error nonzero exit
2
0
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@carolinegluck-8673
Last seen 7.1 years ago
United States

Hello,

I'm trying to install all of the packages needed to run Rnbeads (as described in the vignette). However, for two of them I get an error message saying that I have nonzero exit. I'm not sure how to trouble shoot. Below are the error messages:

> biocLite("IlluminaHumanMethylation450k.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘IlluminaHumanMethylation450k.db’
installing the source package ‘IlluminaHumanMethylation450k.db’

trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/IlluminaHumanMethylation450k.db_2.0.9.tar.gz'
Content type 'application/x-gzip' length 63268317 bytes (60.3 MB)
==================================================
downloaded 60.3 MB

* installing *source* package ‘IlluminaHumanMethylation450k.db’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details:
  call: NULL
  error: 'fun' is defunct.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Defunct")
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/gluckc/Library/R/3.2/library/IlluminaHumanMethylation450k.db’

The downloaded source packages are in
    ‘/private/var/folders/7d/0vtw_7nn29b7nqjjx3yg11brxm3gbj/T/Rtmpp3COYb/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IlluminaHumanMethylation450k.db’ had non-zero exit status

> biocLite("rtracklayer")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘rtracklayer’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/rtracklayer_1.28.8.tgz'
Content type 'text/html' length 7068 bytes
==================================================
downloaded 7068 bytes

tar: Unrecognized archive format
tar: Error exit delayed from previous errors.
Error: file ‘/var/folders/7d/0vtw_7nn29b7nqjjx3yg11brxm3gbj/T//Rtmpp3COYb/downloaded_packages/rtracklayer_1.28.8.tgz’ is not an OS X binary package
In addition: Warning message:
'tar' returned non-zero exit code 1 

 

Thanks!

Caroline

illuminahumanmethylation450k.db rnbeads • 1.8k views
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@martin-morgan-1513
Last seen 18 days ago
United States

The rtracklayer message seems transient; biocLite() is trying to install a version that is (recently) no longer available (see the bottom of the rtracklayer landing page for currently available versions). Try again, perhaps in a new R session.

The IlluminaHumanMethylation450k.db message must be stale instructions in the RnBeads vignette; the IlluminaHumanMethylation450k.db package is defunct, with instructions to use the FDb.* packages and mapToGenome() function instead. Hopefully the RnBeads maintainer will update the vignette.

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Entering edit mode
katwre • 0
@katwre-8264
Last seen 3.8 years ago
Germany

I have exactly the same error after typing:

biocLite("IlluminaHumanMethylation450k.db")

If it is not possible to install IlluminaHumanMethylation450k.db and use it and as you write it's defunct, why is it still on the BioC website? It is confusing

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