Package: qpgraph

Version: 1.10.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_1.10.1.tar.gz

StartedAt: 2012-03-24 02:08:16 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:13:09 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 292.6 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/qpgraph.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.10.1’
* 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 ... 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  EcoliOxygen.RData    1.4Mb    1.2Mb       xz
* 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-2.9-bioc/meat/qpgraph.Rcheck/qpgraph/libs/qpgraph.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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

* 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-2.9-bioc/R/include -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/biocbuild/bbs-2.9-bioc/R/include -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-2.9-bioc/R/include -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_edge_nrr’:
qpgraph.c:2571:12: warning: unused variable ‘l’
qpgraph.c: In function ‘qp_edge_nrr_identicalQs’:
qpgraph.c:2626:11: warning: unused variable ‘m’
qpgraph.c: In function ‘qp_fast_rnd_graph’:
qpgraph.c:5130:5: warning: assignment from incompatible pointer type
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -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-2.9-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.9-bioc/R/lib -lRlapack -lgfortran -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “connection” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “file” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘qpTxRegNet.Rnw’ 
** testing if installed package can be loaded

* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.076	0.004	0.078
qpAnyGraph	0.480	0.012	0.490
qpAvgNrr	2.060	0.012	2.092
qpBoundary	0.34	0.00	0.34
qpCItest	0.028	0.004	0.032
qpClique	0.652	0.008	0.666
qpCliqueNumber	0.436	0.004	0.440
qpCov	0.088	0.004	0.092
qpEdgeNrr	0.036	0.000	0.035
qpFunctionalCoherence	56.436	0.856	58.139
qpG2Sigma	0.032	0.004	0.036
qpGenNrr	6.148	0.012	6.166
qpGetCliques	0.428	0.004	0.432
qpGraph	0.268	0.004	0.270
qpGraphDensity	0.368	0.000	0.367
qpHTF	0.188	0.004	0.189
qpHist	0.292	0.004	0.296
qpIPF	0.212	0.004	0.217
qpK2ParCor	0.056	0.004	0.061
qpNrr	21.230	0.016	21.251
qpPAC	0.516	0.016	0.535
qpPCC	0.164	0.000	0.165
qpPRscoreThreshold	0.172	0.004	0.180
qpPlotNetwork	0.412	0.000	0.447
qpPrecisionRecall	0.292	0.000	0.291
qpRndGraph	0.020	0.000	0.017
qpRndHMGM	0.072	0.000	0.074
qpRndWishart	0.012	0.000	0.012
qpSampleFromHMGM	0.084	0.004	0.087
qpTopPairs	0.004	0.004	0.006
qpUnifRndAssociation	0.004	0.000	0.007
qpUpdateCliquesRemoving	26.233	0.068	26.696