BioC 2.11: CHECK report for qpgraph on lamb1

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/qpgraph.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘1.14.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘qpgraph’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/qpgraph.Rcheck/qpgraph/libs/qpgraph.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Objects: ‘cliquer.o’, ‘graph.o’, ‘qpgraph.o’, ‘reorder.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘cliquer.o’, ‘graph.o’, ‘qpgraph.o’, ‘reorder.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
qpFunctionalCoherence   65.129  0.868  73.156
qpUpdateCliquesRemoving 22.782  0.120  24.978
qpNrr                   19.885  0.096  21.316
qpGenNrr                 5.968  0.088   7.290
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/qpgraph.Rcheck/00check.log’
for details.

* installing *source* package ‘qpgraph’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
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-2.11-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:1787:8: warning: unused variable ‘fp’ [-Wunused-variable]
cliquer.c: In function ‘clique_print_time_always’:
cliquer.c:1836:8: warning: unused variable ‘fp’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-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:4107:19: warning: unused variable ‘k’ [-Wunused-variable]
qpgraph.c:4107:17: warning: unused variable ‘j’ [-Wunused-variable]
qpgraph.c:4107:15: warning: unused variable ‘i’ [-Wunused-variable]
qpgraph.c: In function ‘lr_em’:
qpgraph.c:4149:15: warning: unused variable ‘Y_j’ [-Wunused-variable]
qpgraph.c:4147:39: warning: variable ‘sufStats_ij’ set but not used [-Wunused-but-set-variable]
qpgraph.c:4147:27: warning: variable ‘sufStats_j’ set but not used [-Wunused-but-set-variable]
qpgraph.c:4147:15: warning: variable ‘sufStats_i’ set but not used [-Wunused-but-set-variable]
qpgraph.c: In function ‘qp_fast_rnd_graph’:
qpgraph.c:7959:5: warning: assignment from incompatible pointer type [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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/usr/local/lib64 -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.11-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘qpTxRegNet.Rnw’ 
** testing if installed package can be loaded

* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.128	0.080	0.456
qpAllCItests	0.620	0.012	0.683
qpAnyGraph	0.132	0.004	0.170
qpAvgNrr	1.884	0.012	2.070
qpBoundary	0.332	0.008	0.477
qpCItest	0.036	0.000	0.037
qpClique	0.792	0.008	1.080
qpCliqueNumber	0.124	0.004	0.147
qpCov	0.112	0.008	0.136
qpEdgeNrr	0.036	0.000	0.067
qpFunctionalCoherence	65.129	0.868	73.156
qpG2Sigma	0.040	0.000	0.071
qpGenNrr	5.968	0.088	7.290
qpGetCliques	0.392	0.008	0.474
qpGraph	0.264	0.008	0.335
qpGraphDensity	0.352	0.004	0.370
qpHTF	0.224	0.004	0.234
qpHist	0.304	0.000	0.319
qpIPF	0.208	0.008	0.260
qpK2ParCor	0.060	0.000	0.061
qpNrr	19.885	0.096	21.316
qpPAC	0.376	0.004	0.383
qpPCC	0.136	0.012	0.149
qpPRscoreThreshold	0.168	0.000	0.169
qpPlotMap	0.040	0.004	0.044
qpPlotNetwork	0.452	0.008	0.732
qpPrecisionRecall	0.276	0.000	1.911
qpRndGraph	0.02	0.00	0.02
qpRndHMGM	0.056	0.000	0.055
qpRndWishart	0.012	0.000	0.011
qpSampleFromHMGM	0.072	0.004	0.077
qpTopPairs	0.000	0.000	0.005
qpUnifRndAssociation	0.004	0.000	0.007
qpUpdateCliquesRemoving	22.782	0.120	24.978

Summary

Command output