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Question: DESeq2 installation error
0
gravatar for seeker
2.2 years ago by
seeker0
Netherlands
seeker0 wrote:

Hi,

I m having error in installing DESeq2 on my mac.

 library(DESeq2)
Error: package ‘RcppArmadillo’ required by ‘DESeq2’ could not be found

 

sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rcpp_0.11.6          GenomicRanges_1.20.5 GenomeInfoDb_1.4.2   IRanges_2.2.7       
[5] S4Vectors_0.6.3      BiocGenerics_0.14.0  BiocInstaller_1.18.4

loaded via a namespace (and not attached):
[1] XVector_0.8.0 tools_3.2.0  

ADD COMMENTlink modified 10 days ago by Cheng-Yuan Kao80 • written 2.2 years ago by seeker0
2
gravatar for andrew.j.skelton73
2.2 years ago by
United Kingdom
andrew.j.skelton73290 wrote:

Seems like your instance is able to access the bioconductor library, but can't access CRAN packages. Maybe try a different mirror?

chooseCRANmirror()​
ADD COMMENTlink written 2.2 years ago by andrew.j.skelton73290

HI Andrew,

I selected a different CRAN mirror. Now when im trying install, its showing this message. Do you want to install from sources the packages which need compilation? Should i choose yes or No?

The downloaded binary packages are in
    /var/folders/yf/ylf3ln2508x5_54hmg8m_01m0000gp/T//Rtmppp1FZf/downloaded_packages
Old packages: 'nlme', 'RcppArmadillo'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
                 binary      source needs_compilation
nlme            3.1-121     3.1-122              TRUE
RcppArmadillo 0.5.300.4 0.5.400.2.0              TRUE

Do you want to install from sources the packages which need compilation?

ADD REPLYlink written 2.2 years ago by seeker0

I'd compile from source if you can, if you can't it'll generally pull down pre-compiled binaries 

ADD REPLYlink written 2.2 years ago by andrew.j.skelton73290

HI,

Im not able to install. Yesterday my mac os updated, may be because of that the issue comes.

 

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo’

The downloaded source packages are in
    ‘/private/var/folders/yf/ylf3ln2508x5_54hmg8m_01m0000gp/T/Rtmppp1FZf/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘nlme’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘RcppArmadillo’ had non-zero exit status

 

 

ADD REPLYlink written 2.2 years ago by seeker0

Do you have Xcode installed?

ADD REPLYlink written 2.2 years ago by andrew.j.skelton73290

I really don't think this is a good suggestion for this user -- install the slightly older, binary version and do not try to compile from source.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Martin Morgan ♦♦ 20k

Hi Andrew,

Just now i installed Xcode and i tried .

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 

  there is no package called ‘xtable’
Error: package or namespace load failed for ‘DESeq2

 

 

 

ADD REPLYlink written 2.2 years ago by seeker0

You'd need to do install.packages("xtable") too. I do agree with Martin, that was probably slightly bad advice on my part, installing from binaries may have been easier, but Xcode should be able to handle the compilation now. 

ADD REPLYlink written 2.2 years ago by andrew.j.skelton73290

Now it worked. 

ADD REPLYlink written 2.2 years ago by seeker0

Compiling from source requires additional software. Also, since the system responsible for creating the binary is having trouble creating the binary from the most recent source, this implies there is some extra level of knowledge required to compile from source. if you're struggling with installation, then it is probably much easier to say 'no' you do not want to install from source, and to use the slightly older pre-compiled versions. 

Also, be sure to choose a 'main stream' CRAN mirror, e.g., '0-cloud'

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Martin Morgan ♦♦ 20k
1
gravatar for EagleEye
3 months ago by
EagleEye10
EagleEye10 wrote:

PROBLEM:

DESeq2 (R 3.4.0) had same problem while installation. 


ERROR:

configuration failed for package ‘RcppArmadillo’
dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’

 

SOLUTION:

Installing compiler g++ version 4.6 or greater solved the issue.

ADD COMMENTlink written 3 months ago by EagleEye10
0
gravatar for andrew.j.skelton73
2.2 years ago by
United Kingdom
andrew.j.skelton73290 wrote:
install.packages("RcppArmadillo")
ADD COMMENTlink written 2.2 years ago by andrew.j.skelton73290

i tried that,

> install.packages("RcppArmadillo")
Warning: unable to access index for repository http://cran.gis-lab.info/src/contrib
Warning: unable to access index for repository http://cran.gis-lab.info/bin/macosx/mavericks/contrib/3.2
Warning message:
package ‘RcppArmadillo’ is not available (for R version 3.2.0)

ADD REPLYlink written 2.2 years ago by seeker0

Just to be safe, update to the latest version of R - I've just ran the installation with no problems. 

ADD REPLYlink written 2.2 years ago by andrew.j.skelton73290

Hi andrew,

I updated the latest version of R (3.2.2) and tried it agian.

biocLite("DESeq2")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘DESeq2’
Warning: unable to access index for repository http://cran.gis-lab.info/src/contrib
Warning: dependency ‘RcppArmadillo’ is not available
Warning: unable to access index for repository http://cran.gis-lab.info/bin/macosx/mavericks/contrib/3.2
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/DESeq2_1.8.1.tgz'
Content type 'application/x-gzip' length 1417421 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

install.packages("RcppArmadillo")
Warning: unable to access index for repository http://cran.gis-lab.info/src/contrib
Warning: unable to access index for repository http://cran.gis-lab.info/bin/macosx/mavericks/contrib/3.2
Warning message:
package ‘RcppArmadillo’ is not available (for R version 3.2.2) 

ADD REPLYlink written 2.2 years ago by seeker0

Hi, I had a similar problem. Try to install libarmadillo-dev, and libarmadillo2 before installing the install.packages("RcppArmadillo")

ie. sudo apt-get install libarmadillo-dev; sudo apt-get install libarmadillo2

and then in R try install.packages("RcppArmadillo")

 

ADD REPLYlink written 2.1 years ago by pavlidisp0
0
gravatar for Cheng-Yuan Kao
10 days ago by
Taiwan
Cheng-Yuan Kao80 wrote:

Hi, 

I tried this (Bioconductor version 3.5 (BiocInstaller 1.26.1)).

> install.packages("RcppArmadillo") 

And I keep getting this error: 

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo’
Warning in install.packages :
  installation of package ‘RcppArmadillo’ had non-zero exit status

-------------------------------------------------------------------

It is a most updated MacOS with Xcode installed.

Any suggestions? Thanks.

 

ADD COMMENTlink written 10 days ago by Cheng-Yuan Kao80
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