BioC 3.1: CHECK report for qpgraph on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qpgraph_2.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/qpgraph.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.2.3’
* 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 ... [40s/43s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘GOstats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alleQTL,eQTLnetwork : .local: no visible binding for global variable
  ‘swappedGenesMarkers’
qpNrr,data.frame : .local: no visible binding for global variable ‘m’
reQTLcross,integer-eQTLcross : .local: no visible binding for global
  variable ‘n.eQTL’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘qpgraph/libs/qpgraph.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘reorder.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘reorder.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

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 files in ‘vignettes’ ... OK
* checking examples ... [26s/27s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [21s/21s]
 [22s/22s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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-darwin10.8.0
checking host system type... i686-apple-darwin10.8.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -Wall -pedantic -fPIC  -mtune=core2 -g -O2 -Wall  -c cliquer.c -o cliquer.o
cliquer.c: In function ‘unweighted_clique_search_single’:
cliquer.c:229: warning: implicit declaration of function ‘R_ProcessEvents’
cliquer.c: In function ‘clique_print_time’:
cliquer.c:1802: warning: unused variable ‘fp’
cliquer.c: In function ‘clique_print_time_always’:
cliquer.c:1851: warning: unused variable ‘fp’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -Wall -pedantic -fPIC  -mtune=core2 -g -O2 -Wall  -c graph.c -o graph.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -Wall -pedantic -fPIC  -mtune=core2 -g -O2 -Wall  -c qpgraph.c -o qpgraph.o
qpgraph.c: In function ‘stat_mis’:
qpgraph.c:4247: warning: unused variable ‘k’
qpgraph.c:4247: warning: unused variable ‘j’
qpgraph.c:4247: warning: unused variable ‘i’
qpgraph.c: In function ‘lr_em’:
qpgraph.c:4289: warning: unused variable ‘Y_j’
qpgraph.c: In function ‘ssd_A’:
qpgraph.c:8012: warning: unused variable ‘m’
qpgraph.c:8012: warning: unused variable ‘k’
qpgraph.c: In function ‘qp_fast_rnd_graph’:
qpgraph.c:8141: warning: assignment from incompatible pointer type
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -Wall -pedantic -fPIC  -mtune=core2 -g -O2 -Wall  -c reorder.c -o reorder.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘det’ from package ‘Matrix’ in package ‘qpgraph’
Creating a generic function from function ‘rmvnorm’ in package ‘qpgraph’
Creating a generic function from function ‘sim.cross’ in package ‘qpgraph’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.004	0.001	0.004
qpAllCItests	0.246	0.007	0.253
qpAnyGraph	0.226	0.003	0.229
qpAvgNrr	2.762	0.004	2.766
qpBoundary	1.269	0.004	1.273
qpCItest	0.071	0.001	0.073
qpClique	0.852	0.002	0.965
qpCliqueNumber	0.469	0.014	0.485
qpCov	0.126	0.002	0.128
qpEdgeNrr	0.064	0.001	0.066
qpFunctionalCoherence	0.004	0.000	0.004
qpG2Sigma	0.016	0.001	0.016
qpGenNrr	1.175	0.009	1.202
qpGetCliques	0.470	0.003	0.473
qpGraphDensity	0.664	0.001	0.666
qpHTF	0.177	0.001	0.179
qpHist	0.525	0.003	0.529
qpIPF	0.225	0.001	0.227
qpK2ParCor	0.062	0.001	0.064
qpNrr	0.330	0.001	0.331
qpPAC	0.600	0.014	0.613
qpPCC	0.171	0.002	0.172
qpPRscoreThreshold	0.316	0.002	0.317
qpPlotMap	0.066	0.009	0.075
qpPlotNetwork	0.001	0.000	0.001
qpPrecisionRecall	0.526	0.003	0.529
qpRndGraph	0.015	0.001	0.015
qpRndWishart	0.009	0.001	0.011
qpTopPairs	0.004	0.000	0.004
qpUnifRndAssociation	0.007	0.001	0.007
qpUpdateCliquesRemoving	0.001	0.000	0.002

BioC 3.1: CHECK report for qpgraph on petty

Summary

Command output