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Unable to install rtracklayer #42

Closed klmr closed 8 years ago

klmr commented 8 years ago 
source('http://bioconductor.org/biocLite.R')
biocLite('rtracklayer')

yields

…
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/nfs/research2/marioni/Konrad/opt/R-lib/rtracklayer/libs/rtracklayer.so':
  /nfs/research2/marioni/Konrad/opt/R-lib/rtracklayer/libs/rtracklayer.so: undefined symbol: __fdelt_chk
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/nfs/research2/marioni/Konrad/opt/R-lib/rtracklayer’
> .libPaths()[1]
"/nfs/research2/marioni/Konrad/opt/R-lib"               "/nfs/research2/software/prefix/usr/lib/R/site-library" "/nfs/research2/software/prefix/usr/lib/R/library"
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

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

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

other attached packages:
[1] modules_0.8.2  vimcom_1.2-6   setwidth_1.0-4 colorout_1.1-0

loaded via a namespace (and not attached):
[1] magrittr_1.5 tools_3.2.2

R also wants to update an outdated “Matrix” package even though I had previously successfully reinstalled that manually — there seems to be a confusion with the paths, since trying to update (rather than reinstall) it attempts to write to (readonly) /nfs/research2/software/prefix/usr/lib/R/library:

ERROR: failed to lock directory ‘/nfs/research2/software/prefix/usr/lib/R/library’ for modifying
Try removing ‘/nfs/research2/software/prefix/usr/lib/R/library/00LOCK-Matrix’

The manually reinstalled version (in .libPaths()[1]) is not considered.

mschubert commented 8 years ago

did you try recompile S4Vectors? (that's related to linking glibc with FORTIFY #40 - I set the global flag to be off now, that should serve as a workaround for the time being)

2nd is, if it all, an internal R bug and I can not explain how the setup could have caused this (it should respect .libPaths either way)

klmr commented 8 years ago

Reinstalling S4Vectors doesn’t change anything either, unfortunately.

klmr commented 8 years ago

Worked after the following changes: