How can I use bioconductor and Deseq2 in linux ubuntu 18
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Taufiq • 0
@Taufiq-24701
Last seen 3.8 years ago

I tried several time even using older version of R (3.5) to install bioconductor and deseq2 in my linux ubuntu 18 system but it is not working. I got the error like this-

``` 9: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status
RiboProfiling DESeq2 Bioconductor RNASeqRData • 2.4k views
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Kevin Blighe ★ 4.0k
@kevin
Last seen 23 days ago
Republic of Ireland

Which is your default R? - it should be 4.0.x. There should also be more text in the lines before the error message. Can you please post it, please? Also, please show the command that you used to try to install.
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I am using R version 4.0.3 (ubuntu 18) and I used the command from Bioconductor-

     if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
    BiocManager::install("DESeq2")

    The downloaded source packages are in
        ‘/tmp/RtmphiO50q/downloaded_packages’
    Warning messages:
    1: In install.packages(...) :
      installation of package ‘locfit’ had non-zero exit status
    2: In install.packages(...) :
      installation of package ‘RcppArmadillo’ had non-zero exit status
    3: In install.packages(...) :
      installation of package ‘DelayedArray’ had non-zero exit status
    4: In install.packages(...) :
      installation of package ‘SummarizedExperiment’ had non-zero exit status
    5: In install.packages(...) :
      installation of package ‘genefilter’ had non-zero exit status
    6: In install.packages(...) :
      installation of package ‘geneplotter’ had non-zero exit status
    7: In install.packages(...) :
      installation of package ‘DESeq2’ had non-zero exit status

After running the deseq2 I got the error message-

    > library( "DESeq2" )
    Error in library("DESeq2") : there is no package called ‘DESeq2’
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Tackle the first warning message. Include full output. Here is what I have:

> BiocManager::install("locfit")
Bioconductor version 3.12 (BiocManager 1.30.10.7), R 4.0.3 Patched (2020-10-13
  r79345)
Installing package(s) 'locfit'
trying URL 'https://cran.rstudio.com/src/contrib/locfit_1.5-9.4.tar.gz'
Content type 'application/x-gzip' length 200998 bytes (196 KB)
==================================================
downloaded 196 KB

* installing *source* package 'locfit' ...
** package 'locfit' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c S_enter.c -o S_enter.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c band.c -o band.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c dbinom.c -o dbinom.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c dens_haz.c -o dens_haz.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c dens_int.c -o dens_int.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c dens_odi.c -o dens_odi.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c density.c -o density.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c ev_atree.c -o ev_atree.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c ev_interp.c -o ev_interp.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c ev_kdtre.c -o ev_kdtre.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c ev_main.c -o ev_main.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c ev_sphere.c -o ev_sphere.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c ev_trian.c -o ev_trian.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c family.c -o family.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c fitted.c -o fitted.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c frend.c -o frend.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lf_adap.c -o lf_adap.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lf_dercor.c -o lf_dercor.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lf_fitfun.c -o lf_fitfun.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lf_nbhd.c -o lf_nbhd.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lf_robust.c -o lf_robust.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lf_vari.c -o lf_vari.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lf_wdiag.c -o lf_wdiag.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c lfstr.c -o lfstr.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c locfit.c -o locfit.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_chol.c -o m_chol.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_eigen.c -o m_eigen.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_icirc.c -o m_icirc.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_imont.c -o m_imont.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_isimp.c -o m_isimp.o
m_isimp.c:65:49: warning: too few arguments in call to 'simp3'
      simp3(fd,x,d,resd,delta,wt,i0,j,mg,ct,res2);
      ~~~~~                                     ^
1 warning generated.
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_isphr.c -o m_isphr.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_jacob.c -o m_jacob.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_max.c -o m_max.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_qr.c -o m_qr.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_solve.c -o m_solve.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_svd.c -o m_svd.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c m_vector.c -o m_vector.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c math.c -o math.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c minmax.c -o minmax.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c pcomp.c -o pcomp.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c preplot.c -o preplot.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c prob.c -o prob.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c procv.c -o procv.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c scb.c -o scb.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c scb_cons.c -o scb_cons.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c scb_crit.c -o scb_crit.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c scb_iface.c -o scb_iface.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c simul.c -o simul.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c smisc.c -o smisc.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c startlf.c -o startlf.o
gcc -I"/Users/ma38727/bin/R-4-0-branch/include" -DNDEBUG   -I/usr/local/include   -fPIC  -g -O0  -c weight.c -o weight.o
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/ma38727/bin/R-4-0-branch/lib -L/usr/local/lib -o locfit.so S_enter.o band.o dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o lf_wdiag.o lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o m_isphr.o m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o scb_iface.o simul.o smisc.o startlf.o weight.o -L/Users/ma38727/bin/R-4-0-branch/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Users/ma38727/Library/R/4.0/Bioc/3.12/library/00LOCK-locfit/00new/locfit/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (locfit)

The downloaded source packages are in
    '/private/var/folders/yn/gmsh_22s2c55v816r6d51fx1tnyl61/T/RtmpkHSgoV/downloaded_packages'
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Thanks Martin! It worked. I have done following commands as well.

sudo apt-get install libopenblas-dev

> install.packages("RcppArmadillo", repos="http://R-Forge.R-project.org")
Installing package into ‘/home/cw2/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'http://R-Forge.R-project.org/src/contrib/RcppArmadillo_0.3.920.3.tar.gz'
Content type 'application/x-gzip' length 817992 bytes (798 KB)
==================================================
downloaded 798 KB

* installing *source* package ‘RcppArmadillo’ ...
** using staged installation
** libs

> BiocManager::install("DESeq2")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'DESeq2'
also installing the dependency ‘RcppArmadillo’

trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.10.1.2.2.tar.gz'
Content type 'application/x-gzip' length 1647570 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/DESeq2_1.30.0.tar.gz'
Content type 'application/x-gzip' length 2066943 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
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if(! "pacman" %in% installed.packages()) install.packages("pacman")
pacman::p_load(char = packages)
pacman::p_load(DESeq2)
install.packages("DESeq2")
library("DESeq2")
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