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nuno-agostinho / psichomics

Interactive R package to quantify, analyse and visualise alternative splicing
http://nuno-agostinho.github.io/psichomics/
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Install and start running #423

Closed RFTHK closed 3 years ago

RFTHK commented 3 years ago

Hi,

I'd like to use your psichomics visual interface, but can not install and start the program because of the following message. I am using Windows and RStudio version 4.1.0 (2021-05-18). What is the problem?

library(psichomics) Loading required package: shiny Loading required package: shinyBS Registered S3 method overwritten by 'quantmod': method from as.zoo.data.frame zoo Error: package or namespace load failed for ‘psichomics’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘org.Hs.eg.db’ psichomics() Error in psichomics() : could not find function "psichomics"

Ryo

nuno-agostinho commented 3 years ago

Hey Ryo, what version of psichomics do you have installed? You can check with packageVersion("psichomics"). Please try to update to the latest version.

You can also manually install org.Hs.eg.db via BiocManager::install("org.Hs.eg.db"), although this package is no longer a dependency in the newest version of psichomics.

Please let me know if this solves your issues or not. Cheers!

RFTHK commented 3 years ago

Thank you very much for your quick response. The version is 1.17.0. (installed on 2021/05/21).

packageVersion("psichomics") [1] ‘1.17.0’

Manual installation of org.Hs.eg.db could not improve the problem...

Ryo

nuno-agostinho commented 3 years ago

Okay, so there is a 1.18.0 version of psichomics. Could you try to update to this version using Bioconductor?

BiocManager::install("psichomics")

If that doesn't install the 1.18.0 version, please try to install the latest version directly from GitHub with:

install.packages("remotes"); remotes::install_github("nuno_agostinho/psichomics", ref="master")
RFTHK commented 3 years ago

I have installed and started psichomics version 1.17.0, although a version 1.18.0 cannot be installed in my Windows environment. I will proceed my analysis with 1.17.0. Thank you very much for creating such a great program and for your kind help.

Ryo