reproduce the environment I indicated or if the other packages are compatible.Which is the output of the following commands on the newly installed machine?
R >installed.packages() >sessionInfo()
Ok, I now understand why the versions are different. Your original list reports the R version under which the packages where built and not the package version. Here is the output of your commands:
> installed.packages()
Package LibPath Version Priority
abind "abind" "/usr/local/lib/R/site-library" "1.4-3" NA
bayesmix "bayesmix" "/usr/local/lib/R/site-library" "0.7-3" NA
coda "coda" "/usr/local/lib/R/site-library" "0.17-1" NA
R2jags "R2jags" "/usr/local/lib/R/site-library" "0.5-6" NA
R2WinBUGS "R2WinBUGS" "/usr/local/lib/R/site-library" "2.1-19" NA
rjags "rjags" "/usr/local/lib/R/site-library" "3-15" NA
runjags "runjags" "/usr/local/lib/R/site-library" "2.0.1-4" NA
abind "abind" "/usr/lib/R/site-library" "1.4-0" NA
coda "coda" "/usr/lib/R/site-library" "0.14-5" NA
maptools "maptools" "/usr/lib/R/site-library" "0.7-38" NA
rjags "rjags" "/usr/lib/R/site-library" "3-3" NA
sp "sp" "/usr/lib/R/site-library" "0.9-81" NA
base "base" "/usr/lib/R/library" "2.14.1" "base"
boot "boot" "/usr/lib/R/library" "1.3-3" "recommended"
class "class" "/usr/lib/R/library" "7.3-3" "recommended"
cluster "cluster" "/usr/lib/R/library" "1.14.1" "recommended"
codetools "codetools" "/usr/lib/R/library" "0.2-8" "recommended"
compiler "compiler" "/usr/lib/R/library" "2.14.1" "base"
datasets "datasets" "/usr/lib/R/library" "2.14.1" "base"
foreign "foreign" "/usr/lib/R/library" "0.8-48" "recommended"
graphics "graphics" "/usr/lib/R/library" "2.14.1" "base"
grDevices "grDevices" "/usr/lib/R/library" "2.14.1" "base"
grid "grid" "/usr/lib/R/library" "2.14.1" "base"
KernSmooth "KernSmooth" "/usr/lib/R/library" "2.23-7" "recommended"
lattice "lattice" "/usr/lib/R/library" "0.20-0" "recommended"
MASS "MASS" "/usr/lib/R/library" "7.3-16" "recommended"
Matrix "Matrix" "/usr/lib/R/library" "1.0-2" "recommended"
methods "methods" "/usr/lib/R/library" "2.14.1" "base"
mgcv "mgcv" "/usr/lib/R/library" "1.7-12" "recommended"
nlme "nlme" "/usr/lib/R/library" "3.1-102" "recommended"
nnet "nnet" "/usr/lib/R/library" "7.3-1" "recommended"
parallel "parallel" "/usr/lib/R/library" "2.14.1" "base"
rpart "rpart" "/usr/lib/R/library" "3.1-50" "recommended"
spatial "spatial" "/usr/lib/R/library" "7.3-3" "recommended"
splines "splines" "/usr/lib/R/library" "2.14.1" "base"
stats "stats" "/usr/lib/R/library" "2.14.1" "base"
stats4 "stats4" "/usr/lib/R/library" "2.14.1" "base"
survival "survival" "/usr/lib/R/library" "2.36-10" "recommended"
tcltk "tcltk" "/usr/lib/R/library" "2.14.1" "base"
tools "tools" "/usr/lib/R/library" "2.14.1" "base"
utils "utils" "/usr/lib/R/library" "2.14.1" "base"
Depends
abind "R (>= 1.5.0)"
bayesmix "R (>= 2.10),"
coda "R (>= 2.14.0)"
R2jags "R (>= 2.14.0), rjags (>= 3-3)"
R2WinBUGS "R (>= 2.13.0), coda (>= 0.11-0), boot"
rjags "R (>= 2.14.0), coda (>= 0.13)"
runjags "R (>= 2.14.0)"
abind "R (>= 1.5.0)"
coda "R (>= 2.5.0), lattice"
maptools "R (>= 2.4), foreign (>= 0.8), sp (>= 0.9-47), methods, lattice"
rjags "R (>= 2.9.0), coda (>= 0.13)"
sp "R (>= 2.10.0), methods"
base NA
boot "R (>= 2.14.0), graphics, stats"
class "R (>= 2.5.0), stats, utils"
cluster "R (>= 2.10.0), stats, graphics, utils"
codetools "R (>= 2.1)"
compiler NA
datasets NA
foreign "R (>= 2.13.0), stats"
graphics NA
grDevices NA
grid NA
KernSmooth "R (>= 2.5.0), stats"
lattice "R (>= 2.14.0)"
MASS "R (>= 2.14.0), grDevices, graphics, stats, utils"
Matrix "R (>= 2.12.0), stats, methods, utils, lattice"
methods NA
mgcv "R (>= 2.14.0)"
nlme "graphics, stats, R (>= 2.13)"
nnet "R (>= 2.5.0), stats, utils"
parallel NA
rpart "R (>= 2.13.0), graphics, stats, grDevices"
spatial "R (>= 2.5.0), graphics, stats, utils"
splines NA
stats NA
