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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1533/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plier 1.75.0  (landing page)
Crispin Miller
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/plier
git_branch: devel
git_last_commit: ccc26f1
git_last_commit_date: 2024-04-30 10:13:33 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


BUILD BIN results for plier on palomino4

To the developers/maintainers of the plier package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plier.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: plier
Version: 1.75.0
Command: rm -rf plier.buildbin-libdir && mkdir plier.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=plier.buildbin-libdir plier_1.75.0.tar.gz
StartedAt: 2024-06-10 14:36:01 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 14:37:21 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 79.6 seconds
RetCode: 0
Status:   OK  
PackageFile: plier_1.75.0.zip
PackageFileSize: 99.17 KiB

Command output

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### Running command:
###
###   rm -rf plier.buildbin-libdir && mkdir plier.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=plier.buildbin-libdir plier_1.75.0.tar.gz
###
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* installing *source* package 'plier' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c affyplier.cpp -o affyplier.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c plier_impl.cpp -o plier_impl.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:905:21: warning: variable 'icount' set but not used [-Wunused-but-set-variable]
  905 |         long count, icount;
      |                     ^~~~~~
plieralg.cpp: At global scope:
plieralg.cpp:49:12: warning: 'g_ErrorCode' defined but not used [-Wunused-variable]
   49 | static int g_ErrorCode=NoError;
      |            ^~~~~~~~~~~
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:1257:31: warning: 'LogLikelihood' may be used uninitialized [-Wmaybe-uninitialized]
 1257 |         output = LogLikelihood/nSize;
      |                  ~~~~~~~~~~~~~^~~~~~
plieralg.cpp:910:16: note: 'LogLikelihood' was declared here
  910 |         double LogLikelihood;
      |                ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp: In function 'void one_probeset(bool*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, bool*, bool*, bool*, double*, double*, int*, int*, int*, long int*, double*, double*, double*, double*, int*)':
rwrapper.cpp:192:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  192 |     delete pm_ptr;
      |            ^~~~~~
rwrapper.cpp:151:44: note: returned from 'void* operator new [](std::size_t)'
  151 |     double **pm_ptr = new double *[*num_exp];
      |                                            ^
rwrapper.cpp:193:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  193 |     delete mm_ptr;
      |            ^~~~~~
rwrapper.cpp:152:44: note: returned from 'void* operator new [](std::size_t)'
  152 |     double **mm_ptr = new double *[*num_exp];
      |                                            ^
rwrapper.cpp:194:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  194 |     delete rpct;
      |            ^~~~
rwrapper.cpp:159:39: note: returned from 'void* operator new [](std::size_t)'
  159 |     long    *rpct = new long [*num_exp]; /* the API expects a long array that it wants to delete itself (replicate). We have an int array that R owns so we need to create the long one here, but let the API handle the clean up. Which is nice. */
      |                                       ^
g++ -std=gnu++17 -shared -s -static-libgcc -o plier.dll tmp.def affyplier.o plier_impl.o plieralg.o rwrapper.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/meat/plier.buildbin-libdir/00LOCK-plier/00new/plier/libs/x64
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'plier' as plier_1.75.0.zip
* DONE (plier)