There is no package called "samr"

[Goldstriker2]

Hello Mike,

it seems the package "samr" is no longer available on Cran. When installing samr i get:

Warning in install.packages :
package ‘samr’ is not available (for R version 3.4.0)

I first thought it was an issue with the Version of R so i tried older or newer versions, however none of them worked. I also tried to download the package from the Cran website. However, it has has been removed. The latest Version in the archive is "samr_2.0.tar.gz" so i downloaded this. When i tried to install it however, i get the the Error:

• installing source package 'samr' ...
  ** libs

*** arch - i386
Warnung: Ausführung von Kommando 'make -f "D:/Programs/R-3.4.0/etc/i386/Makeconf" -f "D:/Programs/R-3.4.0/share/make/winshlib.mk" SHLIB="samr.dll" SHLIB_LIBADD='$(FLIBS)' OBJECTS="rankcol.o"' ergab Status 127
ERROR: compilation failed for package 'samr'

• removing 'D:/Programs/R-3.4.0/library/samr'
  Warning in install.packages :
  running command '"D:/Programs/R-3.4.0/bin/x64/R" CMD INSTALL -l "D:\Programs\R-3.4.0\library" "C:/Users/Lukas/Downloads/samr_2.0.tar.gz"' had status 1
  Warning in install.packages :
  installation of package ‘C:/Users/Lukas/Downloads/samr_2.0.tar.gz’ had non-zero exit status

I hope you can help me as i am new to R and SAM

Best regards,
Lukas

[SamGG]

Hi,
If you have already installed the devtools package, just type the following command in order to install the samr package from github.

library(devtools)
install_github("cran/samr")

NB: samr depends on the impute package. impute (previously on CRAN) is available on Bioconductor. Install impute using the command below before installing samr.

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("impute")

HTH

> library(devtools)

Attaching package: ‘devtools’

The following object is masked from ‘package:recipes’:

    check

> install_github("cran/samr")
Downloading GitHub repo cran/samr@master
from URL https://api.github.com/repos/cran/samr/zipball/master
Installing samr
"C:/PROGRA~1/R/R-35~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL  \
  "C:/Users/sampgg/AppData/Local/Temp/RtmpURQAa1/devtools1410685a6781/cran-samr-4f4a4da"  \
  --library="C:/Users/sampgg/Documents/R/win-library/3.5" --install-tests 

* installing *source* package 'samr' ...
** libs
c:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rankcol.f -o rankcol.o
c:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o samr.dll tmp.def rankcol.o -lgfortran -lm -lquadmath -LC:/PROGRA~1/R/R-35~1.0/bin/x64 -lR
installing to C:/Users/sampgg/Documents/R/win-library/3.5/samr/libs/x64
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'samr'
    finding HTML links ... done
    SAM                                     html  
    SAMseq                                  html  
    samr                                    html  
    samr.assess.samplesize                  html  
    samr.assess.samplesize.plot             html  
    samr.compute.delta.table                html  
    samr.compute.siggenes.table             html  
    samr.estimate.depth                     html  
    samr.internal                           html  
    samr.missrate                           html  
    samr.norm.data                          html  
    samr.plot                               html  
    samr.pvalues.from.perms                 html  
    samr.tail.strength                      html  
** building package indices
** testing if installed package can be loaded
* DONE (samr)
In R CMD INSTALL

> library(samr)
Loading required package: impute
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following object is masked from ‘package:dplyr’:

    count

[Goldstriker2]

Thank you very much! Everything seems to be working nicely now