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`VGAM::gaussianff()` dependency requires VGAM version<1.0-6 #211

Open robertamezquita opened 6 years ago

robertamezquita commented 6 years ago

The newest version of VGAM (1.0-6) removes VGAM::gaussianff()and (possibly?) renames to VGAM::inv.gaussianff(). Thus, VGAM version 1.0-5 (or less) is required to install the monocle3-alpha release.

install_version("VGAM", version = "1.0-5", repos = "http://cran.us.r-project.org") installs the appropriate version of VGAM and resolves the monocle3-alpha installation error. Fix would specify in DESCRIPTION the required version of VGAM to be ==1.0-5.

wconnell commented 6 years ago

Was VGAM::gaussianff() employing an inverse Gaussian distribution? For use with Monocle2; thanks in advance statisticians.

vagnec commented 5 years ago

Hi, I did what you suggest : installing manually VGAM. Then I changed the DESCRIPTION file in monocle VGAM (>= 1.0-5) (and MD5 as well). I zipped the folder and I reinstalled it. install.packages("path/R/win-library/monocle2/monocle.zip", repos = NULL, type = "win.binary", lib= "path/R/win-library/monocle2")

Problem, I still have this problem: Error: package ‘VGAM’ 1.0.5 was found, but >= 1.0.6 is required by ‘monocle

Could you help me ? Thank you very much

dwucsf commented 5 years ago

Having the same problem. Had to downgrade VGAM to 1.0-5 but when trying to re-install monocle 3, getting the following error:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘VGAM’ 1.0-5 is being loaded, but >= 1.0.6 is required ERROR: lazy loading failed for package ‘monocle’

dwucsf commented 5 years ago

I think this could be a monocle 3 version issue. I'm currently using monocle 3 version 2.99.3, but perhaps VGAM1.0-5 works for earlier versions of monocle 3?

robertamezquita commented 5 years ago

Taking a quick look at the source, it does seem to be a Monocle 3 issue as the current monocle3_alpha branch has in its DESCRIPTION VGAM >= 1.0-6 in it still, and has not yet incorporated the gaussianff_local() function implemented in 0.99.6 (which has been pushed to Bioconductor (devel)). @wschen this bit of code might be nice to port to monocle3_alpha branch as it should resolve the VGAM dependency

dwucsf commented 5 years ago

This might be a dumb question, but where can I find and import version 2.99.1 or 2.99.2 into RStudio? I'm thinking using an older version of monocle 3 with VGAM 1.0.5 might work.

robertamezquita commented 5 years ago

@dwucsf The latest version of Monocle 2 from Bioconductor should just work as it has removed VGAM. You can install this via the BiocManager::install() function (see https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html)

If you want to use Monocle 3 alpha, then you will still need the specific version of VGAM that works with it as of this writing. To install a specific (older) version make sure first that you uninstall VGAM and reinstall the VGAM 1.0-5 version (see https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages for how to do this). Then proceed to install Monocle 3 alpha via devtools::install_github(..., ref = 'monocle3_alpha')

dwucsf commented 5 years ago

Thanks @robertamezquita for your help! Sorry for the delay in my reply. The current version of monocle 3 that is being installed with devtools::install_github(..., ref = 'monocle3_alpha') is 2.99.3. I believe this version is not compatible with VGAM 1.0-5, since I'm running into problems with trying to import monocle 3 with VGAM 1.0-5 installed. Can you confirm this is the case?