Output from install binary with bioclite

dada2_bioclite_install_output.txt

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("dada2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘dada2’
trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/dada2_1.0.3.tar.gz'
Content type 'application/x-gzip' length 1271470 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

* installing *source* package ‘dada2’ ...
** libs
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c Rmain.cpp -o Rmain.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c chimera.cpp -o chimera.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c cluster.cpp -o cluster.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c error.cpp -o error.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c evaluate.cpp -o evaluate.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c filter.cpp -o filter.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c misc.cpp -o misc.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c nwalign_endsfree.cpp -o nwalign_endsfree.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c nwalign_vectorized.cpp -o nwalign_vectorized.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c pval.cpp -o pval.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c strmap.cpp -o strmap.o
g++ -I/home/josephe/miniconda3/envs/newdada2/lib/R/include -DNDEBUG  -I/home/josephe/miniconda3/envs/newdada2/include -I"/home/josephe/.local/Rpackages/Rcpp/include"   -fpic  -I/home/josephe/miniconda3/envs/newdada2/include  -c taxonomy.cpp -o taxonomy.o
g++ -shared -L/home/josephe/miniconda3/envs/newdada2/lib/R/lib -L/home/josephe/miniconda3/envs/newdada2/lib -lgfortran -o dada2.so RcppExports.o Rmain.o chimera.o cluster.o error.o evaluate.o filter.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o strmap.o taxonomy.o -L/home/josephe/miniconda3/envs/newdada2/lib/R/lib -lR
installing to /home/josephe/.local/Rpackages/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dada2)
The downloaded source packages are in
        ‘/tmp/Rtmp0B0VWA/downloaded_packages’
Old packages: 'curl', 'dplyr', 'httr', 'jsonlite', 'maps', 'mgcv', 'mime',
  'Rcpp', 'repr', 'rmarkdown', 'survival', 'tibble'
Update all/some/none? [a/s/n]: n
> packageVersion("dada2")
[1] ‘1.0.3’

> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Old packages: 'curl', 'dplyr', 'httr', 'jsonlite', 'maps', 'mgcv', 'mime',
  'Rcpp', 'repr', 'rmarkdown', 'survival', 'tibble'
Update all/some/none? [a/s/n]: n

> packageVersion("dada2")
[1] ‘1.0.3’