Rich Savage
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BHC |
| git_branch: devel |
| git_last_commit: 90a9789 |
| git_last_commit_date: 2024-01-11 09:10:55 -0400 (Thu, 11 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:13 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 162/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rich Savage
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BHC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BHC.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BHC |
| Version: 1.55.1 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BHC |
| StartedAt: 2024-03-27 15:30:32 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 15:30:56 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 24.3 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BHC
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from BlockCovarianceMatrix.cpp:15:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from DataSet.cpp:13:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from DirichletProcessMixture.cpp:15:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from MultinomialDataSet.h:4,
from MultinomialDataSet.cpp:1:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from Node.cpp:13:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from RobustSquaredExponentialTimecourseDataSet.h:20,
from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: 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]
339 | double currentLogEvidence, gridLogEvidence,
| ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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,
from TimecourseDataSet.h:20,
from TimecourseDataSet.cpp:13:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c gammaln.cpp -o gammaln.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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:
header.h:16: warning: "NDEBUG" redefined
16 | #define NDEBUG
|
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-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++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -fopenmp -I/usr/local/include -fpic -g -O2 -Wall -c multinomial_binevidence.cpp -o multinomial_binevidence.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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
Warning in fun(libname, pkgname) :
Package 'BHC' is deprecated and will be removed from Bioconductor
version 3.20
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
Package 'BHC' is deprecated and will be removed from Bioconductor
version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (BHC)