Closed onahman closed 4 years ago
RubD
commented
4 years ago Hi Ornit,
Can you let me know how you installed Giotto? Did you use docker or the native installation? The current version of Giotto is 0.3.6 . So I would advise you to first install the newest version. 0.1.0 is quite old and does not work anymore with the current dataset examples.
The examples on this site https://rubd.github.io/Giotto_site/ are currently also more up-to-date.
Ruben
onahman
commented
4 years ago Hi, Thank you very much for the fast reply! I used the naive installation. As is listed here:
Native InstallationGiotto consists of two modules: analyzer and viewer. The requirements of Giotto installation are:
library(remotes)# to install the latest stable version (advised) remotes::install_github("RubD/Giotto")# to install a specific release version (example) remotes::install_github("RubD/Giotto@v0.1.0")# install HMRF required by Giotto install.packages("devtools") library(devtools) install_bitbucket("qzhudfci/smfishhmrf-r", ref="default")
On Sun, Jul 19, 2020 at 7:49 PM Ruben Dries notifications@github.com wrote:
Hi Ornit,
Can you let me know how you installed Giotto? Did you use docker or the native installation? The current version of Giotto is 0.3.6 . So I would advise you to first install the newest version. 0.1.0 is quite old and does not work anymore with the current dataset examples.
Ruben
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/RubD/Giotto/issues/63#issuecomment-660674846, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG6BSDLCXGALEKWFI2Y3FCDR4MP2HANCNFSM4PBN53VQ .
RubD
commented
4 years ago You just have to run the first two lines:
That will install everything you need to run the R package.
If you run this at the end: remotes::install_github("RubD/Giotto@v0.1.0"), then that will install a specific version (0.1.0) of Giotto. And 0.1.0 is an old version.
For more up-to-date installation instructions and potential problems have a look here.
Hopefully this will fix everything. Ruben
onahman
commented
4 years ago I actually did what you suggested before I opened the issue. I will try to remove the package installation and re-install without that line. I believe it will solve it.
Thanks again! Ornit
On Sun, Jul 19, 2020 at 8:33 PM Ruben Dries notifications@github.com wrote:
You just have to run the first two lines:
- library(remotes)
- remotes::install_github("RubD/Giotto")
That will install everything you need to run the R package.
If you run this at the end: remotes::install_github("RubD/Giotto@v0.1.0"), then that will install a specific version (0.1.0) of Giotto. And 0.1.0 is an old version.
For more up-to-date installation instructions and potential problems have a look here https://rubd.github.io/Giotto_site/.
Hopefully this will fix everything. Ruben
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/RubD/Giotto/issues/63#issuecomment-660680562, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG6BSDL7VJILCZH6PONSZTLR4MU53ANCNFSM4PBN53VQ .
Hi, I am trying to work on the tutorial here: http://spatialgiotto.rc.fas.harvard.edu/giotto.visium.brain.html I was able to finish all the installation successfully, but very strangely, I am unable to run some of Giotto functions. for example: createGiottoInstructions, get10Xmatrix are not found. But other seem to be recognized like createGiottoObject. The functions I mentions that were not found, were also not listed here: Documentation for package ‘Giotto’ version 0.1.0. What makes me think you have might have made changes in the package without updating the tutorials. Right now I am unable to run the tutorial - your help in solving this problem would be appreciated.
Ornit