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I am trying to install this on Linux machine:

R CMD INSTALL -l ./ broadgap.utils_1.0.tar.gz

The file was downloaded from here: https://www.broadinstitute.org/birdsuite/birdsuite-downloads

The instructions for installation are here: https://www.broadinstitute.org/birdsuite/birdsuite-install

and I got this:

* installing *source* package ‘broadgap.utils’ ...
 ERROR: a 'NAMESPACE' file is required

I tried solution proposed here:

 https://stackoverflow.com/questions/17196225/error-a-namespace-file-is-required

tar -xzf broadgap.utils_1.0.tar.gz
cd broadgap.utils
echo 'exportPattern( "." )' > NAMESPACE
cd ..
tar -zcf broadgap.utils_1.0.tar.gz broadgap.utils

after trying to install it with the proposed solution again I got this:

* installing *source* package ‘broadgap.utils’ ...
** R
** preparing package for lazy loading
** help
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:11: unexpected TEXT ' ', expecting '{'
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:23: unexpected '}'
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:12: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:13: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:13: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:14: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:14: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:15: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:15: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:16: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:16: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:17: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:17: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:19: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:20: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:21: All text must be in a section
Warning: /tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/broad.utils-package.Rd:22: All text must be in a section
Warning: newline within quoted string at commandLineArg.Rd:29
Error in parse_Rd("/tmp/RtmpfWfEvG/R.INSTALL6da96b32b825/broadgap.utils/man/commandLineArg.Rd",  : 
  Unexpected end of input (in " quoted string opened at commandLineArg.Rd:35:31)
ERROR: installing Rd objects failed for package ‘broadgap.utils’

my R version is: r-3.6.3

anamaria
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    Where did the file `broadgap.utils_1.0.tar.gz` come from? Are you sure it contains a valid R package? The error message seems to indicate it does not. What does `tar --gzip --list --verbose --file=broadgap.utils_1.0.tar.gz` return? – MrFlick Sep 28 '20 at 21:52
  • it comes from here: https://www.broadinstitute.org/birdsuite/birdsuite-downloads – anamaria Sep 28 '20 at 21:58
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    It looks like that software was written back in 2008. You may want to use a version of R from back in that time frame because it looks like it hasn't been updated for modern versions of R in a long time. Unless you want to edit the package contents yourself to bring it up to spec. – MrFlick Sep 28 '20 at 22:09
  • Thanks! any ideas how I can edit that package so that it works? – anamaria Sep 28 '20 at 22:10

0 Answers0