BioC 2.9: CHECK report for qpgraph on moscato1

Package: qpgraph

Version: 1.9.0

Command: mkdir qpgraph.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qpgraph.buildbin-libdir qpgraph_1.9.0.tar.gz >qpgraph-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=qpgraph.buildbin-libdir --install="check:qpgraph-install.out" --force-multiarch --no-vignettes --timings qpgraph_1.9.0.tar.gz && mv qpgraph.buildbin-libdir/* qpgraph.Rcheck/ && rmdir qpgraph.buildbin-libdir

StartedAt: 2011-07-07 05:59:37 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 06:05:41 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 363.9 seconds

RetCode: 0

Status: OK

CheckDir: qpgraph.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/qpgraph.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qpgraph/DESCRIPTION' ... OK
* this is package 'qpgraph' version '1.9.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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
* loading checks for arch 'i386'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 tools::resaveRdaFiles() or 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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


install for i386

* installing *source* package 'qpgraph' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c cliquer.c -o cliquer.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c graph.c -o graph.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'qp_ci_test_hmgm':
qpgraph.c:2089:17: warning: unused variable 'm'
qpgraph.c: In function 'ssd_A':
qpgraph.c:4703:15: warning: unused variable 'k'
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c reorder.c -o reorder.o
gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRblas -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'qpTxRegNet.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'qpgraph' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c cliquer.c -o cliquer.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c graph.c -o graph.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'qp_ci_test_hmgm':
qpgraph.c:2089:17: warning: unused variable 'm'
qpgraph.c: In function 'ssd_A':
qpgraph.c:4703:15: warning: unused variable 'k'
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -std=gnu99 -mtune=core2 -c reorder.c -o reorder.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRblas -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qpgraph' as qpgraph_1.9.0.zip

* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.06	0.00	0.07
qpAnyGraph	0.39	0.01	0.40
qpAvgNrr	1.95	0.00	1.95
qpCItest	0.03	0.00	0.03
qpClique	0.47	0.00	0.47
qpCliqueNumber	0.11	0.00	0.11
qpCov	0.23	0.02	0.25
qpEdgeNrr	0.03	0.00	0.03
qpFunctionalCoherence	49.25	0.11	49.36
qpG2Sigma	0.01	0.00	0.02
qpGenNrr	5.85	0.00	5.85
qpGetCliques	0.42	0.00	0.42
qpGraph	0.46	0.00	0.45
qpGraphDensity	0.51	0.00	0.52
qpHist	0.66	0.00	0.65
qpIPF	0.25	0.00	0.27
qpK2ParCor	0.06	0.00	0.06
qpNrr	18.78	0.03	18.81
qpPAC	1.06	0.00	1.06
qpPCC	0.15	0.02	0.17
qpPRscoreThreshold	0.60	0.00	0.59
qpPlotNetwork	0.29	0.00	0.32
qpPrecisionRecall	0.44	0.00	0.44
qpRndGraph	0.19	0.00	0.18
qpRndHMGM	0.06	0.00	0.07
qpRndWishart	0	0	0
qpSampleFromHMGM	0.07	0.00	0.07
qpTopPairs	0	0	0
qpUnifRndAssociation	0.01	0.00	0.01
qpUpdateCliquesRemoving	18.40	0.06	18.46

Summary

Command output