compiling R package on ubuntu, invalid ELF header - r

Question

I am no longer able to compile an R package from source, and this has never been a problem before today. This is what happens:
R CMD build BAMMtools
* checking for file ‘BAMMtools/DESCRIPTION’ ... OK
* preparing ‘BAMMtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘BAMMtools_2.1.0.tar.gz’
R CMD INSTALL BAMMtools
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘BAMMtools’ ...
** libs
make: Nothing to be done for 'all'.
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so':
/usr/local/lib/R/site-library/BAMMtools/libs/BAMMtools.so: invalid ELF header
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/BAMMtools’
* restoring previous ‘/usr/local/lib/R/site-library/BAMMtools’
This does not seem to be a problem with this R package in particular, as I am able to install the package from within R, as:
> install.packages('BAMMtools_2.1.0.tar.gz', repos=NULL)
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘BAMMtools’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cohort_matrix.c -o cohort_matrix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dtrates.c -o dtrates.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c jenksBrks.c -o jenksBrks.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c treetraverse.c -o treetraverse.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BAMMtools.so cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/BAMMtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BAMMtools)
I am running R v3.2.2, under Ubuntu v15.10 wily. I can't think of anything I've done within the last 24 hours that would have this effect, except updating my system with sudo apt-get update/upgrade.
Although this is not too much of a problem for installing the package, I can't run the R CMD check commands either, and this is a problem for development.
Any suggestions or advice would be greatly appreciated! Thanks!

Answer 1

As was found in the comments to the question, thanks to Jack Wasey, the problem was simply that I was running R CMD INSTALL on the name of the source directory, rather than on the built .tar.gz file.