Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:25 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE BHC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 141/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BHC 1.40.0 Rich Savage
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: BHC |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BHC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BHC_1.40.0.tar.gz |
StartedAt: 2020-10-16 23:11:16 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 23:11:36 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 19.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BHC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BHC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BHC_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/BHC.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BHC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BHC’ version ‘1.40.0’ * 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 ‘BHC’ 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 ... NOTE FindOptimalHyperparameter: no visible global function definition for ‘optimise’ WriteOutClusterLabels : WhereToCut: no visible global function definition for ‘is.leaf’ WriteOutClusterLabels: no visible global function definition for ‘dendrapply’ WriteOutClusterLabels: no visible global function definition for ‘write.table’ Undefined global functions or variables: dendrapply is.leaf optimise write.table Consider adding importFrom("stats", "dendrapply", "is.leaf", "optimise") importFrom("utils", "write.table") 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 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 ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.11-bioc/R/library/BHC/libs/BHC.so’: Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Found ‘rand’, possibly from ‘rand’ (C) Found ‘srand’, possibly from ‘srand’ (C) 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 files in ‘vignettes’ ... OK * checking examples ... 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.11-bioc/meat/BHC.Rcheck/00check.log’ for details.
BHC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BHC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘BHC’ ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 ISO C89... none needed checking for gcc option to support OpenMP... -fopenmp checking whether OpenMP will work in this package... yes configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o In file included from BlockCovarianceMatrix.h:16:0, from BlockCovarianceMatrix.cpp:15: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o In file included from DataSet.h:16:0, from TimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.cpp:15: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c DataSet.cpp -o DataSet.o In file included from DataSet.h:16:0, from DataSet.cpp:13: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o In file included from DirichletProcessMixture.h:4:0, from DirichletProcessMixture.cpp:15: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c MultinomialDataSet.cpp -o MultinomialDataSet.o In file included from DataSet.h:16:0, from MultinomialDataSet.h:4, from MultinomialDataSet.cpp:1: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c Node.cpp -o Node.o In file included from Node.h:16:0, from Node.cpp:13: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o In file included from DataSet.h:16:0, from TimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.h:20, from RobustCubicSplineTimecourseDataSet.h:20, from RobustCubicSplineTimecourseDataSet.cpp:15: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o In file included from SquaredExponentialTimecourseDataSet.h:20:0, from RobustSquaredExponentialTimecourseDataSet.h:20, from RobustSquaredExponentialTimecourseDataSet.cpp:15: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o In file included from SquaredExponentialTimecourseDataSet.h:20:0, from SquaredExponentialTimecourseDataSet.cpp:15: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition SquaredExponentialTimecourseDataSet.cpp: In member function ‘void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector<double>, double&, double&, double&, double)’: SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable ‘gridLogEvidence’ set but not used [-Wunused-but-set-variable] double currentLogEvidence, gridLogEvidence, ^~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c TimecourseDataSet.cpp -o TimecourseDataSet.o In file included from DataSet.h:16:0, from TimecourseDataSet.h:20, from TimecourseDataSet.cpp:13: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c bhc.cpp -o bhc.o In file included from bhc.cpp:17:0: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c gammaln.cpp -o gammaln.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c header.cpp -o header.o In file included from header.cpp:1:0: header.h:16:0: warning: "NDEBUG" redefined #define NDEBUG <command-line>:0:0: note: this is the location of the previous definition g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_binevidence.cpp -o multinomial_binevidence.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o BHC.so BlockCovarianceMatrix.o CubicSplineTimecourseDataSet.o DataSet.o DirichletProcessMixture.o MultinomialDataSet.o Node.o RobustCubicSplineTimecourseDataSet.o RobustSquaredExponentialTimecourseDataSet.o SquaredExponentialTimecourseDataSet.o TimecourseDataSet.o bhc.o gammaln.o header.o multinomial_CalculateHyperparameters.o multinomial_OutputDendrogramInformation.o multinomial_ReadInData.o multinomial_bayeslink_binf.o multinomial_binevidence.o -fopenmp -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-BHC/00new/BHC/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BHC)
BHC.Rcheck/BHC-Ex.timings
name | user | system | elapsed | |
BHC | 2.881 | 0.024 | 1.031 | |