isglobal-brge / brge_data_large Goto Github PK

Hi Carles, @carleshf @isglobal-brge

Please check the build report below and address any issues with the experiment data package.
https://bioconductor.org/checkResults/3.7/data-experiment-LATEST/brgedata/malbec2-buildsrc.html

Warning: file ‘brge_expo.rda’ has magic number 'versi'
  Use of save versions prior to 2 is deprecated
Error in load(zfile, envir = envir) : 
  bad restore file magic number (file may be corrupted) -- no data loaded
ERROR: lazydata failed for package ‘brgedata’

Your omicRexposome package is candidate for deprecation. Please resolve these issues
as soon as possible for your continued inclusion in Bioconductor.

Best regards,
Marcel

Hi, I download the metabol_serum/metabol_urine.Rdata files, and found there is no metabolite names in metabol_serum.Rdata file, only the classe information. And there is metabolite information (name, ID etc) in metabol_urine@featureData@data.

I am using brgedata version 1.10.0 with R version 4.0.2 on Ubuntu 18.04.
I am trying to use read.plink with the obesity files (which are not available in the directory of the package, so I downloaded them manually from the GitHub repository). The problem is that when I try to read obesity.bed I receive the following error message:

Error in scan(..., :
line 1 did not have 3 elements

Any suggestion? Thank you. @isglobal-brge

devtools::install_local("/home/sheyu/Downloads/omic1/brgedata-master.zip")
Skipping 1 packages ahead of CRAN: formatR
Installing package into ‘/home/sheyu/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)

• installing source package ‘brgedata’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  Warning: file ‘asthma.rda’ has magic number 'versi'
  Use of save versions prior to 2 is deprecated
  Error in load(zfile, envir = tmp_env) :
  bad restore file magic number (file may be corrupted) -- no data loaded
  ERROR: lazydata failed for package ‘brgedata’
• removing ‘/home/sheyu/R/x86_64-pc-linux-gnu-library/3.6/brgedata’
  Error: Failed to install 'brgedata-master.zip' from local:
  (converted from warning) installation of package ‘/tmp/RtmpQoSJ4q/remotes1c764cde52e9/brgedata-master’ had non-zero exit status