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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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install error #26

Open slg0904 opened 5 years ago

slg0904 commented 5 years ago

I have done all my efforts to install SingleR package. But it still cannot work. My R is updated to version 3.5.2. And seurat is updated to version 3.0.

Method 1: library(curl) library(devtools) install_github('dviraran/SingleR')

Method 2: devtools::install_github('dviraran/SingleR')

Method 3: I downloaded the package file and installed it by using local files.

Who can help me to solve this problem? Thank you.

dviraran commented 5 years ago

Can you post the error output?

slg0904 commented 5 years ago

Can you post the error output? image

dviraran commented 5 years ago

Not sure why its not installing them automatically, but try to install GSEABase and GSVA first (both from Bioconductor), and then try again.

In the next version I will remove those packages all together.

slg0904 commented 5 years ago

Not sure why its not installing them automatically, but try to install GSEABase and GSVA first (both from Bioconductor), and then try again.

In the next version I will remove those packages all together.

Thank you so much. After installing GSEABase and GSVA, it works.

simon2073 commented 5 years ago

I have done all my efforts to install SingleR package. But it still cannot work. My R is updated to version 3.5.2. And seurat is updated to version 3.0.

Method 1: library(curl) library(devtools) install_github('dviraran/SingleR')

Method 2: devtools::install_github('dviraran/SingleR')

Method 3: I downloaded the package file and installed it by using local files.

Who can help me to solve this problem? Thank you.

I came across the different problem and I have try downloading SingleR zip file,but I can't install it directly using install.package. Library(singR) shows can't find this package.And singleR-master was in Library file . Pretty confused.

dviraran commented 5 years ago

Can you post the log? what exactly is failing?

simon2073 commented 5 years ago

Can you post the log? what exactly is failing?

first problem lies in: Downloading GitHub repo dviraran/SingleR@master Error in utils::download.file(url, path, method = download_method(), quiet = quiet, : download from 'https://api.github.com/repos/dviraran/SingleR/tarball/master' failed

Then I try install from local file and R shows no reponse. Library(singR) shows can't find this package.Error in library(singleR) : 不存在叫‘singleR’这个名字的程辑包

simon2073 commented 5 years ago

Can you post the log? what exactly is failing?

dear I downloaded the software for the first time,the I run the following script: install.packages("Seurat") install.packages("outliers") install.packages("pbmcapply") install.packages("doFuture")

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("singscore") BiocManager::install("GSVA") BiocManager::install("GSEABase") BiocManager::install("limma") install.packages("devtools") library(devtools) devtools::install_github('dviraran/SingleR')

I have browsed the same question like me and tried for a period of time, hope to solved it. Thank all the time.

dviraran commented 5 years ago

It seems that there is a problem downloading the code. I've seen this issue in the past, and restarting RStudio (and sometimes the computer) solves it.

I just tried again to install it and it worked for me, so it doesn't seem to be an issue with the repository.

simon2073 commented 5 years ago

It seems that there is a problem downloading the code. I've seen this issue in the past, and restarting RStudio (and sometimes the computer) solves it.

I just tried again to install it and it worked for me, so it doesn't seem to be an issue with the repository.

thanks ,I installed it this time. the problem lise in the file location of R

saisaitian commented 4 years ago

Hi, I always download error,could you tell me how to fix it?

devtools::install_github('dviraran/SingleR') Downloading GitHub repo dviraran/SingleR@master dviraran-SingleR-adc4a0e/data/immgen.rda: truncated gzip input tar.exe: Error exit delayed from previous errors. Error: Failed to install 'SingleR' from GitHub: Does not appear to be an R package (no DESCRIPTION)