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This page was generated on 2023-04-12 11:05:27 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

BUILD BIN results for CellaRepertorium on palomino4


To the developers/maintainers of the CellaRepertorium package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellaRepertorium.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 272/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellaRepertorium 1.8.0  (landing page)
Andrew McDavid
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/CellaRepertorium
git_branch: RELEASE_3_16
git_last_commit: 5346a3b
git_last_commit_date: 2022-11-01 11:23:20 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CellaRepertorium
Version: 1.8.0
Command: rm -rf CellaRepertorium.buildbin-libdir && mkdir CellaRepertorium.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=CellaRepertorium.buildbin-libdir CellaRepertorium_1.8.0.tar.gz
StartedAt: 2023-04-11 07:42:02 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 07:43:08 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 65.3 seconds
RetCode: 0
Status:   OK  
PackageFile: CellaRepertorium_1.8.0.zip
PackageFileSize: 4.047 MiB

Command output

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### Running command:
###
###   rm -rf CellaRepertorium.buildbin-libdir && mkdir CellaRepertorium.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=CellaRepertorium.buildbin-libdir CellaRepertorium_1.8.0.tar.gz
###
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* installing *source* package 'CellaRepertorium' ...
** using staged installation
** libs
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
  494 |   if( band > options.band_width ) band = options.band_width;
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  160 |   #pragma omp critical
      | 
cdhit-common.cpp:174: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  174 |  #pragma omp critical
      | 
cdhit-common.cpp:2418: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
 2418 |    #pragma omp parallel for schedule( dynamic, 1 )
      | 
cdhit-common.cpp:2435: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
 2435 |    #pragma omp parallel for schedule( dynamic, 1 )
      | 
cdhit-common.cpp:2437: warning: ignoring '#pragma omp flush' [-Wunknown-pragmas]
 2437 |     #pragma omp flush (stop)
      | 
cdhit-common.cpp:2458: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
 2458 |        #pragma omp critical
      | 
cdhit-common.cpp:2467: warning: ignoring '#pragma omp flush' [-Wunknown-pragmas]
 2467 |        #pragma omp flush (stop)
      | 
cdhit-common.cpp:2492: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
 2492 |     #pragma omp parallel for schedule( dynamic, 1 )
      | 
cdhit-common.cpp:3151: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
 3151 |    #pragma omp parallel for schedule( dynamic, 1 )
      | 
In file included from cdhit-common.cpp:37:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
  494 |   if( band > options.band_width ) band = options.band_width;
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:545:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
  545 |  int max_diag = 0;
      |      ^~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:669:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
  669 |  int max_diag = 0;
      |      ^~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)':
cdhit-common.cpp:1774:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
 1774 |   if (len > max_len) max_len = len;
      |       ~~~~^~~~~~~~~
cdhit-common.cpp:1775:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
 1775 |   if (len < min_len) min_len = len;
      |       ~~~~^~~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)':
cdhit-common.cpp:2379:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable]
 2379 |  size_t mem, mega = 1000000;
      |         ^~~
In file included from cdhit-common.cpp:37:
In member function 'void NVector<TYPE>::Resize(int, const TYPE&) [with TYPE = long long int]',
    inlined from 'NVector<TYPE>::NVector(int, const TYPE&) [with TYPE = long long int]' at cdhit-common.h:124:10,
    inlined from 'int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)' at cdhit-common.cpp:802:36:
cdhit-common.h:149:27: warning: argument 1 range [18446744056529682448, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  149 |     items = (TYPE*)realloc( items, capacity*sizeof(TYPE) );
      |                    ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdhit-common.h: In function 'int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)':
cdhit-common.h:149:27: note: in a call to built-in allocation function 'void* __builtin_malloc(long long unsigned int)'
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
  494 |   if( band > options.band_width ) band = options.band_width;
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
  494 |   if( band > options.band_width ) band = options.band_width;
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progress.cpp -o progress.o
g++ -std=gnu++14 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/CellaRepertorium.buildbin-libdir/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 'CellaRepertorium' as CellaRepertorium_1.8.0.zip
* DONE (CellaRepertorium)