Question

Workflows in BioC 3.2

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davide risso ▴ 950

@davide-risso-5075

Last seen 6 weeks ago

University of Padova

Dear BioC community,

I'm trying to install the rnaseqGene workflow in R 3.2.2 with BioC 3.2 and I get the following error:

> source("http://bioconductor.org/workflows.R")
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
Error: BiocInstaller:::BIOC_VERSION == "3.1" is not TRUE

Now, looking inside http://bioconductor.org/workflows.R, I see this

source("http://bioconductor.org/biocLite.R")
# FIXME, don't hardcode version number
stopifnot(BiocInstaller:::BIOC_VERSION == "3.1")

workflowInstall <- function(pkg, ...)
{
    repos <- c(biocinstallRepos(), 
    "http://bioconductor.org/packages/3.1/workflows")
    install.packages(pkg, repos=repos, ...)
}

Copying and pasting the definition of workflowInstall() works in BioC 3.2, but only if using the same URL. If I try to substitute "http://bioconductor.org/packages/3.1/workflows" with "http://bioconductor.org/packages/3.2/workflows", it won't find the package.

Are workflows not available (yet) for BioC 3.2?

workflows installation biocinstaller • 2.5k views

ADD COMMENT • link updated 8.3 years ago by angela.oliveira.pisco • 0 • written 8.5 years ago by davide risso ▴ 950

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angela.oliveira.pisco • 0

@angelaoliveirapisco-8068

Last seen 8.3 years ago

European Union

hi, I'm new to R and I was trying to install the rnaseqGene workflow but it gives me the same error

Bioconductor version 3.1 (BiocInstaller 1.18.3), ?biocLite for help
Error: BiocInstaller:::BIOC_VERSION == "3.2" is not TRUE

do you have any updates? thanks, Angela

ADD COMMENT • link 8.3 years ago angela.oliveira.pisco • 0

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For starters, you should update your version of Bioconductor. The latest version is BioC 3.2, running on R 3.2.2 or higher. You should be able to update by following the instructions, though on occasion, it is necessary to run remove.packages(BiocInstaller) beforehand.

ADD REPLY • link 8.3 years ago Aaron Lun ★ 28k

score 2 · Accepted Answer · 2015-10-21

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 3.2 years ago

United States

They will be soon. The rnaseqGene workflow should be available now. I had upgraded the workflow builder to use BioC 3.2 but needed to trigger a rebuild of each workflow. I'm doing the remaining ones now.

ADD COMMENT • link 8.5 years ago Dan Tenenbaum ★ 8.2k

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Thanks Dan!

ADD REPLY • link 8.5 years ago davide risso ▴ 950

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Hi Dan,

I have been trying to install workflows since yesterday and keep getting an error below. The link seems to be broken. Or am I missing something obvious?


> source("http://bioconductor.org/workflows.R")
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
> 
> workflowInstall("rnaseqGene")
Warning in install.packages :
  package ‘rnaseqGene’ is not available (for R version 3.2.1)
curl: (22) The requested URL returned error: 404 Not Found
Warning in install.packages :
  download had nonzero exit status
Warning in install.packages :
  cannot open compressed file '/var/folders/9p/s1c19c1s1m572pywb2qpqnqw0000gn/T//Rtmp8JldTB/file1d61617f711e', probable reason 'No such file or directory'
curl: (22) The requested URL returned error: 404 Not Found
Warning in install.packages :
  download had nonzero exit status
Warning in install.packages :
  cannot open compressed file '/var/folders/9p/s1c19c1s1m572pywb2qpqnqw0000gn/T//Rtmp8JldTB/file1d61617f711e', probable reason 'No such file or directory'
Error in install.packages : cannot open the connection

> sessionInfo()

R version 3.2.1 (2015-06-18) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.1 (unknown)

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] stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocInstaller_1.20.0

loaded via a namespace (and not attached): [1] tools_3.2.1

ADD REPLY • link 8.5 years ago Alejandro Reyes ★ 1.9k

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An update from this issue. I think it only happens for the latest version of MAC OS 10.11.* (El Capitan). I guess the binaries are not available for this OS? I tried to install it from source but I did not manage:

repos <- c(biocinstallRepos(), "http://bioconductor.org/packages/3.2/workflows")

install.packages("rnaseqGene", repos=repos, type="source")

but the following works:

install.packages("ggplot2", repos=repos, type="source")

ADD REPLY • link 8.5 years ago Alejandro Reyes ★ 1.9k

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I just tried the same lines you did on Yosemite and it worked fine.

In fact I did not even need to specify type="source".

I did get a warning but it did not affect the success of the installation.

ADD REPLY • link 8.5 years ago Dan Tenenbaum ★ 8.2k