R
CRAN local repository
How to set up a package repository
Guide: http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a-package-repository
To create CRAN repository
Before creating a local repository please give a dry run first. You don't want to be surprised how long will it take to mirror a directory.
Dry run
rsync -avn cran.r-project.org::CRAN > crandryrun.txt
To mirror only partial repository, it is necessary to create directories before running rsync command.
mkdir /media/WD640/CRAN mkdir /media/WD640/CRAN/bin mkdir /media/WD640/CRAN/bin/windows mkdir /media/WD640/CRAN/bin/windows/contrib mkdir /media/WD640/CRAN/bin/windows/contrib/2.15 rsync -rtlzv --delete cran.r-project.org::CRAN/bin/windows/contrib/2.15/ /media/WD640/CRAN/bin/windows/contrib/2.15 (one line with space before /media) rsync -rtlzv --delete cran.r-project.org::CRAN/src/ /media/WD640/CRAN/src/
And optionally
library(tools)
write_PACKAGES("/var/www/CRAN/bin/windows/contrib/2.15", type="win.binary")
We can use du -h to check the folder size.
To create Bioconductor repository
Dry run
rsync -avn bioconductor.org::2.11 > biocdryrun.txt
Then creates directories before running rsync.
The software part:
mkdir /media/WD640/Bioc/packages/2.11/bioc mkdir /media/WD640/Bioc/packages/2.11/bioc/bin mkdir /media/WD640/Bioc/packages/2.11/bioc/bin/windows rsync -zrtlv --delete bioconductor.org::2.11/bioc/bin/windows/ /media/WD640/Bioc/packages/2.11/bioc/bin/windows
and annotation part:
mkdir /media/WD640/Bioc/packages/2.11/data mkdir /media/WD640/Bioc/packages/2.11/data/annotation mkdir /media/WD640/Bioc/packages/2.11/data/annotation/bin mkdir /media/WD640/Bioc/packages/2.11/data/annotation/bin/windows rsync -zrtlv --delete bioconductor.org::2.11/data/annotation/bin/windows/ /media/WD640/Bioc/packages/2.11/data/annotation/bin/windows
To test local repository
To test CRAN
r <- getOption("repos"); r["CRAN"] <- "http://arraytools.no-ip.org/CRAN"
options(repos=r)
install.packages("pamr")
To test Bioconductor
options("BioC_mirror" = "http://arraytools.no-ip.org/Bioc")
source("http://bioconductor.org/biocLite.R")
# This source biocLite.R line can be placed either before or after the previous 2 lines
biocLite("aCGH")
If there is a connection problem, check folder attributes.
chmod -R 755 ~/CRAN/bin
Note that if a binary package was created for R 2.15.1, then it can be installed under R 2.15.1 but not R 2.15.2. The R console will show package xxx is not available (for R version 2.15.2).
For binary installs, the function also checks for the availability of a source package on the same repository, and reports if the source package has a later version, or is available but no binary version is. So for example, if the mirror does not have contents under src directory, we need to run the following line in order to successfully run install.packages() function.
options(install.packages.check.source = "no")
Hidden tool: rsync in Rtools
c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/a.exe" "/cygdrive/c/users/limingc/Documents/" sending incremental file list a.exe sent 323142 bytes received 31 bytes 646346.00 bytes/sec total size is 1198416 speedup is 3.71 c:\Rtools\bin>
And rsync works best when we need to sync folder.
c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/binary" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
binary/
binary/Eula.txt
binary/cherrytree.lnk
binary/depends64.chm
binary/depends64.dll
binary/depends64.exe
binary/mtputty.exe
binary/procexp.chm
binary/procexp.exe
binary/pscp.exe
binary/putty.exe
binary/sqlite3.exe
binary/wget.exe
sent 4115294 bytes received 244 bytes 1175868.00 bytes/sec
total size is 8036311 speedup is 1.95
c:\Rtools\bin>rm c:\users\limingc\Documents\binary\procexp.exe
cygwin warning:
MS-DOS style path detected: c:\users\limingc\Documents\binary\procexp.exe
Preferred POSIX equivalent is: /cygdrive/c/users/limingc/Documents/binary/procexp.exe
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/binary" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
binary/
binary/procexp.exe
