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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:21 -0400 (Wed, 16 Oct 2019).
| Package 1286/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qpgraph 2.18.0 Robert Castelo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: qpgraph |
| Version: 2.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qpgraph_2.18.0.tar.gz |
| StartedAt: 2019-10-16 05:52:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:59:44 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 411.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qpgraph.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qpgraph_2.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qpgraph.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * 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 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 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/qpgraph.Rcheck/00check.log’ for details.
qpgraph.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qpgraph
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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... i686-apple-darwin15.6.0
checking host system type... i686-apple-darwin15.6.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2 -Wall -pedantic -fPIC -Wall -g -O2 -c cliquer.c -o cliquer.o
cliquer.c:229:5: warning: implicit declaration of function 'R_ProcessEvents' is invalid in C99 [-Wimplicit-function-declaration]
R_ProcessEvents();
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2 -Wall -pedantic -fPIC -Wall -g -O2 -c graph.c -o graph.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2 -Wall -pedantic -fPIC -Wall -g -O2 -c qpgraph.c -o qpgraph.o
qpgraph.c:5851:19: warning: expression result unused [-Wunused-value]
int i = edges[k, 0];
^
qpgraph.c:5852:19: warning: expression result unused [-Wunused-value]
int j = edges[k, 1];
^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Wall -g -O2 -Wall -pedantic -fPIC -Wall -g -O2 -c reorder.c -o reorder.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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)
qpgraph.Rcheck/tests/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-apple-darwin15.6.0 (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 05:59:33 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
21.737 1.360 23.766
qpgraph.Rcheck/qpgraph-Ex.timings
| name | user | system | elapsed | |
| EcoliOxygen | 0.004 | 0.003 | 0.006 | |
| qpAllCItests | 1.309 | 0.021 | 1.334 | |
| qpAnyGraph | 0.181 | 0.015 | 0.197 | |
| qpAvgNrr | 2.051 | 0.025 | 2.078 | |
| qpBoundary | 0.647 | 0.022 | 0.670 | |
| qpCItest | 0.238 | 0.039 | 0.276 | |
| qpClique | 1.355 | 0.020 | 1.377 | |
| qpCliqueNumber | 0.469 | 0.029 | 0.499 | |
| qpCov | 0.111 | 0.004 | 0.115 | |
| qpEdgeNrr | 0.141 | 0.002 | 0.145 | |
| qpFunctionalCoherence | 0.001 | 0.001 | 0.002 | |
| qpG2Sigma | 0.019 | 0.001 | 0.020 | |
| qpGenNrr | 0.997 | 0.010 | 1.007 | |
| qpGetCliques | 0.375 | 0.017 | 0.392 | |
| qpGraphDensity | 0.527 | 0.007 | 0.533 | |
| qpHTF | 0.162 | 0.012 | 0.175 | |
| qpHist | 0.424 | 0.021 | 0.446 | |
| qpIPF | 0.238 | 0.020 | 0.259 | |
| qpK2ParCor | 0.099 | 0.012 | 0.112 | |
| qpNrr | 0.316 | 0.006 | 0.321 | |
| qpPAC | 0.679 | 0.028 | 0.707 | |
| qpPCC | 0.160 | 0.006 | 0.166 | |
| qpPRscoreThreshold | 0.226 | 0.002 | 0.227 | |
| qpPathWeight | 0.093 | 0.001 | 0.095 | |
| qpPlotMap | 0.045 | 0.015 | 0.061 | |
| qpPlotNetwork | 0.001 | 0.001 | 0.000 | |
| qpPrecisionRecall | 0.360 | 0.007 | 0.366 | |
| qpRndGraph | 0.013 | 0.001 | 0.014 | |
| qpRndWishart | 0.014 | 0.002 | 0.017 | |
| qpTopPairs | 0.005 | 0.001 | 0.005 | |
| qpUnifRndAssociation | 0.005 | 0.001 | 0.007 | |
| qpUpdateCliquesRemoving | 0.001 | 0.000 | 0.000 | |