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BioC 2.14: CHECK report for qpgraph on morelia

This page was generated on 2014-10-08 09:03:49 -0700 (Wed, 08 Oct 2014).

Package 617/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 1.20.2
Robert Castelo
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/qpgraph
Last Changed Rev: 93135 / Revision: 95116
Last Changed Date: 2014-08-01 20:41:40 -0700 (Fri, 01 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: qpgraph
Version: 1.20.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_1.20.2.tar.gz
StartedAt: 2014-10-08 00:54:56 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:59:13 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 256.9 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 --no-multiarch qpgraph_1.20.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/qpgraph.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘1.20.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rlecuyer’
* 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 ... [26s/28s] 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
Unexported object imported by a ':::' call: ‘Matrix:::prMatrix’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 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 ... [19s/19s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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();
    ^
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:4241:17: warning: unused variable 'j' [-Wunused-variable]
  int         i,j,k;
                ^
qpgraph.c:4241:19: warning: unused variable 'k' [-Wunused-variable]
  int         i,j,k;
                  ^
qpgraph.c:4241:15: warning: unused variable 'i' [-Wunused-variable]
  int         i,j,k;
              ^
qpgraph.c:4283:15: warning: unused variable 'Y_j' [-Wunused-variable]
  int*        Y_j = NULL;
              ^
qpgraph.c:7969:15: warning: unused variable 'k' [-Wunused-variable]
  int     i,j,k,m;
              ^
qpgraph.c:7969:17: warning: unused variable 'm' [-Wunused-variable]
  int     i,j,k,m;
                ^
qpgraph.c:8098:5: 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/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-2.14-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)

qpgraph.Rcheck/qpgraph-Ex.timings:

nameusersystemelapsed
EcoliOxygen0.0030.0000.004
qpAllCItests0.2040.0060.211
qpAnyGraph0.1400.0030.143
qpAvgNrr2.2110.0062.222
qpBoundary0.5230.0030.527
qpCItest0.0380.0010.039
qpClique0.5400.0040.545
qpCliqueNumber0.2150.0100.224
qpCov0.0990.0030.102
qpEdgeNrr0.0310.0010.033
qpFunctionalCoherence0.0020.0010.002
qpG2Sigma0.0160.0000.016
qpGenNrr1.1230.0031.128
qpGetCliques0.3030.0040.308
qpGraph0.3070.0060.313
qpGraphDensity0.4890.0020.490
qpHTF0.1240.0040.127
qpHist0.3270.0030.330
qpIPF0.1700.0050.175
qpK2ParCor0.0460.0010.048
qpNrr0.2830.0010.284
qpPAC0.6520.0110.664
qpPCC0.1180.0040.122
qpPRscoreThreshold0.2480.0020.250
qpPlotMap0.2840.0060.290
qpPlotNetwork0.1410.0040.183
qpPrecisionRecall0.3510.0020.354
qpRndGraph0.0100.0000.011
qpRndWishart0.0140.0010.015
qpTopPairs0.0040.0010.005
qpUnifRndAssociation0.0060.0010.007
qpUpdateCliquesRemoving0.0010.0000.002