Question: DeSeq2 installation on ubuntu fails
0
gravatar for drumarsohail
11 months ago by
drumarsohail0 wrote:

Hi everyone

I have tried to install DeSeq2 in R using R studio as well as ubuntu terminal but both doesnt succeed.

On R studio I can not find Deseq2 among the packages list. Rather It says

Warning in install.packages :
  package ‘deseq2’ is not available (for R version 3.4.2) 

 

On ubuntu

I use commands

source("http://bioconductor.org/biocLite.R")

and

biocLite("DESeq2")

Below is a long error which I says that it failed to install all 14 dependencies so failed to install Deseq2. Please help.

 

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘DESeq2’
also installing the dependencies ‘GenomeInfoDb’, ‘XVector’, ‘DelayedArray’, ‘AnnotationDbi’, ‘annotate’, ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocGenerics’, ‘Biobase’, ‘genefilter’, ‘geneplotter’

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomeInfoDb_1.14.0.tar.gz'
Content type 'application/x-gzip' length 3402862 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/XVector_0.18.0.tar.gz'
Content type 'application/x-gzip' length 64711 bytes (63 KB)
==================================================
downloaded 63 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/DelayedArray_0.4.1.tar.gz'
Content type 'application/x-gzip' length 241117 bytes (235 KB)
==================================================
downloaded 235 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/AnnotationDbi_1.40.0.tar.gz'
Content type 'application/x-gzip' length 4336842 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/annotate_1.56.2.tar.gz'
Content type 'application/x-gzip' length 1866282 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz'
Content type 'application/x-gzip' length 432152 bytes (422 KB)
==================================================
downloaded 422 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz'
Content type 'application/x-gzip' length 485066 bytes (473 KB)
==================================================
downloaded 473 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomicRanges_1.30.3.tar.gz'
Content type 'application/x-gzip' length 1116094 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/SummarizedExperiment_1.8.1.tar.gz'
Content type 'application/x-gzip' length 1204201 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocGenerics_0.24.0.tar.gz'
Content type 'application/x-gzip' length 43393 bytes (42 KB)
==================================================
downloaded 42 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Biobase_2.38.0.tar.gz'
Content type 'application/x-gzip' length 1656734 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/genefilter_1.60.0.tar.gz'
Content type 'application/x-gzip' length 1432282 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/geneplotter_1.56.0.tar.gz'
Content type 'application/x-gzip' length 1428448 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/DESeq2_1.18.1.tar.gz'
Content type 'application/x-gzip' length 2139692 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE
Error in apply_hotfix73465(getGeneric("cbind")) :
  hotfix failed for generic function cbind()
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’
ERROR: dependency ‘BiocGenerics’ is not available for package ‘S4Vectors’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
ERROR: dependency ‘BiocGenerics’ is not available for package ‘Biobase’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/Biobase’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’ are not available for package ‘IRanges’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/GenomeInfoDb’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/XVector’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’ are not available for package ‘DelayedArray’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/DelayedArray’
ERROR: dependencies ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’
ERROR: dependencies ‘AnnotationDbi’, ‘Biobase’, ‘BiocGenerics’ are not available for package ‘annotate’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/annotate’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘XVector’ are not available for package ‘GenomicRanges’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/GenomicRanges’
ERROR: dependencies ‘GenomicRanges’, ‘Biobase’, ‘DelayedArray’, ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/SummarizedExperiment’
ERROR: dependencies ‘S4Vectors’, ‘AnnotationDbi’, ‘annotate’, ‘Biobase’ are not available for package ‘genefilter’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/genefilter’
ERROR: dependencies ‘Biobase’, ‘BiocGenerics’, ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/geneplotter’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocGenerics’, ‘Biobase’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/musohail/R/x86_64-pc-linux-gnu-library/3.4/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmptBbVmU/downloaded_packages’
installation path not writeable, unable to update packages: XML, cluster,
  foreign, MASS, Matrix, mgcv, nlme, rpart, survival
Old packages: 'pillar'
Update all/some/none? [a/s/n]: a
also installing the dependency ‘fansi’

trying URL 'https://cran.rstudio.com/src/contrib/fansi_0.2.3.tar.gz'
Content type 'application/x-gzip' length 183361 bytes (179 KB)
==================================================
downloaded 179 KB

trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.3.0.tar.gz'
Content type 'application/x-gzip' length 103104 bytes (100 KB)
==================================================
downloaded 100 KB

* installing *source* package ‘fansi’ ...
** package ‘fansi’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c assumptions.c -o assumptions.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c has.c -o has.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nchar.c -o nchar.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read.c -o read.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rnchar.c -o rnchar.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c state.c -o state.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strip.c -o strip.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strsplit.c -o strsplit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tabs.c -o tabs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tohtml.c -o tohtml.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unhandled.c -o unhandled.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unique.c -o unique.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utf8.c -o utf8.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-1q72bO/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wrap.c -o wrap.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fansi.so assumptions.o has.o init.o nchar.o read.o rnchar.o state.o strip.o strsplit.o tabs.o tohtml.o unhandled.o unique.o utf8.o utils.o wrap.o -L/usr/lib/R/lib -lR
installing to /home/musohail/R/x86_64-pc-linux-gnu-library/3.4/fansi/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fansi)
* installing *source* package ‘pillar’ ...
** package ‘pillar’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (pillar)

The downloaded source packages are in
    ‘/tmp/RtmptBbVmU/downloaded_packages’
There were 14 warnings (use warnings() to see them)

ADD COMMENTlink modified 11 months ago by Michael Love24k • written 11 months ago by drumarsohail0
Answer: DeSeq2 installation on ubuntu fails
0
gravatar for Michael Love
11 months ago by
Michael Love24k
United States
Michael Love24k wrote:
It looks like BiocGenerics is the source of the installation troubles here. Can you try installing this with the latest version of R?
ADD COMMENTlink written 11 months ago by Michael Love24k
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