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BioC 3.4: CHECK report for qpgraph on zin1

This page was generated on 2016-09-21 03:36:42 -0700 (Wed, 21 Sep 2016).

Package 950/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.7.1
Robert Castelo
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qpgraph
Last Changed Rev: 117556 / Revision: 121152
Last Changed Date: 2016-05-16 17:21:54 -0700 (Mon, 16 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qpgraph
Version: 2.7.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_2.7.1.tar.gz
StartedAt: 2016-09-20 11:00:15 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:03:31 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 195.7 seconds
RetCode: 0
Status:  OK 
CheckDir: qpgraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_2.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/qpgraph.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.7.1’
* 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 ... NOTE
.qpAllCItests: no visible global function definition for ‘median’
.qpCItest: no visible global function definition for ‘pt’
.qpCItestHMGM: no visible global function definition for ‘var’
.qpCItestHMGM: no visible global function definition for ‘pbeta’
.qpCItestHMGM: no visible global function definition for ‘pchisq’
.qpEdgeNrr: no visible global function definition for ‘qt’
.qpEdgeNrrHMGM: no visible global function definition for ‘qbeta’
.qpEdgeNrrHMGM: no visible global function definition for ‘qchisq’
.qpEdgeNrrIdenticalQs: no visible global function definition for ‘qt’
.qpGenNrr : <anonymous>: no visible global function definition for
  ‘median’
.qpNrr: no visible global function definition for ‘phyper’
.qpNrr: no visible global function definition for ‘median’
.qpPAC: no visible global function definition for ‘pchisq’
.qpPCC: no visible global function definition for ‘pt’
.qpRndRegularGraph: no visible global function definition for ‘runif’
.replaceFormulaQs: no visible global function definition for ‘formula’
qpBoundary: no visible global function definition for ‘approxfun’
qpBoundary: no visible global function definition for ‘integrate’
qpClique: no visible global function definition for ‘approxfun’
qpClique: no visible global function definition for ‘integrate’
qpGraphDensity: no visible global function definition for ‘approxfun’
qpGraphDensity: no visible global function definition for ‘integrate’
qpPlotMap: no visible global function definition for ‘p.adjust’
qpRndGraph: no visible global function definition for ‘runif’
qpRndWishart: no visible global function definition for ‘rnorm’
qpRndWishart: no visible global function definition for ‘rchisq’
qpUnifRndAssociation: no visible global function definition for ‘runif’
stat_mis: no visible global function definition for ‘cov’
addGenes,eQTLcross-integer : <anonymous>: no visible global function
  definition for ‘runif’
addeQTL,eQTLcross : <anonymous>: no visible global function definition
  for ‘runif’
eQTLnetworkEstimate,eQTLnetworkEstimationParam-formula-eQTLnetwork: no
  visible binding for global variable ‘p.adjust.methods’
eQTLnetworkEstimate,eQTLnetworkEstimationParam-formula-missing: no
  visible binding for global variable ‘p.adjust.methods’
eQTLnetworkEstimate,eQTLnetworkEstimationParam-missing-eQTLnetwork: no
  visible binding for global variable ‘p.adjust.methods’
eQTLnetworkEstimate,eQTLnetworkEstimationParam-missing-eQTLnetwork: no
  visible global function definition for ‘p.adjust’
reQTLcross,integer-eQTLcrossParam : <anonymous>: no visible global
  function definition for ‘runif’
show,SsdMatrix: no visible binding for global variable ‘df’
Undefined global functions or variables:
  approxfun cov df formula integrate median p.adjust p.adjust.methods
  pbeta pchisq phyper pt qbeta qchisq qt rchisq rnorm runif var
Consider adding
  importFrom("stats", "approxfun", "cov", "df", "formula", "integrate",
             "median", "p.adjust", "p.adjust.methods", "pbeta", "pchisq",
             "phyper", "pt", "qbeta", "qchisq", "qt", "rchisq", "rnorm",
             "runif", "var")
to your NAMESPACE file.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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... 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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-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-3.4-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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’
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
EcoliOxygen0.0040.0000.003
qpAllCItests0.4760.0040.478
qpAnyGraph0.1040.0040.116
qpAvgNrr1.4000.0001.405
qpBoundary0.2400.0000.241
qpCItest0.0200.0000.018
qpClique0.2520.0000.252
qpCliqueNumber0.6000.0040.604
qpCov0.0880.0000.089
qpEdgeNrr0.0200.0000.019
qpFunctionalCoherence0.0000.0000.001
qpG2Sigma0.0080.0000.012
qpGenNrr0.7840.0000.787
qpGetCliques0.3000.0000.302
qpGraphDensity0.2400.0000.239
qpHTF0.080.000.08
qpHist0.1760.0000.178
qpIPF0.1280.0040.131
qpK2ParCor0.0440.0000.043
qpNrr0.1280.0000.125
qpPAC0.3000.0000.302
qpPCC0.0840.0000.087
qpPRscoreThreshold0.1240.0000.126
qpPathWeight0.0080.0000.010
qpPlotMap0.0360.0000.034
qpPlotNetwork000
qpPrecisionRecall0.1800.0000.184
qpRndGraph0.0120.0000.011
qpRndWishart0.0080.0000.009
qpTopPairs0.0040.0000.002
qpUnifRndAssociation0.0040.0000.004
qpUpdateCliquesRemoving0.0000.0000.001