Question

Issues installing DESeq2, installation path not writable, package: survival

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hall.brooke33 • 0

@hallbrooke33-23832

Last seen 3.8 years ago

Hello.. I am having trouble properly installing DESeq2. Currently have R version 4.0.2, trying to install with Bioconductor version 3.11. I tried troubleshooting with some info I found online with no luck. I have completely uninstalled R and reinstalled. I have tried commands for installing the package survival individually. The command library('DESeq2') results in an error message: Error in library("DESeq2"): there is no package called ‘DESeq2’. I would appreciate any help with this issue, preferably in non-technical terms when possible. I am unfamiliar with coding and this software. I'm attaching two screenshots of the issues I'm having. Thanks.

deseq2 survival • 5.3k views

ADD COMMENT • link updated 17 months ago by chanoul12 • 0 • written 3.8 years ago by hall.brooke33 • 0

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Are you using R Studio or just plain R? What happens when you enter:

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

BiocManager::install("DESeq2")

If this gives you an error about needing the "survival" package, start a new R session and then try install.packages("survival") and then try the DESeq2 install.

ADD REPLY • link 3.8 years ago max.ferretti • 0

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I am using just plain R. When I enter what you provided above, I get the message: Installation path not writeable, unable to update packages: survival. I tried starting the new session, install.packages("survival") and repeated the install procedure. Afterward, I still received the same message. I'm posting the full output below (after trying to install survival).

if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") BiocManager::install("DESeq2") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22) Installing package(s) 'DESeq2' trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/DESeq21.28.1.zip' Content type 'application/zip' length 2831527 bytes (2.7 MB) downloaded 2.7 MB package ‘DESeq2’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\brook\AppData\Local\Temp\Rtmp0weBM0\downloadedpackages Installation path not writeable, unable to update packages: survival Old packages: 'backports', 'rlang', 'tibble' Update all/some/none? [a/s/n]:

ADD REPLY • link 3.8 years ago hall.brooke33 • 0

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package ‘DESeq2’ successfully unpacked

I think you are all set

ADD REPLY • link 3.8 years ago Michael Love 41k

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Yes, I just realized that everything is working. Thanks for the help.

ADD REPLY • link 3.8 years ago hall.brooke33 • 0

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I have the same problem, but even if I install the survival packages, it still doesn't work. At the end of the Deseq2 installation, it's writen for all the packages that it had non-zero exit status... What does it mean? And do you know what other alternatives I can do? Thank you!

ADD REPLY • link 17 months ago chanoul12 • 0

score 0 · Answer 1 · 2020-07-09

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Michael Love 41k

@mikelove

Last seen 1 day ago

United States

You need to install DESeq2. See the install code on the DESeq2 landing page.

ADD COMMENT • link 3.8 years ago Michael Love 41k