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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SIMLR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SIMLR_1.32.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SIMLR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SIMLR/DESCRIPTION' ... OK
* this is package 'SIMLR' version '1.32.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SIMLR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/SIMLR/libs/x64/SIMLR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             76.23   6.25   82.50
SIMLR                             21.22   4.01   28.19
SIMLR_Estimate_Number_of_Clusters  3.02   0.41    6.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/SIMLR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SIMLR
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'SIMLR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rtsne.cpp -o Rtsne.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c package_init.c -o package_init.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c projsplx_R.c -o projsplx_R.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sptree.cpp -o sptree.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tsne.cpp -o tsne.o
tsne.cpp: In member function 'bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)':
tsne.cpp:979:48: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  979 |   if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
In file included from tsne.cpp:43:
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:484:21:   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:562:21:   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)
      |                ~~~~~~~~~~~~^~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o SIMLR.dll tmp.def RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/R/library/00LOCK-SIMLR/00new/SIMLR/libs/x64
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SIMLR)

R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("SIMLR")
> 
> test_check("SIMLR")
Computing the multiple Kernels.
Performing network diffiusion.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Iteration:  6 
Iteration:  7 
Iteration:  8 
Iteration:  9 
Iteration:  10 
Iteration:  11 
Performing t-SNE.
Epoch: Iteration # 100  error is:  0.1113014 
Epoch: Iteration # 200  error is:  0.05998534 
Epoch: Iteration # 300  error is:  0.05920885 
Epoch: Iteration # 400  error is:  0.05904812 
Epoch: Iteration # 500  error is:  0.05890865 
Epoch: Iteration # 600  error is:  0.05879012 
Epoch: Iteration # 700  error is:  0.05868304 
Epoch: Iteration # 800  error is:  0.05858721 
Epoch: Iteration # 900  error is:  0.05850376 
Epoch: Iteration # 1000  error is:  0.05842733 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.95079 
Epoch: Iteration # 200  error is:  0.7359983 
Epoch: Iteration # 300  error is:  0.6853336 
Epoch: Iteration # 400  error is:  0.5509423 
Epoch: Iteration # 500  error is:  0.4786262 
Epoch: Iteration # 600  error is:  0.538848 
Epoch: Iteration # 700  error is:  1.000587 
Epoch: Iteration # 800  error is:  0.3728656 
Epoch: Iteration # 900  error is:  0.2922579 
Epoch: Iteration # 1000  error is:  0.2763716 
Computing the multiple Kernels.
Performing network diffiusion.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Iteration:  6 
Iteration:  7 
Iteration:  8 
Iteration:  9 
Iteration:  10 
Iteration:  11 
Iteration:  12 
Iteration:  13 
Iteration:  14 
Iteration:  15 
Iteration:  16 
Iteration:  17 
Performing t-SNE.
Epoch: Iteration # 100  error is:  0.08108063 
Epoch: Iteration # 200  error is:  0.07477886 
Epoch: Iteration # 300  error is:  0.0681391 
Epoch: Iteration # 400  error is:  0.06595909 
Epoch: Iteration # 500  error is:  0.06572884 
Epoch: Iteration # 600  error is:  0.06554725 
Epoch: Iteration # 700  error is:  0.06539913 
Epoch: Iteration # 800  error is:  0.06527713 
Epoch: Iteration # 900  error is:  0.06517343 
Epoch: Iteration # 1000  error is:  0.06508542 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  12.01355 
Epoch: Iteration # 200  error is:  1.328447 
Epoch: Iteration # 300  error is:  0.5861971 
Epoch: Iteration # 400  error is:  0.5028052 
Epoch: Iteration # 500  error is:  0.3515077 
Epoch: Iteration # 600  error is:  0.2174782 
Epoch: Iteration # 700  error is:  0.2068553 
Epoch: Iteration # 800  error is:  0.1451337 
Epoch: Iteration # 900  error is:  0.1443683 
Epoch: Iteration # 1000  error is:  0.1437203 
Computing the multiple Kernels.
Performing network diffiusion.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Iteration:  6 
Iteration:  7 
Iteration:  8 
Iteration:  9 
Iteration:  10 
Iteration:  11 
Performing t-SNE.
Epoch: Iteration # 100  error is:  0.1207343 
Epoch: Iteration # 200  error is:  0.07172118 
Epoch: Iteration # 300  error is:  0.06071198 
Epoch: Iteration # 400  error is:  0.06057342 
Epoch: Iteration # 500  error is:  0.06044155 
Epoch: Iteration # 600  error is:  0.06033219 
Epoch: Iteration # 700  error is:  0.06023583 
Epoch: Iteration # 800  error is:  0.06014798 
Epoch: Iteration # 900  error is:  0.06006964 
Epoch: Iteration # 1000  error is:  0.05999928 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.46835 
Epoch: Iteration # 200  error is:  1.087565 
Epoch: Iteration # 300  error is:  0.7984759 
Epoch: Iteration # 400  error is:  0.4699688 
Epoch: Iteration # 500  error is:  0.4493796 
Epoch: Iteration # 600  error is:  0.3127752 
Epoch: Iteration # 700  error is:  0.2979372 
Epoch: Iteration # 800  error is:  0.2864533 
Epoch: Iteration # 900  error is:  0.2731501 
Epoch: Iteration # 1000  error is:  0.1450343 
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 142.89   21.75  173.32