How to download the ChAMP dependency ChAMPdata
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Entering edit mode
Federica ▴ 10
@federica-24874
Last seen 23 days ago
Italy

Hi guys,

I have to make control quality of methylation data by ChAMP bioconductor package.

After running the following commands

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

BiocManager::install("ChAMP")

I found the following error message:

trying URL 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/ChAMPdata_2.22.0.tar.gz'
Content type 'application/x-gzip' length 712982793 bytes (680.0 MB)
===========================================
downloaded 591.0 MB

Error in download.file(url, destfile, method, mode = "wb", ...) :
  download from 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/ChAMPdata_2.22.0.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 619674728 != reported length 712982793
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/ChAMPdata_2.22.0.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘ChAMPdata’ failed

I also tried to download the ChAMPdata dependency through the following command

BiocManager::install("ChAMPdata")

And I found the following error message:

Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.5 (2021-03-31)
Installing package(s) 'ChAMPdata'
trying URL 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/ChAMPdata_2.22.0.tar.gz'
Content type 'application/x-gzip' length 712982793 bytes (680.0 MB)
============================================
downloaded 603.0 MB

Error in download.file(url, destfile, method, mode = "wb", ...) :
  download from 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/ChAMPdata_2.22.0.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 632259966 != reported length 712982793
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/ChAMPdata_2.22.0.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘ChAMPdata’ failed

Could someone help me in solving this problem with ChAMPdata?

I used R in a Unix server. The uname -a output is:

Linux platonesrv1 5.4.0-70-generic #78-Ubuntu SMP Fri Mar 19 13:29:52 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

while my R session info is:

R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.5

Thank u!

ChAMP ChAMPdata • 82 views
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2
Entering edit mode

You could try increasing the timeout limit for downloading files. I increased mine in a .Rprofile script so its persistent in all sessions but I think you can do it interactively for a single session by doing something like options(timeout=300) . its in seconds so this would increase the timeout to 5 minutes instead of 1.

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