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BioC 3.5: CHECK report for qpgraph on oaxaca

This page was generated on 2017-03-04 16:37:28 -0500 (Sat, 04 Mar 2017).

Package 1002/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.9.5
Robert Castelo
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qpgraph
Last Changed Rev: 126746 / Revision: 127142
Last Changed Date: 2017-02-14 08:25:06 -0500 (Tue, 14 Feb 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: qpgraph
Version: 2.9.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qpgraph_2.9.5.tar.gz
StartedAt: 2017-03-04 07:32:02 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 07:36:47 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 284.9 seconds
RetCode: 0
Status:  OK 
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qpgraph_2.9.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/qpgraph.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘2.9.5’
* 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 ... 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 ... 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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-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... i686-apple-darwin13.4.0
checking host system type... i686-apple-darwin13.4.0
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();
    ^
1 warning 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:5849:19: warning: expression result unused [-Wunused-value]
    int i = edges[k, 0];
                  ^
qpgraph.c:5850:19: warning: expression result unused [-Wunused-value]
    int j = edges[k, 1];
                  ^
qpgraph.c:8157:17: warning: unused variable 'm' [-Wunused-variable]
  int     i,j,k,m;
                ^
qpgraph.c:8157:15: warning: unused variable 'k' [-Wunused-variable]
  int     i,j,k,m;
              ^
qpgraph.c:8286:5: warning: incompatible pointer types assigning to 'Rboolean *' from 'int *' [-Wincompatible-pointer-types]
  G = LOGICAL(GR);
    ^ ˜˜˜˜˜˜˜˜˜˜˜
5 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-3.5-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘det’ from package ‘Matrix’ in package ‘qpgraph’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qpgraph)

qpgraph.Rcheck/qpgraph-Ex.timings:

nameusersystemelapsed
EcoliOxygen0.0030.0000.003
qpAllCItests0.6240.0080.647
qpAnyGraph0.6510.0410.692
qpAvgNrr2.1250.0062.132
qpBoundary0.4450.0010.446
qpCItest0.2160.0020.218
qpClique0.5290.0020.530
qpCliqueNumber0.5710.0110.581
qpCov0.0880.0020.090
qpEdgeNrr0.1890.0010.190
qpFunctionalCoherence0.0020.0010.002
qpG2Sigma0.0170.0000.018
qpGenNrr0.7130.0040.717
qpGetCliques0.3550.0030.358
qpGraphDensity0.5500.0010.553
qpHTF0.1140.0030.118
qpHist0.3340.0010.336
qpIPF0.1620.0040.165
qpK2ParCor0.0650.0030.067
qpNrr0.2030.0020.204
qpPAC0.4850.0070.492
qpPCC0.1370.0030.140
qpPRscoreThreshold0.1920.0020.194
qpPathWeight0.0670.0000.067
qpPlotMap0.0440.0080.051
qpPlotNetwork0.0010.0000.001
qpPrecisionRecall0.4360.0020.439
qpRndGraph0.0080.0010.008
qpRndWishart0.0100.0010.011
qpTopPairs0.1880.0010.189
qpUnifRndAssociation0.0030.0000.003
qpUpdateCliquesRemoving0.0000.0000.001