Question: package ‘BSgenome.Hsapiens.UCSC.hg38’ is not available (for R version 3.1.2)
0
gravatar for kylvalda
4.3 years ago by
kylvalda0
United States
kylvalda0 wrote:

Hi,

 

trying to install package ‘BSgenome.Hsapiens.UCSC.hg38’ on R version 3.1.2.:

either

biocLite('BSgenome.Hsapiens.UCSC.hg38')


or

biocLite('BSgenome.Hsapiens.UCSC.hg38', dep=T, INSTALL_opts=c('--no-lock'))


creates 23 warnings:

There were 23 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: package ‘BSgenome.Hsapiens.UCSC.hg38’ is not available (for R version 3.1.2)
2: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘base64enc’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘checkmate’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘cluster’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘colorspace’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘digest’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘foreign’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘lattice’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘limma’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘MASS’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘nnet’ had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘RCurl’ had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘rpart’ had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘survival’ had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘XML’ had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘BBmisc’ had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘edgeR’ had non-zero exit status
18: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘GenomicRanges’ had non-zero exit status
19: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘plyr’ had non-zero exit status
20: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Rsamtools’ had non-zero exit status
21: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘scales’ had non-zero exit status
22: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘GenomicAlignments’ had non-zero exit status
23: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Hmisc’ had non-zero exit status


is this package truly not available for R 3.1.2 or is there something else going on?

 

bsgenome r version 3.1.2 hg38 • 1.1k views
ADD COMMENTlink modified 4.3 years ago by James W. MacDonald52k • written 4.3 years ago by kylvalda0
Answer: package ‘BSgenome.Hsapiens.UCSC.hg38’ is not available (for R version 3.1.2)
1
gravatar for James W. MacDonald
4.3 years ago by
United States
James W. MacDonald52k wrote:

Yes it is truly not available. You should upgrade to R-3.2.1 anyway, in which case it will be available.

ADD COMMENTlink written 4.3 years ago by James W. MacDonald52k
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