Package: qpgraph

Version: 1.12.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_1.12.0.tar.gz

StartedAt: 2012-04-01 02:51:04 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:55:19 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 255.1 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/qpgraph.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qpgraph/DESCRIPTION' ... OK
* this is package 'qpgraph' version '1.12.0'
* 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 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 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 ... NOTE
.qpAvgNrr: warning in assign("clusterSize", clusterSize, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
.qpEdgeNrr: warning in sample(V, q - q.fix, rep = FALSE): partial
  argument match of 'rep' to 'replace'
.qpEdgeNrrHMGM: warning in sample(V, q - q.fix, rep = FALSE): partial
  argument match of 'rep' to 'replace'
.qpEdgeNrrHMGMsml: warning in sample(V, q - q.fix, rep = FALSE):
  partial argument match of 'rep' to 'replace'
.qpGenNrr: warning in assign("clusterSize", clusterSize, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
.qpNrr: warning in assign("clusterSize", clusterSize, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
qpHist: warning in close.screen(all = TRUE): partial argument match of
  'all' to 'all.screens'
* 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/hpages/test-puck5/bbs-2.10-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'
  Found 'stdout', possibly from 'stdout' (C)
    Object: 'cliquer.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
* 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 were 2 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-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/hpages/test-puck5/bbs-2.10-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
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-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/hpages/test-puck5/bbs-2.10-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 'qp_fast_nrr_par':
qpgraph.c:1142:11: warning: variable 'nAdjEtime' set but not used [-Wunused-but-set-variable]
qpgraph.c: In function 'qp_fast_nrr_identicalQs_par':
qpgraph.c:1540:11: warning: variable 'nAdjEtime' set but not used [-Wunused-but-set-variable]
qpgraph.c: In function 'qp_edge_nrr_identicalQs':
qpgraph.c:3269:12: warning: variable 'Q' set but not used [-Wunused-but-set-variable]
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:6004:5: warning: assignment from incompatible pointer type [enabled by default]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-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/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lRblas -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-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	0.142
qpAnyGraph	0.152	0.004	0.173
qpAvgNrr	2.116	0.008	2.135
qpBoundary	0.304	0.004	0.316
qpCItest	0.028	0.004	0.039
qpClique	0.308	0.000	0.317
qpCliqueNumber	0.112	0.000	0.125
qpCov	0.080	0.000	0.098
qpEdgeNrr	0.224	0.000	0.232
qpFunctionalCoherence	46.879	0.756	47.860
qpG2Sigma	0.072	0.000	0.069
qpGenNrr	5.644	0.012	5.666
qpGetCliques	0.388	0.008	0.409
qpGraph	0.216	0.012	0.238
qpGraphDensity	0.296	0.004	0.308
qpHTF	0.100	0.004	0.123
qpHist	0.261	0.004	0.272
qpIPF	0.140	0.004	0.164
qpK2ParCor	0.044	0.000	0.054
qpNrr	14.504	0.012	14.533
qpPAC	0.460	0.000	0.474
qpPCC	0.124	0.008	0.152
qpPRscoreThreshold	0.132	0.004	0.145
qpPlotNetwork	0.340	0.012	0.403
qpPrecisionRecall	0.248	0.000	0.259
qpRndGraph	0.016	0.000	0.015
qpRndHMGM	0.064	0.000	0.062
qpRndWishart	0.008	0.000	0.010
qpSampleFromHMGM	0.060	0.000	0.069
qpTopPairs	0.004	0.000	0.004
qpUnifRndAssociation	0.004	0.000	0.005
qpUpdateCliquesRemoving	15.336	0.040	15.399