sent 1767277 bytes received 35 bytes 3534624.00 bytes/sec
total size is 8036311 speedup is 4.55
c:\Rtools\bin>
Unforunately, if the destination is a network drive, I could get a permission denied (13) error. See also http://superuser.com/questions/69620/rsync-file-permissions-on-windows
Install rgdal package on ubuntu
sudo apt-get install libgdal1-dev libproj-dev
R
> install.packages("rgdal")
Embedding R
Reference http://bioconductor.org/help/course-materials/2012/Seattle-Oct-2012/AdvancedR.pdf
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ export R_HOME=/home/mli/Downloads/R-2.15.2
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/mli/Downloads/R-2.15.2/lib
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ embed.c -I/home/mli/Downloads/R-2.15.2/include -L/home/mli/Downloads/R-2.15.2/lib -lR
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ R CMD ./a.out
WARNING: ignoring environment value of R_HOME
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
ns> require(stats); require(graphics)
ns> ns(women$height, df = 5)
1 2 3 4 5
[1,] 0.000000e+00 0.000000e+00 0.00000000 0.00000000 0.0000000000
[2,] 7.592323e-03 0.000000e+00 -0.08670223 0.26010669 -0.1734044626
[3,] 6.073858e-02 0.000000e+00 -0.15030440 0.45091320 -0.3006088020
[4,] 2.047498e-01 6.073858e-05 -0.16778345 0.50335034 -0.3355668952
[5,] 4.334305e-01 1.311953e-02 -0.13244035 0.39732106 -0.2648807067
[6,] 6.256681e-01 8.084305e-02 -0.07399720 0.22199159 -0.1479943948
[7,] 6.477162e-01 2.468416e-01 -0.02616007 0.07993794 -0.0532919575
[8,] 4.791667e-01 4.791667e-01 0.01406302 0.02031093 -0.0135406187
[9,] 2.468416e-01 6.477162e-01 0.09733619 0.02286023 -0.0152401533
[10,] 8.084305e-02 6.256681e-01 0.27076826 0.06324188 -0.0405213106
[11,] 1.311953e-02 4.334305e-01 0.48059836 0.12526031 -0.0524087186
[12,] 6.073858e-05 2.047498e-01 0.59541597 0.19899261 0.0007809246
[13,] 0.000000e+00 6.073858e-02 0.50097182 0.27551020 0.1627793975
[14,] 0.000000e+00 7.592323e-03 0.22461127 0.35204082 0.4157555879
[15,] 0.000000e+00 0.000000e+00 -0.14285714 0.42857143 0.7142857143
attr(,"degree")
[1] 3
attr(,"knots")
20% 40% 60% 80%
60.8 63.6 66.4 69.2
attr(,"Boundary.knots")
[1] 58 72
attr(,"intercept")
[1] FALSE
attr(,"class")
[1] "ns" "basis" "matrix"
ns> summary(fm1 <- lm(weight ~ ns(height, df = 5), data = women))
Call:
lm(formula = weight ~ ns(height, df = 5), data = women)
Residuals:
Min 1Q Median 3Q Max
-0.38333 -0.12585 0.07083 0.15401 0.30426
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 114.7447 0.2338 490.88 < 2e-16 ***
ns(height, df = 5)1 15.9474 0.3699 43.12 9.69e-12 ***
ns(height, df = 5)2 25.1695 0.4323 58.23 6.55e-13 ***
ns(height, df = 5)3 33.2582 0.3541 93.93 8.91e-15 ***
ns(height, df = 5)4 50.7894 0.6062 83.78 2.49e-14 ***
ns(height, df = 5)5 45.0363 0.2784 161.75 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.2645 on 9 degrees of freedom
Multiple R-squared: 0.9998, Adjusted R-squared: 0.9997
F-statistic: 9609 on 5 and 9 DF, p-value: < 2.2e-16
ns> ## example of safe prediction
ns> plot(women, xlab = "Height (in)", ylab = "Weight (lb)")
ns> ht <- seq(57, 73, length.out = 200)
ns> lines(ht, predict(fm1, data.frame(height=ht)))
ns> ## Don't show:
ns> ## Consistency:
ns> x <- c(1:3,5:6)
ns> stopifnot(identical(ns(x), ns(x, df = 1)),
ns+ identical(ns(x, df=2), ns(x, df=2, knots=NULL)),# not true till 2.15.2
ns+ !is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1
ns+ length(kk) == 0)
ns> ## End Don't show
ns>
ns>
ns>
The above result can be compared with running
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ R WARNING: ignoring environment value of R_HOME
R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
> library(splines) > example("ns")
ns> require(stats); require(graphics)
ns> ns(women$height, df = 5)
