Question

package DESeq2 installation with R.

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layeb • 0

@layeb-15273

Last seen 6.8 years ago

Hi,

I would like to install the package DESeq2, however it doesnt look to work with the last version of R...

> install.packages("DESeq2")
Warning in install.packages :
package ‘DESeq2’ is not available (for R version 3.4.3)

What should I do ?

Many thanks,

Leila

deseq2 R package installation • 26k views

ADD COMMENT • link updated 3.6 years ago by Michael Love 43k • written 6.8 years ago by layeb • 0

score 0 · Answer 1 · 2018-03-16

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thokall ▴ 160

@thokall-14310

Last seen 10 weeks ago

Swedish Museum of Natural History

DESeq2 is part of bioconductor and can be Installed according to the instructions that you find here https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html

ADD COMMENT • link 6.8 years ago thokall ▴ 160

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

BiocManager::install("DESeq2")

I am using this command but still, an error is occurring ERROR: configuration failed for package ‘XML’

removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/XML’ ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/httr’ ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/GenomicRanges’ ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’ ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/SummarizedExperiment’ ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’ ERROR: dependencies ‘AnnotationDbi’, ‘XML’, ‘httr’ are not available for package ‘annotate’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/annotate’ ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/genefilter’ ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/geneplotter’ ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
removing ‘/home/dell/R/x86_64-pc-linux-gnu-library/4.1/DESeq2’

The downloaded source packages are in ‘/tmp/RtmpVSJdAc/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/lib/R/library packages: Matrix, mgcv There were 15 warnings (use warnings() to see them)

What should I do ?

many Thanks

ADD REPLY • link 3.6 years ago Nikha • 0

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See the FAQ about installing on Linux.

ADD REPLY • link 3.6 years ago Michael Love 43k

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Hello Sir,

as per your answer, I am using this command but still not installing my DESeq2 tool ( I am updating my PC too)

http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#i-have-trouble-installing-deseq2-on-ubuntulinux -- FAQ

sudo apt install libxml2-dev sudo apt install llibcurl4-openssl-dev

sessionInfo()

‘/tmp/RtmpTbMiir/downloaded_packages’ Warning messages: 1: In .inet_warning(msg) : installation of package ‘openssl’ had non-zero exit status 2: In .inet_warning(msg) : installation of package ‘httr’ had non-zero exit status 3: In .inet_warning(msg) : installation of package ‘KEGGREST’ had non-zero exit status 4: In .inet_warning(msg) : installation of package ‘AnnotationDbi’ had non-zero exit status 5: In .inet_warning(msg) : installation of package ‘annotate’ had non-zero exit status 6: In .inet_warning(msg) : installation of package ‘genefilter’ had non-zero exit status 7: In .inet_warning(msg) : installation of package ‘geneplotter’ had non-zero exit status 8: In .inet_warning(msg) : installation of package ‘DESeq2’ had non-zero exit status

library(DESeq2) Error in library(DESeq2) : there is no package called ‘DESeq2’

please help me to solve this error

Thanks in advance

ADD REPLY • link 3.6 years ago Nikha • 0

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Find the first error in the installation script and try to work out solving that one. It looks like it is openssl.

ADD REPLY • link 3.6 years ago Michael Love 43k