stats4 "methods, graphics, stats"
survival "stats, utils, graphics, splines, R (>= 2.13.0)"
tcltk NA
tools NA
utils NA
Imports
abind NA
bayesmix "rjags (>= 2.1.0), coda (>= 0.13)"
coda "lattice"
R2jags "abind, coda (>= 0.13), methods, R2WinBUGS, parallel"
R2WinBUGS NA
rjags NA
runjags "parallel, lattice (>= 0.20-10), coda (>= 0.17-1), stats, utils"
abind NA
coda NA
maptools NA
rjags NA
sp "utils, lattice, grid"
base NA
boot NA
class "MASS"
cluster NA
codetools NA
compiler NA
datasets NA
foreign "methods, utils"
graphics "grDevices"
grDevices NA
grid "grDevices"
KernSmooth NA
lattice "grid, grDevices, graphics, stats, utils, methods"
MASS NA
Matrix "graphics, grid"
methods "utils"
mgcv "graphics, stats, nlme, Matrix"
nlme "lattice"
nnet NA
parallel NA
rpart NA
spatial NA
splines "graphics, stats"
stats NA
stats4 NA
survival NA
tcltk NA
tools NA
utils NA
LinkingTo Suggests
abind NA NA
bayesmix NA NA
coda NA NA
R2jags NA NA
R2WinBUGS NA "BRugs (>= 0.3-2)"
rjags NA "tcltk"
runjags NA "rjags, modeest, knitr"
abind NA NA
coda NA NA
maptools NA "spatstat, PBSmapping, maps, gpclib, RArcInfo"
rjags NA NA
sp NA "lattice, RColorBrewer, rgdal"
base NA NA
boot NA "survival"
class NA NA
cluster NA NA
codetools NA NA
compiler NA NA
datasets NA NA
foreign NA NA
graphics NA NA
grDevices NA NA
grid NA "lattice"
KernSmooth NA "MASS"
lattice NA "grid, KernSmooth, MASS"
MASS NA "lattice, nlme, nnet, survival"
Matrix NA "expm"
methods NA NA
mgcv NA "nlme (>= 3.1-64), splines, Matrix, parallel"
nlme NA "Hmisc"
nnet NA "MASS"
parallel NA NA
rpart NA "survival"
spatial NA "MASS"
splines NA NA
stats NA NA
stats4 NA NA
survival NA NA
tcltk NA NA
tools NA NA
utils NA NA
Enhances OS_type
abind NA NA
bayesmix NA NA
coda NA NA
R2jags NA NA
R2WinBUGS NA NA
rjags NA NA
runjags NA NA
abind NA NA
coda NA NA
maptools NA NA
rjags NA NA
sp NA NA
base NA NA
boot NA NA
class NA NA
cluster "MASS" NA
codetools NA NA
compiler NA NA
datasets NA NA
foreign NA NA
graphics NA NA
grDevices NA NA
grid NA NA
KernSmooth NA NA
lattice "chron" NA
MASS NA NA
Matrix "MatrixModels, graph, SparseM (>= 0.87), sfsmisc" NA
methods NA NA
mgcv NA NA
nlme NA NA
nnet NA NA
parallel "snow" NA
rpart NA NA
spatial NA NA
splines NA NA
stats NA NA
stats4 NA NA
survival NA NA
tcltk NA NA
tools NA NA
utils NA NA
License Built
abind "LGPL (>= 2)" "2.14.1"
bayesmix "GPL (>= 2)" "2.14.1"
coda "GPL (>= 2)" "2.14.1"
R2jags "GPL (>= 2)" "2.14.1"
R2WinBUGS "GPL-2" "2.14.1"
rjags "GPL (== 2)" "2.14.1"
runjags "GPL-2" "2.14.1"
abind "LGPL (>= 2)" "2.14.0"
coda "GPL (>= 2)" "2.14.0"
maptools "GPL (>= 2)" "2.12.0"
rjags "GPL (== 2)" "2.13.1"
sp "GPL (>= 2)" "2.13.0"
base "Part of R 2.14.1" "2.14.1"
boot "Unlimited" "2.14.0"
class "GPL-2 | GPL-3" "2.12.0"
cluster "GPL (>= 2)" "2.13.2"
codetools "GPL" "2.12.1"
compiler "Part of R 2.14.1" "2.14.1"
datasets "Part of R 2.14.1" "2.14.1"
foreign "GPL (>= 2)" "2.14.0"
graphics "Part of R 2.14.1" "2.14.1"
grDevices "Part of R 2.14.1" "2.14.1"
grid "Part of R 2.14.1" "2.14.1"
KernSmooth "Unlimited" "2.14.0"
lattice "GPL (>= 2)" "2.14.0"
MASS "GPL-2 | GPL-3" "2.14.0"
Matrix "GPL (>= 2)" "2.14.0"
methods "Part of R 2.14.1" "2.14.1"
mgcv "GPL (>= 2)" "2.14.0"
nlme "GPL (>= 2)" "2.13.1"
nnet "GPL-2 | GPL-3" "2.13.2"
parallel "Part of R 2.14.1" "2.14.1"
rpart "GPL-2 | GPL-3" "2.13.0"
spatial "GPL-2 | GPL-3" "2.14.0"
splines "Part of R 2.14.1" "2.14.1"
stats "Part of R 2.14.1" "2.14.1"
stats4 "Part of R 2.14.1" "2.14.1"
survival "GPL (>= 2)" "2.13.2"
tcltk "Part of R 2.14.1" "2.14.1"
tools "Part of R 2.14.1" "2.14.1"
utils "Part of R 2.14.1" "2.14.1"
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.14.1
Updated by Andrea Dell'Amico over 10 years ago
- Related to Task #140: 36 new smartgears VMs are needed added
Updated by Gianpaolo Coro over 10 years ago
- Status changed from In Progress to Closed
