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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SIMLR_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SIMLR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SIMLR’ can be installed ... OK
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
* 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 loading without being on the library search path ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
SIMLR_Feature_Ranking             56.644  0.677  32.630
SIMLR                             31.818  0.277  33.355
SIMLR_Estimate_Number_of_Clusters  3.588  0.157   6.394
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/SIMLR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL SIMLR
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Rtsne.cpp -o Rtsne.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c package_init.c -o package_init.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c projsplx_R.c -o projsplx_R.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c sptree.cpp -o sptree.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -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 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]'
  131 |         search(_root, target, k, heap);
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:484:21:   required from here
  484 |         tree->search(obj_X[n], K + 1, &indices, &distances);
      |         ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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 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]'
  131 |         search(_root, target, k, heap);
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
tsne.cpp:562:21:   required from here
  562 |         tree->search(obj_X[n], K + 1, &indices, &distances);
      |         ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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 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 -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-SIMLR/00new/SIMLR/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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:  0.1002465 
Epoch: Iteration # 200  error is:  0.05982035 
Epoch: Iteration # 300  error is:  0.05947052 
Epoch: Iteration # 400  error is:  0.05926682 
Epoch: Iteration # 500  error is:  0.05909646 
Epoch: Iteration # 600  error is:  0.05895061 
Epoch: Iteration # 700  error is:  0.0588265 
Epoch: Iteration # 800  error is:  0.05871539 
Epoch: Iteration # 900  error is:  0.05861945 
Epoch: Iteration # 1000  error is:  0.05853214 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.15156 
Epoch: Iteration # 200  error is:  0.8363414 
Epoch: Iteration # 300  error is:  0.5525973 
Epoch: Iteration # 400  error is:  0.4777885 
Epoch: Iteration # 500  error is:  0.5100297 
Epoch: Iteration # 600  error is:  0.3934903 
Epoch: Iteration # 700  error is:  0.3069014 
Epoch: Iteration # 800  error is:  0.28956 
Epoch: Iteration # 900  error is:  0.2799138 
Epoch: Iteration # 1000  error is:  0.269573 
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:  0.07985683 
Epoch: Iteration # 200  error is:  0.07405478 
Epoch: Iteration # 300  error is:  0.06712199 
Epoch: Iteration # 400  error is:  0.06481996 
Epoch: Iteration # 500  error is:  0.06459687 
Epoch: Iteration # 600  error is:  0.0644226 
Epoch: Iteration # 700  error is:  0.06427758 
Epoch: Iteration # 800  error is:  0.06415905 
Epoch: Iteration # 900  error is:  0.06405579 
Epoch: Iteration # 1000  error is:  0.06396948 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.72457 
Epoch: Iteration # 200  error is:  0.8013585 
Epoch: Iteration # 300  error is:  0.6146086 
Epoch: Iteration # 400  error is:  0.6885311 
Epoch: Iteration # 500  error is:  0.5652767 
Epoch: Iteration # 600  error is:  0.6047624 
Epoch: Iteration # 700  error is:  0.4821472 
Epoch: Iteration # 800  error is:  0.4932905 
Epoch: Iteration # 900  error is:  0.4597804 
Epoch: Iteration # 1000  error is:  0.3645012 
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:  0.1071239 
Epoch: Iteration # 200  error is:  0.06081309 
Epoch: Iteration # 300  error is:  0.06036734 
Epoch: Iteration # 400  error is:  0.06020438 
Epoch: Iteration # 500  error is:  0.06006716 
Epoch: Iteration # 600  error is:  0.05994882 
Epoch: Iteration # 700  error is:  0.05984484 
Epoch: Iteration # 800  error is:  0.05975454 
Epoch: Iteration # 900  error is:  0.05966999 
Epoch: Iteration # 1000  error is:  0.05959479 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.82814 
Epoch: Iteration # 200  error is:  0.6511501 
Epoch: Iteration # 300  error is:  0.7541452 
Epoch: Iteration # 400  error is:  0.8754104 
Epoch: Iteration # 500  error is:  0.437819 
Epoch: Iteration # 600  error is:  0.4551979 
Epoch: Iteration # 700  error is:  0.3800435 
Epoch: Iteration # 800  error is:  0.5683826 
Epoch: Iteration # 900  error is:  0.3282436 
Epoch: Iteration # 1000  error is:  0.3056316 
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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 
157.513   2.258 138.830