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Question

Error when loading DMRcate

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Bazingastats • 0

@966ac971

Last seen 22 months ago

United Kingdom

Hi all,

I am fairly new to bioconductor packages but have had some experience in R. My R version is 2022.07.2 so it is the latest.

When trying to load DMRcate library, I am getting the same error over and over again and I have tried to uninstall package and reinstall and it still gives me this error. I am not sure what to do and I was wondering if you all had any suggestions? FYI i am currently trying to follow the tutorial for methylation analysis from the paper " A cross-package Bioconductor workflow for analysing methylation array data"

Code should be placed in three backticks as shown below

library(minfi)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(IlluminaHumanMethylation450kmanifest)
library(RColorBrewer)
library(missMethyl)
library(matrixStats)
library(minfiData)
library(Gviz)
library(DMRcate)
library(stringr)

Error when I run this code:

Error: package or namespace load failed for 'DMRcate' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'httpuv'

I even tried to install httpuv but with no luck still.

Any suggestions of what to do?

DMRcate • 2.4k views

ADD COMMENT • link 22 months ago Bazingastats • 0

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Hi, adding the error you have when installing httpuv would be informative.

ADD REPLY • link 22 months ago Basti ▴ 780

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> install.packages("httpuv")

`There is a binary version available but the source version is later: binary source needs_compilation httpuv 1.6.8 1.6.9 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) library(DMRcate)

Error in install.packages : Unrecognized response "library(DMRcate)" `

ADD REPLY • link 22 months ago Bazingastats • 0

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What did happen after "Do you want to install from sources the package which needs compilation? (Yes/no/cancel)" ? Have you tried to input "Yes" ? I think you should

ADD REPLY • link 22 months ago Basti ▴ 780

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I cant actually tried inputting as before I can it just comes up with the last line "error in install.package : Unrecognized response "library(DMRcate)"

ADD REPLY • link 22 months ago Bazingastats • 0

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You need to run each line independently. Run install.packages("httpuv")alone and you will be able to run "Yes" for the compilation

ADD REPLY • link 22 months ago Basti ▴ 780

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I tried that too. It comes up with the error:

"Error: package or namespace load failed for 'DMRcate' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'httpuv'"

Even after I install httpuv and input Yes

ADD REPLY • link 22 months ago Bazingastats • 0

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This is very strange. I suggest you to close your R session, restart a new one and only run install.packages("httpuv"). I do not understand why DMRcate comes up here

ADD REPLY • link 22 months ago Basti ▴ 780

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really annoying. I've tried this just now and only ran that.

I then ran all the libraries and got the same error.

ADD REPLY • link 22 months ago Bazingastats • 0

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We need to know the message you have after running ONLY : install.packages("httpuv")

ADD REPLY • link 22 months ago Basti ▴ 780

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Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes

installing the source package ‘httpuv’

trying URL 'https://cran.rstudio.com/src/contrib/httpuv_1.6.9.tar.gz'

Content type 'application/x-gzip' length 1875081 bytes (1.8 MB)

downloaded 1.8 MB

installing source package ‘httpuv’ ... package ‘httpuv’ successfully unpacked and MD5 sums checked using staged installation ** libs xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ERROR: compilation failed for package ‘httpuv’
removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/httpuv’ Warning in install.packages : installation of package ‘httpuv’ had non-zero exit status

The downloaded source packages are in ‘/private/var/folders/j1/k4c93kqx0qq3f7ctvbqcngt80000gn/T/RtmpFRiGQA/downloaded_packages’

ADD REPLY • link 22 months ago Bazingastats • 0

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Thanks. Now we know that xcrun is missing and httpuv cannot be installed until this error is unsolved. Are you working on macOS ? If yes you can try the solutions proposed here to overcome this issue : https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a Notably opening a terminal and run xcode-select --install