Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:22:37 -0400 (Wed, 17 Oct 2018).
Package 1158/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
qpgraph 2.14.0 Robert Castelo
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: qpgraph |
Version: 2.14.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings qpgraph_2.14.0.tar.gz |
StartedAt: 2018-10-16 02:57:44 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 03:01:03 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 198.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qpgraph.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:qpgraph.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings qpgraph_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/qpgraph.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘2.14.0’ * 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-3.7-bioc/meat/qpgraph.Rcheck/00check.log’ for details.
qpgraph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL qpgraph ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * 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-3.7-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-3.7-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-3.7-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-3.7-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-3.7-bioc/R/lib -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/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 No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’ * DONE (qpgraph)
qpgraph.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" 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") 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 -- Tue Oct 16 03:00:59 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 10.668 0.316 11.009
qpgraph.Rcheck/qpgraph-Ex.timings
name | user | system | elapsed | |
EcoliOxygen | 0.004 | 0.000 | 0.003 | |
qpAllCItests | 0.232 | 0.000 | 0.230 | |
qpAnyGraph | 0.088 | 0.000 | 0.086 | |
qpAvgNrr | 1.212 | 0.000 | 1.210 | |
qpBoundary | 0.212 | 0.004 | 0.216 | |
qpCItest | 0.084 | 0.000 | 0.083 | |
qpClique | 0.212 | 0.000 | 0.211 | |
qpCliqueNumber | 0.352 | 0.000 | 0.349 | |
qpCov | 0.052 | 0.004 | 0.056 | |
qpEdgeNrr | 0.056 | 0.000 | 0.057 | |
qpFunctionalCoherence | 0.004 | 0.000 | 0.001 | |
qpG2Sigma | 0.008 | 0.000 | 0.009 | |
qpGenNrr | 0.392 | 0.004 | 0.395 | |
qpGetCliques | 0.876 | 0.000 | 0.875 | |
qpGraphDensity | 0.200 | 0.000 | 0.201 | |
qpHTF | 0.068 | 0.000 | 0.067 | |
qpHist | 0.160 | 0.000 | 0.158 | |
qpIPF | 0.100 | 0.000 | 0.099 | |
qpK2ParCor | 0.036 | 0.000 | 0.034 | |
qpNrr | 0.104 | 0.000 | 0.102 | |
qpPAC | 0.200 | 0.000 | 0.201 | |
qpPCC | 0.064 | 0.000 | 0.063 | |
qpPRscoreThreshold | 0.092 | 0.004 | 0.098 | |
qpPathWeight | 0.044 | 0.004 | 0.048 | |
qpPlotMap | 0.020 | 0.008 | 0.028 | |
qpPlotNetwork | 0 | 0 | 0 | |
qpPrecisionRecall | 0.156 | 0.004 | 0.160 | |
qpRndGraph | 0.012 | 0.000 | 0.010 | |
qpRndWishart | 0.008 | 0.000 | 0.008 | |
qpTopPairs | 0.004 | 0.000 | 0.002 | |
qpUnifRndAssociation | 0.004 | 0.000 | 0.003 | |
qpUpdateCliquesRemoving | 0.000 | 0.000 | 0.001 | |