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Question: Can't get the lumi and methylumi packages to work.
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gravatar for gitteba
17 months ago by
gitteba0
gitteba0 wrote:

Hi

I hope you are able to help me with my problem, and sorry in advance if it is me who have done something wrong in R. It does not always come intuitive to me, working with R.

I have installed R on a new computer, and also needs the Bioconductor packages lumi and methylumi to get some scripts to work. I have installed the packages the way you say at this website. Installing lumina's works fine, however when installing methylumi I get several errors:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("methylumi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘methylumi’
also installing the dependencies ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘FDb.InfiniumMethylation.hg19’

trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/el-capitan/contrib/3.4/methylumi_2.22.0.tgz'
Content type 'application/x-gzip' length 6720081 bytes (6.4 MB)
==================================================
downloaded 6.4 MB


The downloaded binary packages are in
    /var/folders/jf/8lcnlvcx1ps967rq3dv79pxh5s2dkp/T//RtmpnTFLNw/downloaded_packages
installing the source packages ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘FDb.InfiniumMethylation.hg19’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz'
Content type 'application/x-gzip' length 18669702 bytes (17.8 MB)
==================================================
downloaded 17.8 MB

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz'
Content type 'application/x-gzip' length 38996322 bytes (37.2 MB)
==================================================
downloaded 37.2 MB

* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for ‘GenomicFeatures’ in dyn.load(file, DLLpath = DLLpath, ...):
 kan ikke indlæse delt objekt '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
  Reason: image not found
Error : package ‘GenomicFeatures’ could not be loaded
ERROR: lazy loading failed for package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/TxDb.Hsapiens.UCSC.hg19.knownGene’
ERROR: dependency ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ is not available for package ‘FDb.InfiniumMethylation.hg19’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/FDb.InfiniumMethylation.hg19’

The downloaded source packages are in
    ‘/private/var/folders/jf/8lcnlvcx1ps967rq3dv79pxh5s2dkp/T/RtmpnTFLNw/downloaded_packages’
Advarselsbeskeder: (Warnings)
1: I install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
2: I install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘FDb.InfiniumMethylation.hg19’ had non-zero exit status

When trying to run my script which needs lumi and methylumi I get these errors:

Indlæser krævet pakke: lumi (Loading required package: lumi)
Error: package or namespace load failed for ‘lumi’ in dyn.load(file, DLLpath = DLLpath, ...):
 kan ikke indlæse delt objekt (Can't load this object) '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
  Reason: image not found
> require(methylumi)
Indlæser krævet pakke: methylumi (Loading required package: methylumi)
Failed with error:  ‘pakke ‘FDb.InfiniumMethylation.hg19’ krævet af ‘methylumi’ kunne ikke findes’ (Package "FDb.InfiniumMethylation.hg19" required by "methylumi" could not be found)

 

 

I have tried downloading tracklayer.so as you have described in the post "Question: "minfi" loading problem because of couldn't "bumphunter" load". But this does not help.

I have used the bioconductor packages on my old computer many times, and have just checked them now. And they work perfectly.

Do you have any idea why I can't get the two packages to work on my new computer and how to get around this problem?

Thank you in advance!

Kind regards

Gitte B. Andersen

ADD COMMENTlink written 17 months ago by gitteba0
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