Error installing chromVAR, GO.db not installed

[timydaley]

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘GO.db’
ERROR: lazy loading failed for package ‘chromVAR’

[AliciaSchep]

What was the installation mechanism here that lead to this error? i.e. was this result from calling install_github?

[timydaley]

Yes. Do you have another way to install it?

[caleblareau]

If I recall correctly, GO.db is a nested dependency of one of the packages that chromVAR depends on. @timydaley does the following work?

source("https://bioconductor.org/biocLite.R")
biocLite("GO.db")
devtools::install_github("GreenleafLab/chromVAR")

[timydaley]

Yes. But I wanted y'all to be aware of the issue.

[AliciaSchep]

You can also install packages from Github using biocLite, e.g. BiocInstaller::biocLite("GreenleafLab/chromVAR"). This may do better at installing the BioC dependencies, but I'm not sure. Anyways I don't think this is really chromVAR problem, except for the documentation & what recommendation for installation is.

[timydaley]

That's good to know. I'll change my scripts to reflect this change. Thank you.

[ttriche]

if there are BioC dependencies or imports declared for a package on GitHub, biocLite("author/package") will indeed do a better job of chasing them down.

…

--t

On Tue, Aug 8, 2017 at 4:00 PM, Alicia Schep ***@***.***> wrote: You can also install packages from Github using biocLite, e.g. BiocInstaller::biocLite("GreenleafLab/chromVAR"). This may do better at installing the BioC dependencies, but I'm not sure. Anyways I don't think this is really chromVAR problem, except for the documentation & what recommendation for installation is. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAARIvSdpVCXlVbh4TuDL_abz_5K7B1_ks5sWOhvgaJpZM4OwGIb> .

[AliciaSchep]

Thanks @ttriche for confirmation (and @timydaley for bringing up the issue), I'll re-open this issue as a reminder to update docs to recommend biocLite installation instead of install_github.

[AliciaSchep]

readme updated to recommend biocLite

[Funshope]

Thanks alot! I have finally installed chromVAR on my computer.

[Funshope]

Is there a course organized or going to be organized on ATAC-Seq data analysis? My colleagues and I are really interested in attending.

[AliciaSchep]

@Funshope I would ask that question on the ATAC-seq forum. I think various places have hosted related courses, but don't know specifically.