package not available for R version 3.1.2

[TrofimovAssya]

Hi!

I am trying to install genefu and it doesn't seem to work for the new version of R 3.2.2. I tried on another machine as well, with R running 3.1.2. I also tried installing from url: > install.packages(url="http://bioconductor.org/packages/genefu/", 'genefu') Warning in install.packages : package ‘genefu’ is not available (for R version 3.1.2)

Thanks in advance!

[bhaibeka]

can you try the following?

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

[TrofimovAssya]

Hi! It doesnt work!

source("https://bioconductor.org/biocLite.R") Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) : unsupported URL scheme

On Wed, Apr 19, 2017 at 11:22 AM, Benjamin Haibe-Kains < notifications@github.com> wrote:

can you try the following?

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

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bhklab/genefu/issues/10#issuecomment-295308328, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQn-kBCpvR02OyGPjt55ODPiCH46EWqks5rxiahgaJpZM4NB1oc .

[TrofimovAssya]

Update: For R 3.2.2, it doesn't support https, so the non-secure one worked:

source("http://bioconductor.org/biocLite.R")

However, when I do

biocLite("genefu") it gives me the following error for the lava package dependency.

Error: file ‘/var/folders/y0/f_41pv_13kj5j6nj_dh8w2h80000gp/T//RtmpByxAH0/downloaded_packages/lava_1.4.1.tgz’ is not an OS X binary package In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 32832 != reported length 1036121 2: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 24104 != reported length 282678 3: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 33724 != reported length 790087 4: 'tar' returned non-zero exit code 1

Can the package run without?

[bhaibeka]

We do not use lava, but it could be a dependency of one of our dependencies. Try to install it from source: https://cran.r-project.org/web/packages/lava/index.html

[TrofimovAssya]

Update: In order for everything to install and load, I have done the following steps:

• install lava from source
• install prodlim from source
• re-install Rcpp and update the file
• re-install genefu

The package loaded with warnings about dependency versions. Will close issue when I test the package.

Thanks for the support!