I need to install development version of bioconductor package - ggbio.
@lawremi suggested to install development version (1.23.1) to resolve X-axis zoom issues here.
From the installation manuals, it says, I need to install r-devel. Then biocLite() will install development version automatically. I tried, installation failed. I am on Windows.
Let me know if you need more details.
Edit 1:
Attempt to install using R-devel version for Windows:
> source("https://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help Bioconductor does not yet support R version 3.4.0 > biocLite("ggbio") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R Under development (unstable) (2016-10-18 r71535). Installing package(s) ‘ggbio’ also installing the dependencies ‘XVector’, ‘zlibbioc’, ‘biomaRt’, ‘graph’, ‘RBGL’, ‘AnnotationHub’, ‘biovizBase’, ‘Biobase’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Biostrings’, ‘Rsamtools’, ‘GenomicAlignments’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’, ‘AnnotationDbi’ Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4: cannot open URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/annotation/bin/windows/contrib/3.4: cannot open URL 'https://bioconductor.org/packages/3.4/data/annotation/bin/windows/contrib/3.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4: cannot open URL 'https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4: cannot open URL 'https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4/PACKAGES' Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘XVector’ ‘zlibbioc’ ‘graph’ ‘RBGL’ ‘AnnotationHub’ ‘biovizBase’ ‘Biobase’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’ ‘GenomicAlignments’ ‘VariantAnnotation’ ‘rtracklayer’ These will not be installed installing the source packages ‘biomaRt’, ‘GenomeInfoDb’, ‘SummarizedExperiment’, ‘BSgenome’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’, ‘AnnotationDbi’, ‘ggbio’ trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/biomaRt_2.30.0.tar.gz' Content type 'application/x-gzip' length 75971 bytes (74 KB) downloaded 74 KB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GenomeInfoDb_1.10.0.tar.gz' Content type 'application/x-gzip' length 14545873 bytes (13.9 MB) downloaded 13.9 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/SummarizedExperiment_1.4.0.tar.gz' Content type 'application/x-gzip' length 978079 bytes (955 KB) downloaded 955 KB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BSgenome_1.42.0.tar.gz' Content type 'application/x-gzip' length 6057978 bytes (5.8 MB) downloaded 5.8 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GenomicFeatures_1.26.0.tar.gz' Content type 'application/x-gzip' length 831031 bytes (811 KB) downloaded 811 KB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/OrganismDbi_1.16.0.tar.gz' Content type 'application/x-gzip' length 194540 bytes (189 KB) downloaded 189 KB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/ensembldb_1.6.0.tar.gz' Content type 'application/x-gzip' length 1744721 bytes (1.7 MB) downloaded 1.7 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/AnnotationDbi_1.36.0.tar.gz' Content type 'application/x-gzip' length 4273002 bytes (4.1 MB) downloaded 4.1 MB trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/ggbio_1.22.0.tar.gz' Content type 'application/x-gzip' length 1519369 bytes (1.4 MB) downloaded 1.4 MB ERROR: dependencies 'S4Vectors', 'IRanges' are not available for package 'GenomeInfoDb' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/GenomeInfoDb' ERROR: dependencies 'Biobase', 'IRanges', 'S4Vectors' are not available for package 'AnnotationDbi' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/AnnotationDbi' ERROR: dependency 'AnnotationDbi' is not available for package 'biomaRt' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/biomaRt' ERROR: dependencies 'GenomicRanges', 'Biobase', 'S4Vectors', 'IRanges', 'GenomeInfoDb' are not available for package 'SummarizedExperiment' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/SummarizedExperiment' ERROR: dependencies 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'Biostrings', 'rtracklayer', 'XVector', 'Rsamtools' are not available for package 'BSgenome' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/BSgenome' ERROR: dependencies 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'AnnotationDbi', 'XVector', 'Biostrings', 'rtracklayer', 'biomaRt', 'Biobase' are not available for package 'GenomicFeatures' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/GenomicFeatures' ERROR: dependencies 'AnnotationDbi', 'GenomicFeatures', 'Biobase', 'GenomicRanges', 'graph', 'IRanges', 'RBGL', 'S4Vectors' are not available for package 'OrganismDbi' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/OrganismDbi' ERROR: dependencies 'GenomicRanges', 'GenomicFeatures', 'Biobase', 'GenomeInfoDb', 'AnnotationDbi', 'rtracklayer', 'S4Vectors', 'AnnotationHub', 'Rsamtools', 'IRanges' are not available for package 'ensembldb' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/ensembldb' ERROR: dependencies 'biovizBase', 'Biobase', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools', 'GenomicAlignments', 'BSgenome', 'VariantAnnotation', 'rtracklayer', 'GenomicFeatures', 'OrganismDbi', 'ensembldb', 'AnnotationDbi' are not available for package 'ggbio' * removing 'C:/Users/tdadaev/Documents/R/win-library/3.4/ggbio' The downloaded source packages are in ‘C:\Users\tdadaev\AppData\Local\Temp\RtmpOU5gy0\downloaded_packages’ There were 18 warnings (use warnings() to see them) > sessionInfo() R Under development (unstable) (2016-10-18 r71535) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.24.0 loaded via a namespace (and not attached): [1] tools_3.4.0 > library(ggbio) Error in library(ggbio) : there is no package called ‘ggbio’
Edit 2:
Also found this repo, I think this the one where Michael Lawrence fixed the issue. How do I install this version?
provide enough detail, e.g., copy and paste (no need for a screen shot) of your attempt at
so that at least a few problems can be ruled out. Please edit your post rather than adding a comment or 'answer'.
See edits, thank you.
You're going to need to call
useDevel(TRUE)
to get the development version. That doesn't explain the above errors though.I am on R.3.3.1, re-installed "BiocInstaller", then tried "useDevel(TRUE)", but it is saying I need "more recent R". Then tried latest R for Windows (R Under development (unstable) (2016-10-18 r71535)), and tried to re-install "BiocInstaller", but it failed. Could you tell with which R version the "ggbio_1.23.1" version would work? Maybe, I am asking about your current R set up :)
By the way below gives '404 Not Found' error:
source("http://www.tengfei.name/projects/ggbio/utils/installer.R")
I guess you found that in that old README.md file, which I've now removed.