Question

ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'

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shenjun_renji • 0

@shenjun_renji-23314

Last seen 4.0 years ago

> eset=rma(Data)
installing the source package ‘hgu133plus2cdf’

试开URL’https://bioconductor.org/packages/3.10/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 4353300 bytes (4.2 MB)
downloaded 4.2 MB

ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'
* removing 'D:/我的文档/R/win-library/3.6/hgu133plus2cdf'

The downloaded source packages are in
    ‘C:\Users\Jiao\AppData\Local\Temp\RtmpE9p4tm\downloaded_packages’
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG-U133_Plus_2
Library - package hgu133plus2cdf not installed
Library - package hgu133plus2cdf not installed
此外: Warning message:
In install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu133plus2cdf’ had non-zero exit status

normalization • 1.1k views

ADD COMMENT • link updated 4.0 years ago by Gordon Smyth 50k • written 4.0 years ago by shenjun_renji • 0

Martin Morgan · Answer 1 · 2020-04-12

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Gordon Smyth 50k

@gordon-smyth

Last seen 3 hours ago

WEHI, Melbourne, Australia

The message is telling you that the AnnotationDbi package isn't available on your computer. So you need to install it.

One could argue that if rma() installs the cdf package automatically, without asking the user whether to do so, then it should also install the necessary dependencies, but that's a matter for the developers.

ADD COMMENT • link 4.0 years ago Gordon Smyth 50k

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Thank you. But I've installed the AnnotationDbi package, it still has an error . How can I solve this?

library(AnnotationDbi)
> eset=rma(Data)
installing the source package ‘hgu133plus2cdf’

试开URL’https://bioconductor.org/packages/3.10/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 4353300 bytes (4.2 MB)
downloaded 4.2 MB

ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'
* removing 'D:/我的文档/R/win-library/3.6/hgu133plus2cdf'

The downloaded source packages are in
    ‘C:\Users\Jiao\AppData\Local\Temp\Rtmp8utWl1\downloaded_packages’
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG-U133_Plus_2
Library - package hgu133plus2cdf not installed
Library - package hgu133plus2cdf not installed
此外: Warning message:
In install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu133plus2cdf’ had non-zero exit status

ADD REPLY • link updated 4.0 years ago by Martin Morgan 25k • written 4.0 years ago by shenjun_renji • 0

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Try simplifying. First confirm that

library(AnnotationDbi)

loads into your R session. Then try to install the cdf package using 'standard' procedures

BiocManager::install("hgu133plus2cdf")

I suspect that this fails. I suspect it is because of the non-ASCII characters in the file path D:/我的文档/ and that the solution is to use a path for your library that uses only ASCII characters.

I believe that the ASCII character issue has been addressed in R-4.0, which is due for release at the end of this month.

ADD REPLY • link 4.0 years ago Martin Morgan 25k