##############################################################################
##############################################################################
###
### 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_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SIMLR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.33.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  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             36.006  0.373  36.680
SIMLR                             29.439  0.371  32.783
SIMLR_Estimate_Number_of_Clusters  2.660  0.029   5.602
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SIMLR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SIMLR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c Rtsne.cpp -o Rtsne.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c package_init.c -o package_init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c projsplx_R.c -o projsplx_R.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c sptree.cpp -o sptree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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)
      |                ~~~~~~~~~~~~^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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:  0.1166379 
Epoch: Iteration # 200  error is:  0.06147658 
Epoch: Iteration # 300  error is:  0.05998078 
Epoch: Iteration # 400  error is:  0.05981972 
Epoch: Iteration # 500  error is:  0.05968298 
Epoch: Iteration # 600  error is:  0.05956356 
Epoch: Iteration # 700  error is:  0.0594614 
Epoch: Iteration # 800  error is:  0.05937002 
Epoch: Iteration # 900  error is:  0.05929013 
Epoch: Iteration # 1000  error is:  0.05921645 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.54068 
Epoch: Iteration # 200  error is:  0.9100059 
Epoch: Iteration # 300  error is:  0.4332803 
Epoch: Iteration # 400  error is:  0.5446613 
Epoch: Iteration # 500  error is:  0.4101855 
Epoch: Iteration # 600  error is:  0.3787689 
Epoch: Iteration # 700  error is:  0.3616095 
Epoch: Iteration # 800  error is:  0.3843966 
Epoch: Iteration # 900  error is:  0.3518734 
Epoch: Iteration # 1000  error is:  0.3182997 
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:  0.08058122 
Epoch: Iteration # 200  error is:  0.07349299 
Epoch: Iteration # 300  error is:  0.06658213 
Epoch: Iteration # 400  error is:  0.06416662 
Epoch: Iteration # 500  error is:  0.06394168 
Epoch: Iteration # 600  error is:  0.06376247 
Epoch: Iteration # 700  error is:  0.06361992 
Epoch: Iteration # 800  error is:  0.06350109 
Epoch: Iteration # 900  error is:  0.06340161 
Epoch: Iteration # 1000  error is:  0.06331447 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.70413 
Epoch: Iteration # 200  error is:  0.9865564 
Epoch: Iteration # 300  error is:  0.6600015 
Epoch: Iteration # 400  error is:  0.515049 
Epoch: Iteration # 500  error is:  0.3711811 
Epoch: Iteration # 600  error is:  0.2871871 
Epoch: Iteration # 700  error is:  0.1459756 
Epoch: Iteration # 800  error is:  0.1452945 
Epoch: Iteration # 900  error is:  0.144824 
Epoch: Iteration # 1000  error is:  0.1443256 
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:  0.08010113 
Epoch: Iteration # 200  error is:  0.06151627 
Epoch: Iteration # 300  error is:  0.06081965 
Epoch: Iteration # 400  error is:  0.06033519 
Epoch: Iteration # 500  error is:  0.05997822 
Epoch: Iteration # 600  error is:  0.05970198 
Epoch: Iteration # 700  error is:  0.05948038 
Epoch: Iteration # 800  error is:  0.05929918 
Epoch: Iteration # 900  error is:  0.05913881 
Epoch: Iteration # 1000  error is:  0.05900059 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.89311 
Epoch: Iteration # 200  error is:  0.9198741 
Epoch: Iteration # 300  error is:  0.6363923 
Epoch: Iteration # 400  error is:  0.405209 
Epoch: Iteration # 500  error is:  0.3631498 
Epoch: Iteration # 600  error is:  0.406208 
Epoch: Iteration # 700  error is:  0.4177793 
Epoch: Iteration # 800  error is:  0.5016554 
Epoch: Iteration # 900  error is:  0.6021663 
Epoch: Iteration # 1000  error is:  0.5482259 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
19 
20 
21 
22 
23 
24 
25 
26 
27 
28 
29 
30 
31 
32 
33 
34 
35 
36 
37 
38 
39 
40 
41 
42 
43 
44 
45 
46 
47 
48 
49 
50 
51 
52 
53 
54 
55 
56 
57 
58 
59 
60 
61 
62 
63 
64 
65 
66 
67 
68 
69 
70 
71 
72 
73 
74 
75 
76 
77 
78 
79 
80 
81 
82 
83 
84 
85 
86 
87 
88 
89 
90 
91 
92 
93 
94 
95 
96 
97 
98 
99 
100 
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
129.843   0.802 140.002