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Question: package ‘TCGAbiolinks’ is not available (for R version 3.2.0)
0
gravatar for yizhong2md
2.8 years ago by
yizhong2md0
yizhong2md0 wrote:

I try to install TCGAbiolinks but

> biocLite("TCGAbiolinks")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0.
Installing package(s) 'TCGAbiolinks'
Warning message:
package ‘TCGAbiolinks’ is not available (for R version 3.2.0)

anyone can help me, many thanks

ADD COMMENTlink modified 2.8 years ago by Martin Morgan ♦♦ 22k • written 2.8 years ago by yizhong2md0
0
gravatar for Martin Morgan
2.8 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Your version of Bioconductor (and R) is too old. Install the latest R (version 3.2.3; it might not be necessary to update R) then in a new R session

  remove.packages("BiocInstaller")
  source("http://bioconductor.org/biocLite.R")
  ## should install BiocInstaller 1.20.1 / Bioconductor v. 3.2
  ## if not, troubleshoot.
  biocLite()    ## to update old packages
  biocLite("TCGAbiolinks")
ADD COMMENTlink written 2.8 years ago by Martin Morgan ♦♦ 22k

I also have trouble in install TCGAbiolinks, Here is the error:

> biocLite("TCGAbiolinks")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.2), R Under development (unstable) (2015-12-28 r69816).
Installing package(s) ‘TCGAbiolinks’
trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/TCGAbiolinks_1.1.15.tar.gz'
Content type 'application/x-gzip' length 18935234 bytes (18.1 MB)
==================================================
downloaded 18.1 MB

* installing *source* package ‘TCGAbiolinks’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : object ‘subsetByOverlaps’ is not exported by 'namespace:SummarizedExperiment'
ERROR: lazy loading failed for package ‘TCGAbiolinks’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/TCGAbiolinks’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/TCGAbiolinks’

The downloaded source packages are in
    ‘/private/var/folders/n4/11sc2xz13k56hl85z_h2rgq00000gn/T/RtmpwGkxW0/downloaded_packages’
Old packages: 'genoset', 'git2r'
Update all/some/none? [a/s/n]:
n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TCGAbiolinks’ had non-zero exit status
> packageVersion("SummarizedExperiment")
[1] ‘1.1.14’
> sessionInfo()
R Under development (unstable) (2015-12-28 r69816)
Platform: x86_64-apple-darwin12.5.0 (64-bit)
Running under: OS X 10.8.5 (Mountain Lion)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.21.2

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.1.14             genefilter_1.53.0                       circlize_0.3.4                         
 [4] shape_1.4.2                             GetoptLong_0.1.1                        splines_3.3.0                          
 [7] lattice_0.20-33                         colorspace_1.2-6                        EDASeq_2.5.1                           
[10] stats4_3.3.0                            rtracklayer_1.31.3                      GenomicFeatures_1.23.17                
[13] XML_3.98-1.3                            survival_2.38-3                         R.oo_1.19.0                            
[16] DBI_0.3.1                               R.utils_2.2.0                           BiocParallel_1.5.12                    
[19] BiocGenerics_0.17.2                     aroma.light_3.1.1                       RColorBrewer_1.1-2                     
[22] matrixStats_0.50.1                      plyr_1.8.3                              zlibbioc_1.17.0                        
[25] Biostrings_2.39.6                       sjmisc_1.4                              munsell_0.4.2                          
[28] gtable_0.1.2                            hwriter_1.3.2                           R.methodsS3_1.7.0                      
[31] GlobalOptions_0.0.8                     GGally_1.0.1                            latticeExtra_0.6-26                    
[34] Biobase_2.31.3                          ComplexHeatmap_1.9.1                    geneplotter_1.49.0                     
[37] IRanges_2.5.20                          biomaRt_2.27.2                          GenomeInfoDb_1.7.3                     
[40] parallel_3.3.0                          AnnotationDbi_1.33.6                    TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[43] Rcpp_0.12.3                             xtable_1.8-0                            scales_0.3.0                           
[46] S4Vectors_0.9.19                        CNTools_1.27.0                          annotate_1.49.0                        
[49] XVector_0.11.2                          ShortRead_1.29.1                        Rsamtools_1.23.1                       
[52] rjson_0.2.15                            ggplot2_2.0.0                           ConsensusClusterPlus_1.35.0            
[55] DESeq_1.23.1                            GenomicRanges_1.23.11                   grid_3.3.0                             
[58] bitops_1.0-6                            magrittr_1.5                            RCurl_1.95-4.7                         
[61] RSQLite_1.0.0                           cluster_2.0.3                           whisker_0.3-2                          
[64] dendextend_1.1.2                        MASS_7.3-45                             reshape_0.8.5                          
[67] GenomicAlignments_1.7.12               

 

ADD REPLYlink written 2.8 years ago by Ou, Jianhong1.1k
1

Your problem is on the other end of the specturm. You are using the development version of Bioconductor, which is less stable than the release version. As a developer, the best thing to do is to check the package build report, where you'll see that the package is failing to build. This is a problem for the package developer, who has checked in a change yesterday. The change will propagate when today's builds complete in a few hours. If the package builds successfully, you should be able to use biocLite() later today.

ADD REPLYlink written 2.8 years ago by Martin Morgan ♦♦ 22k
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