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BenvenLab / eSNPKaryotyping

Analysis of Chromosomal Aberrations from RNA-Seq sequencing data.
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Unable to install package #3

Open galanisl opened 5 years ago

galanisl commented 5 years ago

Hi,

I tried to install eSNPKaryotyping using the provided instructions but I get the following error:

install_github("BenvenLab/eSNPKaryotyping/eSNPKaryotyping")
Downloading GitHub repo BenvenLab/eSNPKaryotyping@master
Skipping 1 packages not available: Depends: zoo
Installing 1 packages: Depends: zoo
Installing package into ‘/home/lobatog/R/x86_64-redhat-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
Error: (converted from warning) package ‘Depends: zoo’ is not available (for R version 3.5.2)

If I install the dependencies myself and set dependencies to FALSE in install_github, I get the following:

install_github("BenvenLab/eSNPKaryotyping/eSNPKaryotyping", dependencies = FALSE)
Downloading GitHub repo BenvenLab/eSNPKaryotyping@master
✔  checking for file ‘/tmp/RtmpaN2Q9E/remotes12d7a5ac00522/BenvenLab-eSNPKaryotyping-1d890ef/eSNPKaryotyping/DESCRIPTION’ ...
─  preparing ‘eSNPKaryotyping’:
E  checking DESCRIPTION meta-information
   Malformed Depends or Suggests or Imports or Enhances field.
   Offending entries:
     Depends: zoo
   Entries must be names of packages optionally followed by '<=' or '>=',
   white space, and a valid version number in parentheses.

   See section 'The DESCRIPTION file' in the 'Writing R Extensions'
   manual.

Error in (function (command = NULL, args = character(), error_on_status = TRUE,  : 
  System command error
BenvenLab commented 5 years ago

Hi, Please try install the package now. I remove the dependencies requirement for the package. If it works please make sure you install the packages gplots and zoo separately. Thanks

galanisl commented 5 years ago

Thanks! It worked. However, I ended up cloning the GitHub repository because the working directory assumptions made by the package were giving me a headache.

Function TopHat, for example, doesn't work at all with relative paths and function CreateVCF assumes that my working directory is ~/. I suggest that you specify that full paths are required.