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Cannot install ifnb dataset #15

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Cannot install ifnb dataset#15
@molecules

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@molecules
molecules
opened on Dec 10, 2019 · edited by molecules

When we tried to install the ifnb dataset, we got the following error:

> InstallData('ifnb')
trying URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz': HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘ifnb.SeuratData’ failed
Error in loadNamespace(name) :
  there is no package called ‘ifnb.SeuratData’

I tried wget https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz and found that it did not exist. However, the older version does: (i.e. wget https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz works).

UPDATE:
InstallData('infb') did not work on Linux nor Windows, so it is not system dependent.

Activity

Seojoonho001

Seojoonho001 commented on Dec 12, 2019

@Seojoonho001
Seojoonho001
on Dec 12, 2019

I can confirm this...can you tell me how I can install data from https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz?

bbarthold

bbarthold commented on Dec 12, 2019

@bbarthold
bbarthold
on Dec 12, 2019

...can you tell me how I can install data from https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz?

This is a source package. You can install it as any other source package from the file path where you downloaded it:
install.packages("download.dir/ifnb.SeuratData_3.0.0.tar.gz", repos = NULL, type = "source")
Then load it
library(ifnb.SeuratData),
load the data
data("ifnb")
and follow the vignette from there on.

Seojoonho001

Seojoonho001 commented on Dec 12, 2019

@Seojoonho001
Seojoonho001
on Dec 12, 2019

install.packages("https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz", repos = NULL, type = "source") worked. Thanks!

vHelmholtz
mentioned this in 2 issues on Jan 31, 2020
lengfei5

lengfei5 commented on Apr 3, 2020

@lengfei5
lengfei5
on Apr 3, 2020

Dear Seurat team,
I failed to open https://seurat.nygenome.org/src/contrib/panc8.SeuratData_3.0.0.tar.gz
But other datasets can be well downloaded.
Any idea ?
Thanks.

Dragonmasterx87

Dragonmasterx87 commented on Apr 22, 2020

@Dragonmasterx87
Dragonmasterx87
on Apr 22, 2020

Hi @lengfei5 I am not a Seurat Dev but here is your solution (works for Seurat versions > v3.1):

# Devtools
install.packages('devtools')
library(devtools)

# Seuratdata
devtools::install_github('satijalab/seurat-data')

# Seurat wrappers
devtools::install_github('satijalab/seurat-wrappers')

# Load packages
library(Seurat)
library(ggplot2)
library(patchwork)
library(SeuratData)
library(SeuratWrappers)

# Load Panc8 data
InstallData('panc8')
data("panc8")

Enjoy!

🐲

yanwei-li

yanwei-li commented on May 16, 2020

@yanwei-li
yanwei-li
on May 16, 2020

Dear Seurat team,
I failed to open https://seurat.nygenome.org/src/contrib/panc8.SeuratData_3.0.0.tar.gz
But other datasets can be well downloaded.
Any idea ?
Thanks.

Hi! you can find the panc8data at https://seurat.nygenome.org/src/contrib/panc8.SeuratData_3.0.2.tar.gz

kant
added a commit that references this issue on Jul 28, 2020

Added closing ) to paragraph satijalab#15

3bd9029
mojaveazure
added a commit that references this issue on Sep 18, 2020

Merge pull request #25 from kant/patch-1

c633765
thkuo

thkuo commented on Jan 16, 2022

@thkuo
thkuo
on Jan 16, 2022

Below is the method that worked fine with me. To install the 'ifnb' dataset:

install.packages("https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz", repos = NULL, type = "source")

and to use it:

library(ifnb.SeuratData)
ifnb<-LoadData("ifnb")
molecules

molecules commented on Apr 11, 2022

@molecules
molecules
on Apr 11, 2022
Author

I think that this issue has been resolved (for example, wget https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz works).

molecules
closed this as completedon Apr 11, 2022
AzureLii
mentioned this on Jun 21, 2024
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          Cannot install ifnb dataset · Issue #15 · satijalab/seurat-data