BioC 3.0: CHECK report for qpgraph on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_2.0.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/qpgraph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.0.5’
* 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 ... [39s/40s] 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
eQTLnetworkEstimationParam: no visible global function definition for
  ‘seqinfo’
show,eQTLnetwork: no visible global function definition for ‘genome’
show,eQTLnetworkEstimationParam: no visible global function definition
  for ‘genome’
* 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 ... [25s/25s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/21s]
 [21s/21s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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-darwin13.1.0
checking host system type... i686-apple-darwin13.1.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -Wall -mtune=core2 -g -O2  -c cliquer.c -o cliquer.o
cliquer.c:229:5: warning: implicit declaration of function 'R_ProcessEvents' is invalid in C99 [-Wimplicit-function-declaration]
    R_ProcessEvents();
    ^
cliquer.c:1802:8: warning: unused variable 'fp' [-Wunused-variable]
        FILE *fp=opts->output;
              ^
cliquer.c:1851:8: warning: unused variable 'fp' [-Wunused-variable]
        FILE *fp=opts->output;
              ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -Wall -mtune=core2 -g -O2  -c graph.c -o graph.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -Wall -mtune=core2 -g -O2  -c qpgraph.c -o qpgraph.o
qpgraph.c:4247:19: warning: unused variable 'k' [-Wunused-variable]
  int         i,j,k;
                  ^
qpgraph.c:4247:17: warning: unused variable 'j' [-Wunused-variable]
  int         i,j,k;
                ^
qpgraph.c:4247:15: warning: unused variable 'i' [-Wunused-variable]
  int         i,j,k;
              ^
qpgraph.c:4289:15: warning: unused variable 'Y_j' [-Wunused-variable]
  int*        Y_j = NULL;
              ^
qpgraph.c:8012:17: warning: unused variable 'm' [-Wunused-variable]
  int     i,j,k,m;
                ^
qpgraph.c:8012:15: warning: unused variable 'k' [-Wunused-variable]
  int     i,j,k,m;
              ^
qpgraph.c:8141:5: warning: incompatible pointer types assigning to 'Rboolean *' from 'int *' [-Wincompatible-pointer-types]
  G = LOGICAL(GR);
    ^ ˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -Wall -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -Wall -mtune=core2 -g -O2  -c reorder.c -o reorder.o
clang -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 -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/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
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
* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.003	0.001	0.004
qpAllCItests	0.198	0.012	0.223
qpAnyGraph	0.114	0.003	0.117
qpAvgNrr	2.092	0.005	2.112
qpBoundary	0.563	0.003	0.569
qpCItest	0.049	0.001	0.051
qpClique	0.577	0.003	0.592
qpCliqueNumber	0.672	0.009	0.700
qpCov	0.090	0.003	0.094
qpEdgeNrr	0.032	0.001	0.034
qpFunctionalCoherence	0.002	0.000	0.002
qpG2Sigma	0.012	0.001	0.012
qpGenNrr	0.914	0.003	0.941
qpGetCliques	0.711	0.004	0.716
qpGraphDensity	0.533	0.003	0.548
qpHTF	0.102	0.003	0.105
qpHist	0.367	0.006	0.372
qpIPF	0.166	0.004	0.171
qpK2ParCor	0.038	0.002	0.040
qpNrr	0.312	0.001	0.313
qpPAC	0.708	0.015	0.728
qpPCC	0.104	0.003	0.107
qpPRscoreThreshold	0.269	0.002	0.270
qpPlotMap	0.063	0.008	0.078
qpPlotNetwork	0.001	0.001	0.000
qpPrecisionRecall	0.358	0.002	0.361
qpRndGraph	0.010	0.000	0.011
qpRndWishart	0.010	0.001	0.011
qpTopPairs	0.004	0.000	0.004
qpUnifRndAssociation	0.005	0.000	0.005
qpUpdateCliquesRemoving	0.001	0.000	0.001

BioC 3.0: CHECK report for qpgraph on oaxaca

Summary

Command output