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This page was generated on 2023-01-02 09:00:51 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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BUILD results for SIMLR on palomino5


To the developers/maintainers of the SIMLR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1863/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.25.0  (landing page)
Luca De Sano
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/SIMLR
git_branch: master
git_last_commit: 4b1f409
git_last_commit_date: 2022-11-01 11:14:30 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped

Summary

Package: SIMLR
Version: 1.25.0
Command: chmod a+r SIMLR -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SIMLR
StartedAt: 2022-12-28 20:38:49 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 20:39:06 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 17.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r SIMLR -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SIMLR
###
##############################################################################
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* checking for file 'SIMLR/DESCRIPTION' ... OK
* preparing 'SIMLR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'SIMLR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-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++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rtsne.cpp -o Rtsne.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c package_init.c -o package_init.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c projsplx_R.c -o projsplx_R.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sptree.cpp -o sptree.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tsne.cpp -o tsne.o
tsne.cpp: In member function 'void TSNE::computeSquaredEuclideanDistance(double*, int, int, double*)':
tsne.cpp:883:11: error: too few arguments to function 'void dgemm_(const char*, const char*, const int*, const int*, const int*, const double*, const double*, const int*, const double*, const int*, const double*, double*, const int*, size_t, size_t)'
  883 |     dgemm_("T", "N", &N, &N, &D, &a1, X, &D, X, &D, &a2, DD, &N);
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.17-bioc/R/include/R.h:78,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from tsne.cpp:39:
F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      |          ^~~~~
F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro 'F77_CALL'
   77 | # define F77_CALL(x)    x ## _
      |                         ^
F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro 'F77_NAME'
  207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
      | ^~~~~~~~
tsne.cpp: In member function 'bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)':
tsne.cpp:967:48: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  967 |   if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
In file included from tsne.cpp:41:
vptree.h: In instantiation of 'void VpTree<T, distance>::search(Node*, const T&, int, std::priority_queue<HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance; typename std::vector<HeapItem, std::allocator<HeapItem> >::value_type = VpTree<DataPoint, precomputed_distance>::HeapItem]':
vptree.h:131:15:   required from 'void VpTree<T, distance>::search(const T&, int, std::vector<T>*, std::vector<double>*) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance]'
tsne.cpp:472:21:   required from here
vptree.h:237:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, precomputed_distance>::HeapItem, std::vector<VpTree<DataPoint, precomputed_distance>::HeapItem, std::allocator<VpTree<DataPoint, precomputed_distance>::HeapItem> >, std::less<VpTree<DataPoint, precomputed_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  237 |             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
      |                ~~~~~~~~~~~~^~~~
vptree.h:239:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, precomputed_distance>::HeapItem, std::vector<VpTree<DataPoint, precomputed_distance>::HeapItem, std::allocator<VpTree<DataPoint, precomputed_distance>::HeapItem> >, std::less<VpTree<DataPoint, precomputed_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  239 |             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
      |                ~~~~~~~~~~~~^~~~
vptree.h: In instantiation of 'void VpTree<T, distance>::search(Node*, const T&, int, std::priority_queue<HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance; typename std::vector<HeapItem, std::allocator<HeapItem> >::value_type = VpTree<DataPoint, euclidean_distance>::HeapItem]':
vptree.h:131:15:   required from 'void VpTree<T, distance>::search(const T&, int, std::vector<T>*, std::vector<double>*) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance]'
tsne.cpp:550:21:   required from here
vptree.h:237:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, euclidean_distance>::HeapItem, std::vector<VpTree<DataPoint, euclidean_distance>::HeapItem, std::allocator<VpTree<DataPoint, euclidean_distance>::HeapItem> >, std::less<VpTree<DataPoint, euclidean_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  237 |             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
      |                ~~~~~~~~~~~~^~~~
vptree.h:239:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue<VpTree<DataPoint, euclidean_distance>::HeapItem, std::vector<VpTree<DataPoint, euclidean_distance>::HeapItem, std::allocator<VpTree<DataPoint, euclidean_distance>::HeapItem> >, std::less<VpTree<DataPoint, euclidean_distance>::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  239 |             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
      |                ~~~~~~~~~~~~^~~~
make: *** [F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf:264: tsne.o] Error 1
ERROR: compilation failed for package 'SIMLR'
* removing 'F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpaavDRb/Rinst3e7c6a6424a4/SIMLR'
      -----------------------------------
ERROR: package installation failed