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CHECK report for qpgraph on malbec2

This page was generated on 2018-10-17 08:22:37 -0400 (Wed, 17 Oct 2018).

Package 1158/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.14.0
Robert Castelo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/qpgraph
Branch: RELEASE_3_7
Last Commit: 96d71a2
Last Changed Date: 2018-04-30 10:35:10 -0400 (Mon, 30 Apr 2018)
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  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qpgraph
Version: 2.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings qpgraph_2.14.0.tar.gz
StartedAt: 2018-10-16 02:57:44 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 03:01:03 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 198.9 seconds
RetCode: 0
Status:  OK 
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings qpgraph_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/qpgraph.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘2.14.0’
* 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 ... OK
* 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 shell scripts ... 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
Note: information on .o files is not available
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/qpgraph.Rcheck/00check.log’
for details.



Installation output

qpgraph.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL qpgraph
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* 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... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c cliquer.c -o cliquer.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c qpgraph.c -o qpgraph.o
qpgraph.c: In function ‘qp_fast_path_weight’:
qpgraph.c:5851:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int i = edges[k, 0];
                    ^
qpgraph.c:5852:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int j = edges[k, 1];
                    ^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include  -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c reorder.c -o reorder.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
Creating a generic function for ‘det’ from package ‘Matrix’ in package ‘qpgraph’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘eQTLnetworks.Rnw’ 
   ‘qpTxRegNet.Rnw’ 
   ‘qpgraphSimulate.Rnw’ 
** testing if installed package can be loaded
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
* DONE (qpgraph)

Tests output

qpgraph.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("qpgraph")
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.


RUNIT TEST PROTOCOL -- Tue Oct 16 03:00:59 2018 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
qpgraph RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 10.668   0.316  11.009 

Example timings

qpgraph.Rcheck/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.0040.0000.003
qpAllCItests0.2320.0000.230
qpAnyGraph0.0880.0000.086
qpAvgNrr1.2120.0001.210
qpBoundary0.2120.0040.216
qpCItest0.0840.0000.083
qpClique0.2120.0000.211
qpCliqueNumber0.3520.0000.349
qpCov0.0520.0040.056
qpEdgeNrr0.0560.0000.057
qpFunctionalCoherence0.0040.0000.001
qpG2Sigma0.0080.0000.009
qpGenNrr0.3920.0040.395
qpGetCliques0.8760.0000.875
qpGraphDensity0.2000.0000.201
qpHTF0.0680.0000.067
qpHist0.1600.0000.158
qpIPF0.1000.0000.099
qpK2ParCor0.0360.0000.034
qpNrr0.1040.0000.102
qpPAC0.2000.0000.201
qpPCC0.0640.0000.063
qpPRscoreThreshold0.0920.0040.098
qpPathWeight0.0440.0040.048
qpPlotMap0.0200.0080.028
qpPlotNetwork000
qpPrecisionRecall0.1560.0040.160
qpRndGraph0.0120.0000.010
qpRndWishart0.0080.0000.008
qpTopPairs0.0040.0000.002
qpUnifRndAssociation0.0040.0000.003
qpUpdateCliquesRemoving0.0000.0000.001