BioC 3.1: INSTALL report for qpgraph on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL qpgraph
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* installing to library ‘/home/biocbuild/bbs-3.1-bioc/R/library’
* installing *source* package ‘qpgraph’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c cliquer.c -o cliquer.o
cliquer.c: In function ‘clique_print_time’:
cliquer.c:1802:8: warning: unused variable ‘fp’ [-Wunused-variable]
  FILE *fp=opts->output;
        ^
cliquer.c: In function ‘clique_print_time_always’:
cliquer.c:1851:8: warning: unused variable ‘fp’ [-Wunused-variable]
  FILE *fp=opts->output;
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c qpgraph.c -o qpgraph.o
qpgraph.c: In function ‘stat_mis’:
qpgraph.c:4247:19: warning: unused variable ‘k’ [-Wunused-variable]
   int         i,j,k;
                   ^
qpgraph.c:4247:17: warning: unused variable ‘j’ [-Wunused-variable]
   int         i,j,k;
                 ^
qpgraph.c:4247:15: warning: unused variable ‘i’ [-Wunused-variable]
   int         i,j,k;
               ^
qpgraph.c: In function ‘lr_em’:
qpgraph.c:4289:15: warning: unused variable ‘Y_j’ [-Wunused-variable]
   int*        Y_j = NULL;
               ^
qpgraph.c:4287:39: warning: variable ‘sufStats_ij’ set but not used [-Wunused-but-set-variable]
   suf_stats_t sufStats_i, sufStats_j, sufStats_ij;
                                       ^
qpgraph.c:4287:27: warning: variable ‘sufStats_j’ set but not used [-Wunused-but-set-variable]
   suf_stats_t sufStats_i, sufStats_j, sufStats_ij;
                           ^
qpgraph.c:4287:15: warning: variable ‘sufStats_i’ set but not used [-Wunused-but-set-variable]
   suf_stats_t sufStats_i, sufStats_j, sufStats_ij;
               ^
qpgraph.c: In function ‘ssd_A’:
qpgraph.c:8012:17: warning: unused variable ‘m’ [-Wunused-variable]
   int     i,j,k,m;
                 ^
qpgraph.c:8012:15: warning: unused variable ‘k’ [-Wunused-variable]
   int     i,j,k,m;
               ^
qpgraph.c: In function ‘qp_fast_rnd_graph’:
qpgraph.c:8141:5: warning: assignment from incompatible pointer type [enabled by default]
   G = LOGICAL(GR);
     ^
qpgraph.c: In function ‘qp_edge_nrr’:
qpgraph.c:5121:67: warning: ‘Rf_df’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       pcor[nTests+k] = n == NA_INTEGER ? NA_REAL : 2.0 * (1.0 - pt(fabs(t_value), df, 1, 0));
                                                                   ^
qpgraph.c: In function ‘qp_fast_edge_nrr’:
qpgraph.c:5442:11: warning: ‘pcorR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   SEXP    pcorR;
           ^
qpgraph.c: In function ‘qp_ci_test_hmgm.isra.9’:
qpgraph.c:3967:36: warning: ‘rss1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       *partial_eta_squared = (rss1 - rss2) / rss0;
                                    ^
qpgraph.c:3694:11: note: ‘rss1’ was declared here
   double  rss1, rss2;
           ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/R/library/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘det’ from package ‘Matrix’ in package ‘qpgraph’
Creating a generic function from function ‘rmvnorm’ in package ‘qpgraph’
Creating a generic function from function ‘sim.cross’ in package ‘qpgraph’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘eQTLnetworks.Rnw’ 
   ‘qpTxRegNet.Rnw’ 
   ‘qpgraphSimulate.Rnw’ 
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (qpgraph)
BioC 3.1: INSTALL report for qpgraph on zin2

Summary

Command output
