Multiple platform build/check report for BioC 3.6 - CHECK report for qpgraph on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_2.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/qpgraph.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.12.0’
* 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 ... 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 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 ... 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/qpgraph.Rcheck/00check.log’
for details.

Installation output

* 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-3.6-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-3.6-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-3.6-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:5849:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int i = edges[k, 0];
                    ^
qpgraph.c:5850:20: warning: left-hand operand of comma expression has no effect [-Wunused-value]
     int j = edges[k, 1];
                    ^
qpgraph.c: In function ‘ssd_A’:
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: In function ‘qp_fast_rnd_graph’:
qpgraph.c:8286:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   G = LOGICAL(GR);
     ^
In file included from qpgraph.c:27:0:
qpgraph.c: In function ‘qp_edge_nrr’:
/home/biocbuild/bbs-3.6-bioc/R/include/Rmath.h:302:13: warning: ‘Rf_df’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define pt  Rf_pt
             ^
/home/biocbuild/bbs-3.6-bioc/R/include/Rmath.h:236:13: note: ‘Rf_df’ was declared here
 #define df  Rf_df
             ^
qpgraph.c:5082:16: note: in expansion of macro ‘df’
   int    k, l, df, n_upper_tri;
                ^
qpgraph.c: In function ‘qp_fast_edge_nrr’:
qpgraph.c:5534:12: warning: ‘pcorR’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     return pcorR;
            ^
qpgraph.c: In function ‘qp_ci_test_hmgm.isra.9’:
qpgraph.c:3976:36: warning: ‘rss1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       *partial_eta_squared = (rss1 - rss2) / rss0;
                                    ^
qpgraph.c:3703:11: note: ‘rss1’ was declared here
   double  rss1, rss2;
           ^
gcc -I/home/biocbuild/bbs-3.6-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
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)

Tests output


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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")
Using t tests for zero partial regression coefficients.
Using exact likelihood ratio tests.


RUNIT TEST PROTOCOL -- Thu Apr 12 02:06:24 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 
 13.144   0.160  13.319

Example timings

name	user	system	elapsed
EcoliOxygen	0.000	0.004	0.002
qpAllCItests	0.848	0.012	0.859
qpAnyGraph	0.480	0.012	0.493
qpAvgNrr	1.596	0.000	1.596
qpBoundary	0.272	0.000	0.273
qpCItest	0.548	0.000	0.547
qpClique	0.316	0.000	0.312
qpCliqueNumber	0.916	0.012	0.928
qpCov	0.068	0.004	0.069
qpEdgeNrr	0.136	0.000	0.136
qpFunctionalCoherence	0.004	0.000	0.002
qpG2Sigma	0.008	0.000	0.009
qpGenNrr	0.432	0.000	0.431
qpGetCliques	0.32	0.00	0.32
qpGraphDensity	0.252	0.000	0.255
qpHTF	0.100	0.000	0.101
qpHist	0.160	0.000	0.162
qpIPF	0.132	0.000	0.128
qpK2ParCor	0.048	0.000	0.050
qpNrr	0.112	0.000	0.114
qpPAC	0.212	0.000	0.212
qpPCC	0.564	0.000	0.564
qpPRscoreThreshold	0.116	0.000	0.114
qpPathWeight	0.044	0.000	0.045
qpPlotMap	0.024	0.000	0.024
qpPlotNetwork	0	0	0
qpPrecisionRecall	0.256	0.000	0.256
qpRndGraph	0.008	0.000	0.009
qpRndWishart	0.004	0.000	0.007
qpTopPairs	0.136	0.004	0.143
qpUnifRndAssociation	0.000	0.000	0.003
qpUpdateCliquesRemoving	0.004	0.000	0.001

CHECK report for qpgraph on malbec1

Summary

Command output

Installation output

Tests output

Example timings