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Question: Workflows in BioC 3.2
0
gravatar for davide risso
2.1 years ago by
davide risso490
Weill Cornell Medicine
davide risso490 wrote:

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?

ADD COMMENTlink modified 22 months ago by angela.oliveira.pisco0 • written 2.1 years ago by davide risso490
2
gravatar for Dan Tenenbaum
2.1 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

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 COMMENTlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k

Thanks Dan!

ADD REPLYlink written 2.1 years ago by davide risso490

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 REPLYlink written 2.0 years ago by Alejandro Reyes1.5k

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 REPLYlink written 2.0 years ago by Alejandro Reyes1.5k

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 REPLYlink written 2.0 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for angela.oliveira.pisco
22 months ago by
European Union
angela.oliveira.pisco0 wrote:

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 COMMENTlink written 22 months ago by angela.oliveira.pisco0
1

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 REPLYlink written 22 months ago by Aaron Lun17k
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