1 2 3 4 5 [1,] 0.000000e+00 0.000000e+00 0.00000000 0.00000000 0.0000000000 [2,] 7.592323e-03 0.000000e+00 -0.08670223 0.26010669 -0.1734044626 [3,] 6.073858e-02 0.000000e+00 -0.15030440 0.45091320 -0.3006088020 [4,] 2.047498e-01 6.073858e-05 -0.16778345 0.50335034 -0.3355668952 [5,] 4.334305e-01 1.311953e-02 -0.13244035 0.39732106 -0.2648807067 [6,] 6.256681e-01 8.084305e-02 -0.07399720 0.22199159 -0.1479943948 [7,] 6.477162e-01 2.468416e-01 -0.02616007 0.07993794 -0.0532919575 [8,] 4.791667e-01 4.791667e-01 0.01406302 0.02031093 -0.0135406187 [9,] 2.468416e-01 6.477162e-01 0.09733619 0.02286023 -0.0152401533
[10,] 8.084305e-02 6.256681e-01 0.27076826 0.06324188 -0.0405213106 [11,] 1.311953e-02 4.334305e-01 0.48059836 0.12526031 -0.0524087186 [12,] 6.073858e-05 2.047498e-01 0.59541597 0.19899261 0.0007809246 [13,] 0.000000e+00 6.073858e-02 0.50097182 0.27551020 0.1627793975 [14,] 0.000000e+00 7.592323e-03 0.22461127 0.35204082 0.4157555879 [15,] 0.000000e+00 0.000000e+00 -0.14285714 0.42857143 0.7142857143 attr(,"degree") [1] 3 attr(,"knots")
20% 40% 60% 80%
60.8 63.6 66.4 69.2 attr(,"Boundary.knots") [1] 58 72 attr(,"intercept") [1] FALSE attr(,"class") [1] "ns" "basis" "matrix"
ns> summary(fm1 <- lm(weight ~ ns(height, df = 5), data = women))
Call: lm(formula = weight ~ ns(height, df = 5), data = women)
Residuals:
Min 1Q Median 3Q Max
-0.38333 -0.12585 0.07083 0.15401 0.30426
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 114.7447 0.2338 490.88 < 2e-16 *** ns(height, df = 5)1 15.9474 0.3699 43.12 9.69e-12 *** ns(height, df = 5)2 25.1695 0.4323 58.23 6.55e-13 *** ns(height, df = 5)3 33.2582 0.3541 93.93 8.91e-15 *** ns(height, df = 5)4 50.7894 0.6062 83.78 2.49e-14 *** ns(height, df = 5)5 45.0363 0.2784 161.75 < 2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.2645 on 9 degrees of freedom Multiple R-squared: 0.9998, Adjusted R-squared: 0.9997 F-statistic: 9609 on 5 and 9 DF, p-value: < 2.2e-16
ns> ## example of safe prediction
ns> plot(women, xlab = "Height (in)", ylab = "Weight (lb)")
ns> ht <- seq(57, 73, length.out = 200)
ns> lines(ht, predict(fm1, data.frame(height=ht)))
ns> ## Don't show: ns> ## Consistency: ns> x <- c(1:3,5:6)
ns> stopifnot(identical(ns(x), ns(x, df = 1)), ns+ identical(ns(x, df=2), ns(x, df=2, knots=NULL)),# not true till 2.15.2 ns+ !is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1 ns+ length(kk) == 0)
ns> ## End Don't show ns> ns> ns>
Note that if I follow the instruction to put embed.c at the end of g++ command, I will get an error.
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ -I/home/mli/Downloads/R-2.15.2/include -L/home/mli/Downloads/R-2.15.2/lib -lR embed.c /tmp/cc7Vum5j.o: In function `main': embed.c:(.text+0x1c): undefined reference to `Rf_initEmbeddedR' embed.c:(.text+0x2b): undefined reference to `Rf_endEmbeddedR' /tmp/cc7Vum5j.o: In function `doSplinesExample()': embed.c:(.text+0x45): undefined reference to `Rf_mkString' embed.c:(.text+0x52): undefined reference to `Rf_install' embed.c:(.text+0x5d): undefined reference to `Rf_lang2' embed.c:(.text+0x6d): undefined reference to `Rf_protect' embed.c:(.text+0x74): undefined reference to `R_GlobalEnv' embed.c:(.text+0x87): undefined reference to `R_tryEval' embed.c:(.text+0x91): undefined reference to `Rf_unprotect' embed.c:(.text+0x9b): undefined reference to `Rf_ScalarLogical' embed.c:(.text+0xa8): undefined reference to `Rf_install' embed.c:(.text+0xb3): undefined reference to `Rf_lang2' embed.c:(.text+0xc3): undefined reference to `Rf_protect' embed.c:(.text+0xcd): undefined reference to `Rf_install' embed.c:(.text+0xdc): undefined reference to `CDR' embed.c:(.text+0xe7): undefined reference to `SET_TAG' embed.c:(.text+0xee): undefined reference to `R_GlobalEnv' embed.c:(.text+0x102): undefined reference to `R_tryEval' embed.c:(.text+0x10c): undefined reference to `Rf_unprotect' embed.c:(.text+0x116): undefined reference to `Rf_mkString' embed.c:(.text+0x123): undefined reference to `Rf_install' embed.c:(.text+0x12e): undefined reference to `Rf_lang2' embed.c:(.text+0x13e): undefined reference to `Rf_protect' embed.c:(.text+0x145): undefined reference to `R_GlobalEnv' embed.c:(.text+0x158): undefined reference to `R_tryEval' embed.c:(.text+0x162): undefined reference to `Rf_unprotect' collect2: ld returned 1 exit status