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BioC 3.0: CHECK report for qpgraph on perceval

This page was generated on 2015-04-10 09:54:18 -0700 (Fri, 10 Apr 2015).

Package 701/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.0.5
Robert Castelo
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/qpgraph
Last Changed Rev: 97847 / Revision: 102249
Last Changed Date: 2014-12-22 06:59:43 -0800 (Mon, 22 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: qpgraph
Version: 2.0.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_2.0.5.tar.gz
StartedAt: 2015-04-10 05:13:48 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:22:25 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 516.5 seconds
RetCode: 0
Status:  OK 
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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-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 ‘2.0.5’
* 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 ... [50s/55s] 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 ... [33s/33s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [29s/29s]
 [29s/29s] 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.

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-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-3.0-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)

qpgraph.Rcheck/qpgraph-Ex.timings:

nameusersystemelapsed
EcoliOxygen0.0030.0000.004
qpAllCItests0.2270.0080.237
qpAnyGraph0.2120.0090.221
qpAvgNrr2.3290.0052.334
qpBoundary0.5210.0020.524
qpCItest0.0610.0020.063
qpClique1.3150.0061.321
qpCliqueNumber1.3250.0171.344
qpCov0.1260.0070.132
qpEdgeNrr0.0530.0030.055
qpFunctionalCoherence0.0030.0010.003
qpG2Sigma0.0130.0010.015
qpGenNrr0.8840.0110.904
qpGetCliques0.4000.0040.406
qpGraphDensity0.5140.0020.516
qpHTF0.1640.0050.169
qpHist0.3760.0050.381
qpIPF0.2250.0030.228
qpK2ParCor0.0660.0020.069
qpNrr0.2660.0010.267
qpPAC0.5590.0220.581
qpPCC0.1580.0040.161
qpPRscoreThreshold0.2880.0050.292
qpPlotMap0.0700.0120.091
qpPlotNetwork000
qpPrecisionRecall0.3830.0030.386
qpRndGraph0.0110.0010.012
qpRndWishart0.0090.0010.011
qpTopPairs0.0040.0000.004
qpUnifRndAssociation0.0070.0000.007
qpUpdateCliquesRemoving0.0010.0000.002