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This page was generated on 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 163/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BHC 1.56.0  (landing page)
Rich Savage
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/BHC
git_branch: RELEASE_3_19
git_last_commit: 29dfdc8
git_last_commit_date: 2024-04-30 10:22:12 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  ERROR    ERROR  skippedskipped

BUILD BIN results for BHC on palomino7

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.

raw results


Summary

Package: BHC
Version: 1.56.0
Command: rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=BHC.buildbin-libdir BHC_1.56.0.tar.gz
StartedAt: 2024-10-17 07:23:44 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 07:24:24 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 39.6 seconds
RetCode: 0
Status:   OK  
PackageFile: BHC_1.56.0.zip
PackageFileSize: 508.6 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=BHC.buildbin-libdir BHC_1.56.0.tar.gz
###
##############################################################################
##############################################################################


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

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


** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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
DirichletProcessMixture.cpp:187: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  187 | #pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
      | 
DirichletProcessMixture.cpp:272: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  272 | #pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
      | 
DirichletProcessMixture.cpp:299: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  299 | #pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1)
      | 
DirichletProcessMixture.cpp:375: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  375 | #pragma omp parallel for default(shared) private(j) schedule(dynamic,1)
      | 
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gammaln.cpp -o gammaln.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multinomial_binevidence.cpp -o multinomial_binevidence.o
g++ -std=gnu++17 -shared -s -static-libgcc -o BHC.dll tmp.def 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.19-bioc/meat/BHC.buildbin-libdir/00LOCK-BHC/00new/BHC/libs/x64
** R
** inst
** 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
** 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
* MD5 sums
packaged installation of 'BHC' as BHC_1.56.0.zip
* DONE (BHC)