Package: qpgraph

Version: 2.20.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings qpgraph_2.20.0.tar.gz

StartedAt: 2020-04-15 00:35:12 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:40:07 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 295.1 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings qpgraph_2.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/qpgraph.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.20.0’
* 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-3.10-bioc/meat/qpgraph.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL qpgraph
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘qpgraph’ ...
** using staged installation
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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-qpgraph/00new/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 from temporary location
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
** testing if installed package keeps a record of temporary installation path
* DONE (qpgraph)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 -- Wed Apr 15 00:40:02 2020 
*********************************************** 
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 
 17.636   0.456  18.195 

name	user	system	elapsed
EcoliOxygen	0.000	0.000	0.002
qpAllCItests	0.360	0.020	0.377
qpAnyGraph	0.220	0.004	0.224
qpAvgNrr	1.908	0.000	1.907
qpBoundary	0.264	0.000	0.264
qpCItest	0.144	0.000	0.143
qpClique	0.384	0.000	0.384
qpCliqueNumber	0.584	0.016	0.599
qpCov	0.080	0.000	0.082
qpEdgeNrr	0.076	0.000	0.075
qpFunctionalCoherence	0	0	0
qpG2Sigma	0.012	0.000	0.011
qpGenNrr	0.672	0.000	0.672
qpGetCliques	0.356	0.004	0.360
qpGraphDensity	0.348	0.008	0.355
qpHTF	0.120	0.012	0.132
qpHist	0.280	0.004	0.284
qpIPF	0.192	0.004	0.197
qpK2ParCor	0.100	0.004	0.105
qpNrr	0.160	0.000	0.161
qpPAC	0.196	0.004	0.202
qpPCC	0.08	0.00	0.08
qpPRscoreThreshold	0.092	0.000	0.092
qpPathWeight	0.06	0.00	0.06
qpPlotMap	0.036	0.000	0.040
qpPlotNetwork	0.000	0.000	0.001
qpPrecisionRecall	0.248	0.000	0.250
qpRndGraph	0.044	0.000	0.041
qpRndWishart	0.008	0.000	0.011
qpTopPairs	0.004	0.000	0.004
qpUnifRndAssociation	0.004	0.000	0.004
qpUpdateCliquesRemoving	0	0	0