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Package 479/631HostnameOS / ArchBUILDCHECKBUILD BIN
qpgraph 1.15.0
Robert Castelo
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qpgraph
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: qpgraph
Version: 1.15.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_1.15.0.tar.gz
StartedAt: 2013-01-16 05:30:39 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 05:37:12 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 392.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: qpgraph.Rcheck
Warnings: 1

Command output

* 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.

qpgraph.Rcheck/00install.out:

* 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)

qpgraph.Rcheck/qpgraph-Ex.timings:

nameusersystemelapsed
EcoliOxygen0.1320.0080.141
qpAllCItests0.7080.0240.732
qpAnyGraph0.1520.0080.159
qpAvgNrr2.5000.0002.497
qpBoundary0.3640.0000.365
qpCItest0.0480.0080.055
qpClique0.3690.0000.374
qpCliqueNumber0.1560.0080.167
qpCov0.1240.0120.139
qpEdgeNrr0.060.000.06
qpFunctionalCoherence66.972 0.64067.750
qpG2Sigma0.1320.0000.134
qpGenNrr6.2920.0206.321
qpGetCliques0.4720.0040.479
qpGraph0.3880.0000.389
qpGraphDensity1.2080.0041.214
qpHTF0.1880.0000.189
qpHist0.3080.0080.321
qpIPF0.2360.0040.238
qpK2ParCor0.0800.0000.078
qpNrr18.089 0.00418.091
qpPAC0.4480.0040.451
qpPCC0.2080.0040.209
qpPRscoreThreshold0.2040.0080.212
qpPlotMap0.1160.0080.124
qpPlotNetwork0.4850.0000.489
qpPrecisionRecall0.3400.0000.339
qpRndGraph0.0520.0000.054
qpRndHMGM0.0560.0000.054
qpRndWishart0.0480.0040.051
qpSampleFromHMGM0.0840.0000.082
qpTopPairs0.0080.0000.008
qpUnifRndAssociation0.0120.0000.012
qpUpdateCliquesRemoving25.329 0.12825.461