BioC 2.12: CHECK report for qpgraph on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/qpgraph.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.15.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘qpgraph’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... WARNING
File ‘/loc/home/biocbuild/bbs-2.12-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   66.972  0.640  67.750
qpUpdateCliquesRemoving 25.329  0.128  25.461
qpNrr                   18.089  0.004  18.091
qpGenNrr                 6.292  0.020   6.321
* 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

WARNING: There was 1 warning.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/qpgraph.Rcheck/00check.log’
for details.

* 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-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -c cliquer.c -o cliquer.o
cliquer.c: In function ‘clique_print_time’:
cliquer.c:1787:8: warning: unused variable ‘fp’
cliquer.c: In function ‘clique_print_time_always’:
cliquer.c:1836:8: warning: unused variable ‘fp’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -c qpgraph.c -o qpgraph.o
qpgraph.c: In function ‘stat_mis’:
qpgraph.c:4104:19: warning: unused variable ‘k’
qpgraph.c:4104:17: warning: unused variable ‘j’
qpgraph.c:4104:15: warning: unused variable ‘i’
qpgraph.c: In function ‘lr_em’:
qpgraph.c:4146:15: warning: unused variable ‘Y_j’
qpgraph.c: In function ‘qp_fast_rnd_graph’:
qpgraph.c:7947:5: warning: assignment from incompatible pointer type
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2  -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-2.12-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -lgfortran -lm -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-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	0.132	0.008	0.141
qpAllCItests	0.708	0.024	0.732
qpAnyGraph	0.152	0.008	0.159
qpAvgNrr	2.500	0.000	2.497
qpBoundary	0.364	0.000	0.365
qpCItest	0.048	0.008	0.055
qpClique	0.369	0.000	0.374
qpCliqueNumber	0.156	0.008	0.167
qpCov	0.124	0.012	0.139
qpEdgeNrr	0.06	0.00	0.06
qpFunctionalCoherence	66.972	0.640	67.750
qpG2Sigma	0.132	0.000	0.134
qpGenNrr	6.292	0.020	6.321
qpGetCliques	0.472	0.004	0.479
qpGraph	0.388	0.000	0.389
qpGraphDensity	1.208	0.004	1.214
qpHTF	0.188	0.000	0.189
qpHist	0.308	0.008	0.321
qpIPF	0.236	0.004	0.238
qpK2ParCor	0.080	0.000	0.078
qpNrr	18.089	0.004	18.091
qpPAC	0.448	0.004	0.451
qpPCC	0.208	0.004	0.209
qpPRscoreThreshold	0.204	0.008	0.212
qpPlotMap	0.116	0.008	0.124
qpPlotNetwork	0.485	0.000	0.489
qpPrecisionRecall	0.340	0.000	0.339
qpRndGraph	0.052	0.000	0.054
qpRndHMGM	0.056	0.000	0.054
qpRndWishart	0.048	0.004	0.051
qpSampleFromHMGM	0.084	0.000	0.082
qpTopPairs	0.008	0.000	0.008
qpUnifRndAssociation	0.012	0.000	0.012
qpUpdateCliquesRemoving	25.329	0.128	25.461

Summary

Command output