Package: qpgraph

Version: 1.14.4

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_1.14.4.tar.gz

StartedAt: 2013-03-25 00:54:59 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:01:29 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 390.7 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/qpgraph.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 '/Users/biocbuild/bbs-2.11-bioc/meat/qpgraph.Rcheck/qpgraph/libs/i386/qpgraph.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Objects: 'cliquer.o', 'graph.o', 'qpgraph.o', 'reorder.o'
  Found '_abort', possibly from 'abort' (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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
qpFunctionalCoherence   67.324  3.256  71.544
qpUpdateCliquesRemoving 21.281  0.705  22.390
qpNrr                   20.707  0.229  21.289
qpGenNrr                 6.545  0.085   6.792
* 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
  '/Users/biocbuild/bbs-2.11-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... i686-apple-darwin9.8.0
checking host system type... i686-apple-darwin9.8.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic  -c cliquer.c -o cliquer.o
cliquer.c: In function 'clique_print_time':
cliquer.c:1787: warning: unused variable 'fp'
cliquer.c: In function 'clique_print_time_always':
cliquer.c:1836: warning: unused variable 'fp'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic  -c graph.c -o graph.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic  -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'stat_mis':
qpgraph.c:4107: warning: unused variable 'k'
qpgraph.c:4107: warning: unused variable 'j'
qpgraph.c:4107: warning: unused variable 'i'
qpgraph.c: In function 'lr_em':
qpgraph.c:4149: warning: unused variable 'Y_j'
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:7959: warning: assignment from incompatible pointer type
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic  -c reorder.c -o reorder.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/qpgraph.Rcheck/qpgraph/libs/i386
** 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	0.490	0.014	0.507
qpAllCItests	0.227	0.028	0.255
qpAnyGraph	0.112	0.012	0.124
qpAvgNrr	2.397	0.017	2.426
qpBoundary	0.874	0.015	0.893
qpCItest	0.043	0.005	0.074
qpClique	0.585	0.013	0.608
qpCliqueNumber	0.135	0.011	0.153
qpCov	0.113	0.013	0.146
qpEdgeNrr	0.034	0.003	0.040
qpFunctionalCoherence	67.324	3.256	71.544
qpG2Sigma	0.041	0.003	0.049
qpGenNrr	6.545	0.085	6.792
qpGetCliques	0.432	0.008	0.452
qpGraph	0.401	0.012	0.423
qpGraphDensity	0.636	0.015	0.666
qpHTF	0.206	0.017	0.226
qpHist	0.425	0.012	0.437
qpIPF	0.262	0.172	0.436
qpK2ParCor	0.060	0.003	0.063
qpNrr	20.707	0.229	21.289
qpPAC	0.581	0.036	0.636
qpPCC	0.219	0.014	0.236
qpPRscoreThreshold	0.292	0.012	0.305
qpPlotMap	0.083	0.022	0.106
qpPlotNetwork	0.504	0.031	0.542
qpPrecisionRecall	0.501	0.018	0.525
qpRndGraph	0.013	0.006	0.019
qpRndHMGM	0.155	0.005	0.162
qpRndWishart	0.011	0.001	0.012
qpSampleFromHMGM	0.075	0.003	0.080
qpTopPairs	0.003	0.000	0.004
qpUnifRndAssociation	0.006	0.001	0.007
qpUpdateCliquesRemoving	21.281	0.705	22.390