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yizhong2md
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@yizhong2md-9509
Last seen 9.2 years ago
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
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
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.