Question: [Resolved] RcppArmadillo pckg ERRORS : non-zero exit status (and so DESeq2 also)
0
gravatar for RS1
5 weeks ago by
RS10
RS10 wrote:

I am facing problems to install the DESeq2 package on my linux laptop. I have read many posts and tried the different tips across, but none have worked so far.

Here are the DESEq2 installation errors:

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("DESeq2", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'DESeq2'
also installing the dependency ‘RcppArmadillo’

essai de l'URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.9.200.7.0.tar.gz'
Content type 'application/x-gzip' length 1333647 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

essai de l'URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/DESeq2_1.22.2.tar.gz'
Content type 'application/x-gzip' length 2062838 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ correctement décompressé et sommes MD5 vérifiées
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... yes, with OpenMP as version 5.4.0
checking for macOS... checking LAPACK_LIBS... system LAPACK found
checking for OpenMP... found and suitable
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/me/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include"   -I../inst/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/me/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include"   -I../inst/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/me/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include"   -I../inst/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld : ne peut trouver -llapack
/usr/bin/ld : ne peut trouver -lblas
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6 : la recette pour la cible « RcppArmadillo.so » a échouée
make: *** [RcppArmadillo.so] Erreur 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/home/me/R/x86_64-pc-linux-gnu-library/3.5/RcppArmadillo’
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’
* removing ‘/home/me/R/x86_64-pc-linux-gnu-library/3.5/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmpPTfc02/downloaded_packages’
installation path not writeable, unable to update packages: evaluate
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘RcppArmadillo’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

Here are the essential info of my configuration:

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8    LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.2     tools_3.5.2        yaml_2.2.0

Few installations already done and tested but none solved the problem (I got the same errors after trying to reinstall DESeq2):

me@xmglaptop:~$ sudo apt-get install libcurl4-openssl-dev libxml2-dev
me@xmglaptop:~$  sudo apt install gfortran
me@xmglaptop:~$ curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
me@xmglaptop:~$ sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /

me@xmglaptop:~$ g++ --version
g++ (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609
Copyright (C) 2015 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.

me@xmglaptop:~$ gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609
Copyright (C) 2015 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.

me@xmglaptop:~$ gfortran --version
GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING


Few related posts without found solution in my case: https://support.bioconductor.org/p/90994/ https://stackoverflow.com/questions/421 … -not-found https://github.com/sagemath/cloud/issues/114 https://stackoverflow.com/questions/206 … -and-rcurl https://support.bioconductor.org/p/100517/ https://support.bioconductor.org/p/54381/ https://support.bioconductor.org/p/76093/ http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#FAQ

If you have any solution, tips, idea, suggestion, whatever, I would be very grateful, I really need to use urgently the package. Many thanks in advance for your help. Best regards.

deseq2 linux R rcpparmadillo • 85 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by RS10
Answer: C: Error in DESeq2 installation with linux env.: non zero exit status (and RcppArma
0
gravatar for Mike Smith
5 weeks ago by
Mike Smith3.3k
EMBL Heidelberg / de.NBI
Mike Smith3.3k wrote:

The first thing to note is that this isn't a problem with DESeq2. The message ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’ tells you that the reason DESeq2 isn't being installed is because RcppArmadillo isn't available. So you really want to focus on sorting that out first, and hopefully installation of DESeq2 will just follow smoothly.

It looks like you have system level BLAS and LAPACK libraries installed, which are found during configuration, but then fail at the linking step - this is the ne peut trouver -llapack and ne peut trouver -lblas messagages. I would try installing the development versions of those system libraries. Do do that, open a Linux terminal and run:

sudo apt-get install libopenblas-dev

then restart R and try installing RcppArmadillo again.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Mike Smith3.3k
Answer: Error in DESeq2 installation with linux env.: non zero exit status (and RcppArma
0
gravatar for RS1
5 weeks ago by
RS10
RS10 wrote:

Thank you so much it has worked:

sudo apt-get install libopenblas-dev

And then the DESeq installation is processed correctly.

I still have warning issues but I can now load the DEseq2 package. I will then see if it works properly. I will try to install the requested additional packages, but for now I consider the problem as solved ! Many thanks.

For info:

> library("DESeq2")
Le chargement a nécessité le package : S4Vectors
Le chargement a nécessité le package : stats4
Le chargement a nécessité le package : BiocGenerics
Le chargement a nécessité le package : parallel

Attachement du package : ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated,
    eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min


Attachement du package : ‘S4Vectors’

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

    expand.grid

Le chargement a nécessité le package : IRanges
Le chargement a nécessité le package : GenomicRanges
Le chargement a nécessité le package : GenomeInfoDb
Le chargement a nécessité le package : SummarizedExperiment
Le chargement a nécessité le package : Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Le chargement a nécessité le package : DelayedArray
Le chargement a nécessité le package : matrixStats

Attachement du package : ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Le chargement a nécessité le package : BiocParallel

Attachement du package : ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by RS10
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