Error during installation of GEOquery package (R 4.0.3, Bioconduct 3.11)
1
0
Entering edit mode
@zhangzhuo77-24384
Last seen 4.1 years ago

I installed R 4.0.3 and Rstudio. Then I installed BiocManager by the following command.

Operation:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version="3.11")

The response:

Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)

So it seems ok.

But I CAN'T succeed to install GEOquery.

Operation:

BiocManager::install("GEOquery" ) 

Responses:

URL’https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/4.0/curl_4.3.zip'
Content type 'application/zip' length 4126745 bytes (3.9 MB)
downloaded 3.9 MB
......
URL’https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/GEOquery_2.56.0.zip'
Content type 'application/zip' length 13932568 bytes (13.3 MB)
downloaded 164 KB

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
Cann't open the link.
Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 536576 != reported length 746705
2: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 442368 != reported length 2418713
3: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 49152 != reported length 3167021
4: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 167936 != reported length 13932568
5: In unzip(zipname, exdir = dest) : Error in extracting 1  from zip file.
6: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  Can't open the compressed file 'BiocGenerics/DESCRIPTION',Possible due to 'No such file or directory'

It seems something wrong is with BiocGeneric.

Could anyone help me? Thank you in advance. I spent a few hours on it but just cann't solve it.

software error GEOquery • 2.4k views
ADD COMMENT
0
Entering edit mode
@laurent-gatto-5645
Last seen 4 weeks ago
Belgium

This looks like a download issue. I can't reproduce the error with Bioconductor 3.11 installing GEOquery and BiocGenerics. I would suggest you try again.

ADD COMMENT
0
Entering edit mode

Thank you sincerely, Laurent.

ADD REPLY

Login before adding your answer.

Traffic: 674 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6