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

I try to install TCGAbiolinks but

> biocLite("TCGAbiolinks")
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 2.6 years ago by Martin Morgan ♦♦ 22k • written 2.6 years ago by yizhong2md0
gravatar for Martin Morgan
2.6 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

  ## should install BiocInstaller 1.20.1 / Bioconductor v. 3.2
  ## if not, troubleshoot.
  biocLite()    ## to update old packages
ADD COMMENTlink written 2.6 years ago by Martin Morgan ♦♦ 22k

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

> biocLite("TCGAbiolinks")
Using Bioconductor 3.3 (BiocInstaller 1.21.2), R Under development (unstable) (2015-12-28 r69816).
Installing package(s) ‘TCGAbiolinks’
trying URL ''
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
Old packages: 'genoset', 'git2r'
Update all/some/none? [a/s/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)

[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 2.6 years ago by Ou, Jianhong1.1k

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 2.6 years ago by Martin Morgan ♦♦ 22k
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