Hi all,
I am not an admin expert, so the question might be beginner level, sorry of so.
I am having difficulties upgrading flowCore package.
System: Ubuntu 14.04.5 LTS (GNU/Linux 3.13.0-66-generic x86_64)
R version 3.3.2
Typing
source("https://bioconductor.org/biocLite.R"); biocLite("flowCore")
led to error:
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/BH/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hyperlogTransform.cpp -o hyperlogTransform.o
In file included from /usr/share/R/include/R.h:40:0,
from hyperlogTransform.cpp:14:
/usr/include/c++/4.8/cstdlib: In function ‘long long int std::abs(long long int)’:
/usr/include/c++/4.8/cstdlib:174:20: error: declaration of C function ‘long long int std::abs(long long int)’ conflicts with
abs(long long __x) { return __builtin_llabs (__x); }
followed by a (too-)long list of similar errors.
biocValid() does not seem to indicate the problem (except many packages out of date)
> biocValid()
* sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.18.5
loaded via a namespace (and not attached):
[1] tools_3.3.2
I also updated/upgraded and rebooted my system, and got the same problem.
Any hint?
Thanks
