Workflows in BioC 3.2
2
0
Entering edit mode
davide risso ▴ 890
@davide-risso-5075
Last seen 7 months 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 • 1.8k views
ADD COMMENT
2
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 15 months 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
0
Entering edit mode

Thanks Dan!

ADD REPLY
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode
@angelaoliveirapisco-8068
Last seen 6.4 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
1
Entering edit mode

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

Login before adding your answer.

Traffic: 169 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6