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CHECK report for qpgraph on tokay2

This page was generated on 2019-10-16 12:22:20 -0400 (Wed, 16 Oct 2019).

Package 1286/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qpgraph 2.18.0
Robert Castelo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/qpgraph
Branch: RELEASE_3_9
Last Commit: db07b68
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qpgraph
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qpgraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qpgraph_2.18.0.tar.gz
StartedAt: 2019-10-16 06:15:41 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:21:52 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 370.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: qpgraph.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qpgraph.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qpgraph_2.18.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/qpgraph.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qpgraph/DESCRIPTION' ... OK
* this is package 'qpgraph' version '2.18.0'
* 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 whether package 'qpgraph' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/HMgmm-class.Rd:65: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/SsdMatrix-class.Rd:14: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/SsdMatrix-class.Rd:27: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/UGgmm-class.Rd:56: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/qpG2Sigma.Rd:51: file link 'rmvnorm' in package 'mvtnorm' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/qpK2ParCor.Rd:17: file link 'cov2cor' in package 'stats' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/qpgraph.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qpgraph/libs/i386/qpgraph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qpgraph/libs/x64/qpgraph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/qpgraph.Rcheck/00check.log'
for details.



Installation output

qpgraph.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/qpgraph_2.18.0.tar.gz && rm -rf qpgraph.buildbin-libdir && mkdir qpgraph.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qpgraph.buildbin-libdir qpgraph_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL qpgraph_2.18.0.zip && rm qpgraph_2.18.0.tar.gz qpgraph_2.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1855k  100 1855k    0     0  16.8M      0 --:--:-- --:--:-- --:--:-- 17.9M

install for i386

* installing *source* package 'qpgraph' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c cliquer.c -o cliquer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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];
                    ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/qpgraph.buildbin-libdir/00LOCK-qpgraph/00new/qpgraph/libs/i386
** 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
  converting help for package 'qpgraph'
    finding HTML links ... done
    EcoliOxygen                             html  
    HMgmm-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/HMgmm-class.Rd:65: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
    SsdMatrix-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/SsdMatrix-class.Rd:14: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/SsdMatrix-class.Rd:27: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
    UGgmm-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/UGgmm-class.Rd:56: file link 'dspMatrix-class' in package 'Matrix' does not exist and so has been treated as a topic
    eQTLcross-class                         html  
    eQTLnetwork-class                       html  
    eQTLnetworkEstimate                     html  
    eQTLnetworkEstimationParam-class        html  
    graphParam-class                        html  
    qpAllCItests                            html  
    qpAnyGraph                              html  
    qpAvgNrr                                html  
    qpBoundary                              html  
    qpCItest                                html  
    qpClique                                html  
    qpCliqueNumber                          html  
    qpCov                                   html  
    qpEdgeNrr                               html  
    qpFunctionalCoherence                   html  
    qpG2Sigma                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/qpG2Sigma.Rd:51: file link 'rmvnorm' in package 'mvtnorm' does not exist and so has been treated as a topic
    qpGenNrr                                html  
    qpGetCliques                            html  
    qpGraph-class                           html  
    qpGraphDensity                          html  
    qpHTF                                   html  
    qpHist                                  html  
    qpIPF                                   html  
    qpImportNrr                             html  
    qpK2ParCor                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMvE68s/R.INSTALL22e47e0d4f50/qpgraph/man/qpK2ParCor.Rd:17: file link 'cov2cor' in package 'stats' does not exist and so has been treated as a topic
    qpNrr                                   html  
    qpPAC                                   html  
    qpPCC                                   html  
    qpPRscoreThreshold                      html  
    qpPathWeight                            html  
    qpPlotMap                               html  
    qpPlotNetwork                           html  
    qpPrecisionRecall                       html  
    qpRndGraph                              html  
    qpRndWishart                            html  
    qpTopPairs                              html  
    qpUnifRndAssociation                    html  
    qpUpdateCliquesRemoving                 html  
    qpgraph-package                         html  
** 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'
** 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

install for x64

* installing *source* package 'qpgraph' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cliquer.c -o cliquer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c graph.c -o graph.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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];
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c reorder.c -o reorder.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o qpgraph.dll tmp.def cliquer.o graph.o qpgraph.o reorder.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/qpgraph.buildbin-libdir/qpgraph/libs/x64
** testing if installed package can be loaded
No methods found in package 'GenomicRanges' for request: 'c' when loading 'qpgraph'
* MD5 sums
packaged installation of 'qpgraph' as qpgraph_2.18.0.zip
* DONE (qpgraph)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'qpgraph' successfully unpacked and MD5 sums checked

Tests output

qpgraph.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 Oct 16 06:21:25 2019 
*********************************************** 
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 
  12.59    0.75   13.35 

qpgraph.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 Oct 16 06:21:39 2019 
*********************************************** 
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 
  12.90    0.34   13.50 

Example timings

qpgraph.Rcheck/examples_i386/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.010.000.01
qpAllCItests0.400.010.41
qpAnyGraph0.730.020.75
qpAvgNrr1.560.001.56
qpBoundary0.330.000.33
qpCItest0.060.060.12
qpClique0.250.030.29
qpCliqueNumber0.280.030.31
qpCov0.070.000.06
qpEdgeNrr0.040.000.05
qpFunctionalCoherence000
qpG2Sigma0.020.000.01
qpGenNrr0.470.000.47
qpGetCliques0.250.020.27
qpGraphDensity0.230.000.23
qpHTF0.050.030.08
qpHist0.220.020.23
qpIPF0.120.000.13
qpK2ParCor0.070.000.06
qpNrr0.170.000.17
qpPAC0.260.000.27
qpPCC0.070.000.06
qpPRscoreThreshold0.100.010.13
qpPathWeight0.040.020.04
qpPlotMap0.620.000.63
qpPlotNetwork000
qpPrecisionRecall0.330.000.33
qpRndGraph000
qpRndWishart000
qpTopPairs000
qpUnifRndAssociation000
qpUpdateCliquesRemoving000

qpgraph.Rcheck/examples_x64/qpgraph-Ex.timings

nameusersystemelapsed
EcoliOxygen0.000.020.02
qpAllCItests0.410.000.40
qpAnyGraph0.110.000.11
qpAvgNrr1.660.001.65
qpBoundary0.200.000.21
qpCItest0.090.000.10
qpClique101
qpCliqueNumber0.290.000.28
qpCov0.060.020.08
qpEdgeNrr0.060.000.06
qpFunctionalCoherence000
qpG2Sigma0.020.000.01
qpGenNrr0.360.000.36
qpGetCliques0.290.010.32
qpGraphDensity0.190.000.18
qpHTF0.080.000.08
qpHist0.150.000.16
qpIPF0.110.000.11
qpK2ParCor0.020.020.03
qpNrr0.070.000.08
qpPAC0.240.000.24
qpPCC0.080.020.09
qpPRscoreThreshold0.070.000.08
qpPathWeight0.070.000.06
qpPlotMap0.030.010.05
qpPlotNetwork000
qpPrecisionRecall0.140.000.14
qpRndGraph000
qpRndWishart0.010.000.01
qpTopPairs000
qpUnifRndAssociation000
qpUpdateCliquesRemoving000