Question: Fail to install "AnnotationHub"
1
gravatar for Lian Liu
3.1 years ago by
Lian Liu20
Tokyo
Lian Liu20 wrote:

Dear all,

I am a new user of Bioconductor and I want to normalize and perform gene filtering of HTA 2.0 array.

I used oligo to perform RMA, my codes are:

> GSE1234cels = list.celfiles()
> GSE1234raw = read.celfiles(GSE1234cels) 
> GSE1234.eset = rma(GSE1234raw, target='core')
> GSE1234f <- nsFilter(GSE1234.eset)

And here is the error:

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘columns’ for signature ‘"AffyHTAPDInfo"’

Then I tried to install "affycoretools", and it reminded me to install "AnnotationHub" package. (Sorry, the error is in Chinese, so I don't show it here. But it means no package "AnnotationHub".)

But when I installed "AnnotationHub", I failed and the error was:

 > biocLite("AnnotationHub")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.23.9), R 3.3.1 (2016-06-21).
Installing package(s) ‘AnnotationHub’
Package which is only available in source form, and may need compilation of C/C++/Fortran:
  ‘AnnotationHub’
  These will not be installed
installation path not writeable, unable to update packages: foreign, lattice, Matrix, mgcv, survival
Old packages: 'affy', 'affyio', 'AnnotationDbi', 'Biobase', 'Biostrings', 'CLL', 'crossmeta',
  'DynDoc', 'gcrma', 'GEOquery', 'IRanges', 'MergeMaid', 'metaArray', 'multtest', 'oligoClasses',
  'preprocessCore', 'S4Vectors', 'stringi', 'tkWidgets', 'widgetTools', 'XVector', 'zlibbioc'

Update all/some/none? [a/s/n]:

I don't know what to do. Could anyone help me and give me some clues?

Thank you very much.

 

ADD COMMENTlink modified 3.1 years ago by Martin Morgan ♦♦ 24k • written 3.1 years ago by Lian Liu20
Answer: Fail to install "AnnotationHub"
1
gravatar for Martin Morgan
3.1 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

You are using the 'devel' version of AnnotationHub, and in devel AnnotationHub is currently only available as a 'source' tarball (see the nightly build report for details). A temporary solution is to install AnnotationHub from source, e.g.,

biocLite("AnnotationHub", type="source")

See the 'Binary packages' section of ?install.packages for additional detail.

ADD COMMENTlink written 3.1 years ago by Martin Morgan ♦♦ 24k

Thank you very much! Mr. Morgan. Your answer has been very helpful.

I installed "AnnotationHub" successfully with your code.

And may I ask you another question?

Yes, I installed development version of Bioconductor. But when I installed R again, I didn't see any difference between the two Rs on my PC. It lookes they are both development versions. They both have same packages installed. And at most times, I don't feel any inconvenience use either of them… Do you know how I can install another oridinary version of R?  And what's the main difference of their functions?

Thank you!

ADD REPLYlink written 3.1 years ago by Lian Liu20
1

You are actually using the 'release' version of R (3.3.1). Currently (until mid-October), the 'release' and 'devel' versions of Bioconductor both use the release version of R.

The version of Bioconductor in use is determined by the version of the BiocInstaller package you have installed. At some point, the version BiocInstaller installed with source("https://bioconductor.org/biocLite.R") was updated using a command like BiocInstaller::useDevel(). Normally, one would then need to update other packages to the devel version, as indicated by BiocInstaller::biocValid().

You could revert to the release version with BiocInstaller::useDevel(FALSE), then execute BiocInstaller::biocValid() and follow the advice (probably to re-install many packages).

We are nearly at the next release; personally, I would continue  to use devel until the next release, and then be sure to use the release version after that.

Packages in bioc 'devel' differ from those in release in two major ways. First, new features can be introduced into individual packages. There are many new features across all packages; individually these are often summarized in a package NEWS file and collectively at the time of each release. Second, new packages are introduced into the 'devel' branch, and only made available when the devel branch is made into the next release (approximately every April and October).

ADD REPLYlink written 3.1 years ago by Martin Morgan ♦♦ 24k

Thank you. Mr. Morgan.

Do you mean that I'm using 'release' version of R with 'devel' version of Bioconductor?

And after mid-October, I'd better use 'release' version of Bioconductor with code: BiocInstaller::useDevel(FALSE) and BiocInstaller::useDevel(FALSE)?

Thank you very much.

 

ADD REPLYlink written 3.1 years ago by Lian Liu20

I'm sorry, but the first error still exists and I have no idea what the cause is.

Could you please give me some suggestions?

Thank you.

ADD REPLYlink written 3.1 years ago by Lian Liu20
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