Question: Install ggbio development version
1
gravatar for zx8754
2.6 years ago by
zx875410
United Kingdom
zx875410 wrote:

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?

https://github.com/Bioconductor-mirror/ggbio

ADD COMMENTlink modified 2.6 years ago by Martin Morgan ♦♦ 23k • written 2.6 years ago by zx875410
1

provide enough detail, e.g., copy and paste (no need for a screen shot) of your attempt at

source("https://bioconductor.org/biocLite.R")
biocLite("ggbio")
sessionInfo()

so that at least a few problems can be ruled out. Please edit your post rather than adding a comment or 'answer'.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Martin Morgan ♦♦ 23k

See edits, thank you.

ADD REPLYlink written 2.6 years ago by zx875410
1

You're going to need to call useDevel(TRUE) to get the development version. That doesn't explain the above errors though.

ADD REPLYlink written 2.6 years ago by Michael Lawrence11k

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 :)

ADD REPLYlink written 2.6 years ago by zx875410

By the way below gives '404 Not Found' error:

source("http://www.tengfei.name/projects/ggbio/utils/installer.R")

ADD REPLYlink written 2.6 years ago by zx875410
1

I guess you found that in that old README.md file, which I've now removed.

ADD REPLYlink written 2.6 years ago by Michael Lawrence11k
Answer: Install ggbio development version
2
gravatar for Martin Morgan
2.6 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Your BiocInstaller is incorrect for the version of R you are using, probably because it was installed before the devel branch of Bioconductor started to use R-devel. Remove BiocInstaller and verify that it is removed. Then install it again

remove.packages("BiocInstaller")
remove.packages("BiocInstaller")  # fails -- no package named BiocInstaller
source("https://bioconductor.org/biocLite.R")

Look for Bioconductor version 3.5.

The rest of the errors are because of the  joys of living on the devel branch, where S4Vectors and its dependencies have not built successfully; see http://bioconductor.org/checkResults/3.5/bioc-LATEST/S4Vectors/malbec2-checksrc.html

The best strategy is to wait until S4Vectors does build successfully, perhaps overnight but there has not been a commit to address the problem, at least not in S4Vectors; it's up to the maintainers of the package to correct this problem.

ADD COMMENTlink written 2.6 years ago by Martin Morgan ♦♦ 23k

Did you manage to install devel version of ggbio? If yes, could you please share your system set up? R version, OS, any other relevant detail? Oh, re-reading your answer, Michael's changes didn't take place yet in "devel world", and need to wait a bit?

ADD REPLYlink written 2.6 years ago by zx875410
1

The short answer is no, S4Vectors is as unavailable to me as it is to you.

The long answer is yes, I installed S4Vectors and other packages from the SVN source tree. But this requires that you have the appropriate version of R compiler tools installed on your system (see here for Windows) as well as knowledge of our version control system -- unless you're keen, you're better waiting.

ADD REPLYlink written 2.6 years ago by Martin Morgan ♦♦ 23k
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