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Question: Error with DESeq2 installation
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gravatar for chitsazanalex
8 weeks ago by
chitsazanalex0 wrote:

Im getting the error when trying to install DESeq. I'm installing this on a university cluster interactive node.

 

> biocLite("DESeq2")                                                                             

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).

Installing package(s) ‘DESeq2’

Warning: dependency ‘RcppArmadillo’ is not available

--2017-02-28 13:25:27--  https://bioconductor.org/packages/3.4/bioc/src/contrib/DESeq2_1.14.1.tar.gz

Resolving bioconductor.org... 52.84.24.166, 52.84.24.137, 52.84.24.129, ...

Connecting to bioconductor.org|52.84.24.166|:443... connected.

HTTP request sent, awaiting response... 200 OK

Length: 1406022 (1.3M) [application/x-gzip]

Saving to: “/tmp/RtmpDgcIaT/downloaded_packages/DESeq2_1.14.1.tar.gz”


100%[=========================================================================================================================================>] 1,406,022   --.-K/s   in 0.1s    


2017-02-28 13:25:28 (10.6 MB/s) - “/tmp/RtmpDgcIaT/downloaded_packages/DESeq2_1.14.1.tar.gz” saved [1406022/1406022]


ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’

* removing ‘/gscratch/hpc/achits/rpackages/DESeq2’


The downloaded source packages are in

    ‘/tmp/RtmpDgcIaT/downloaded_packages’

Warning message:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘DESeq2’ had non-zero exit status

> sessionInfo()

R version 3.3.2 (2016-10-31)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS release 6.8 (Final)


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=en_US.UTF-8       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     


other attached packages:

[1] BiocInstaller_1.24.0 Rcpp_0.12.9         


loaded via a namespace (and not attached):

[1] tools_3.3.2

> 

 

Further when trying to install RccpArmadillo, I'm getting the error:

> install.packages('RcppArmadillo', dependencies = TRUE, repos="http://ftp.osuosl.org/pub/cran/")

Installing package into ‘/gscratch/hpc/achits/rpackages’

(as ‘lib’ is unspecified)

--2017-02-28 13:29:07--  http://ftp.osuosl.org/pub/cran/src/contrib/RcppArmadillo_0.7.700.0.0.tar.gz

Resolving ftp.osuosl.org... 64.50.236.52, 64.50.233.100, 140.211.166.134, ...

Connecting to ftp.osuosl.org|64.50.236.52|:80... connected.

HTTP request sent, awaiting response... 200 OK

Length: 1075328 (1.0M) [application/x-gzip]

Saving to: “/tmp/RtmpDgcIaT/downloaded_packages/RcppArmadillo_0.7.700.0.0.tar.gz”


100%[=========================================================================================================================================>] 1,075,328   1.68M/s   in 0.6s    


2017-02-28 13:29:08 (1.68 MB/s) - “/tmp/RtmpDgcIaT/downloaded_packages/RcppArmadillo_0.7.700.0.0.tar.gz” saved [1075328/1075328]


* installing *source* package ‘RcppArmadillo’ ...

** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking how to run the C++ preprocessor... g++ -E

checking whether we are using the GNU C++ compiler... (cached) yes

checking whether g++ accepts -g... (cached) yes

checking whether g++ version is sufficient... no

configure: WARNING: Only g++ version 4.6 or greater can be used with RcppArmadillo.

configure: error: Please use a different compiler.

ERROR: configuration failed for package ‘RcppArmadillo’

* removing ‘/gscratch/hpc/achits/rpackages/RcppArmadillo’


The downloaded source packages are in

    ‘/tmp/RtmpDgcIaT/downloaded_packages’

Warning message:

In install.packages("RcppArmadillo", dependencies = TRUE, repos = "http://ftp.osuosl.org/pub/cran/") :

  installation of package ‘RcppArmadillo’ had non-zero exit status

 

Like I said, I'm doing this on a unviersity cluster so It would be weird to me if I it was in fact the compiler causing the problem. Thanks for your help!

 

Alex

ADD COMMENTlink modified 8 weeks ago by JunLVI40 • written 8 weeks ago by chitsazanalex0
0
gravatar for JunLVI
8 weeks ago by
JunLVI40
Japan
JunLVI40 wrote:

Hi, Alex. I had a similar issue when trying to install DiffBind. 

Basically, "RcppArmadillo" requires a newer version of gcc. 

I resolved the issue by installing a current version of gcc.

You could just check the version of gcc you are using by 

 gcc --version

 

You should see something like:


​ $ gcc --version

    gcc (GCC) 6.1.0

    Copyright (C) 2016 Free Software Foundation, Inc.

    This is free software; see the source for copying conditions.  There is NO

    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

also you could check which gcc using are using by

    $ which gcc
/$HOME/Programme/gcc-6.1.0/bin//gcc # if you installed a gcc in your own directory, this is what you would see. 

if you find the version of gcc is too old, either you could ask the administrator install a current one for the system, or you could install one in your own directory. 

For details, you could check my post on "stackoverflow" .

HTH,

Jun

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by JunLVI40
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