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

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.

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