Multiple platform build/check report for BioC 3.14 - CHECK results for SIMLR on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: SIMLR

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SIMLR_1.20.0.tar.gz

StartedAt: 2022-04-13 03:01:02 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 03:10:33 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 571.3 seconds

RetCode: 0

Status: OK

CheckDir: SIMLR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SIMLR_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SIMLR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SIMLR/DESCRIPTION' ... OK
* this is package 'SIMLR' version '1.20.0'
* 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
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.1Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/SIMLR/libs/i386/SIMLR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/SIMLR/libs/x64/SIMLR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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' ... NOTE
Files named as vignettes but with no recognized vignette engine:
   'vignettes/1_introduction.Rmd'
   'vignettes/2_running_SIMLR.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             58.60   2.85   61.50
SIMLR                             20.23   0.72   23.61
SIMLR_Estimate_Number_of_Clusters  3.27   0.16    6.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             61.73   3.03   64.78
SIMLR                             21.44   0.52   24.73
SIMLR_Estimate_Number_of_Clusters  3.48   0.15    6.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SIMLR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SIMLR_1.20.0.tar.gz && rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMLR.buildbin-libdir SIMLR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SIMLR_1.20.0.zip && rm SIMLR_1.20.0.tar.gz SIMLR_1.20.0.zip
###
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 50 3397k   50 1722k    0     0  1539k      0  0:00:02  0:00:01  0:00:01 1539k
100 3397k  100 3397k    0     0  1902k      0  0:00:01  0:00:01 --:--:-- 1902k

install for i386

* installing *source* package 'SIMLR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rtsne.cpp -o Rtsne.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c package_init.c -o package_init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c projsplx_R.c -o projsplx_R.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sptree.cpp -o sptree.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/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:967:48: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   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(VpTree<T, distance>::Node*, const T&, int, std::priority_queue<VpTree<T, distance>::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance; typename std::vector<VpTree<T, distance>::HeapItem, std::allocator<VpTree<T, distance>::HeapItem> >::value_type = VpTree<DataPoint, precomputed_distance>::HeapItem]':
vptree.h:131:9:   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:472:59:   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 'unsigned int'} and 'int' [-Wsign-compare]
             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
In file included from tsne.cpp:41:
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 'unsigned int'} and 'int' [-Wsign-compare]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
In file included from tsne.cpp:41:
vptree.h: In instantiation of 'void VpTree<T, distance>::search(VpTree<T, distance>::Node*, const T&, int, std::priority_queue<VpTree<T, distance>::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance; typename std::vector<VpTree<T, distance>::HeapItem, std::allocator<VpTree<T, distance>::HeapItem> >::value_type = VpTree<DataPoint, euclidean_distance>::HeapItem]':
vptree.h:131:9:   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:550:59:   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 'unsigned int'} and 'int' [-Wsign-compare]
             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
In file included from tsne.cpp:41:
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 'unsigned int'} and 'int' [-Wsign-compare]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SIMLR.dll tmp.def RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SIMLR.buildbin-libdir/00LOCK-SIMLR/00new/SIMLR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SIMLR'
    finding HTML links ... done
    BuettnerFlorian                         html  
    CIMLR                                   html  
    CIMLR_Estimate_Number_of_Clusters       html  
    SIMLR                                   html  
    SIMLR_Estimate_Number_of_Clusters       html  
    SIMLR_Feature_Ranking                   html  
    SIMLR_Large_Scale                       html  
    ZeiselAmit                              html  
** 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

install for x64

* installing *source* package 'SIMLR' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rtsne.cpp -o Rtsne.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c package_init.c -o package_init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c projsplx_R.c -o projsplx_R.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sptree.cpp -o sptree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/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:967:48: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   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(VpTree<T, distance>::Node*, const T&, int, std::priority_queue<VpTree<T, distance>::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance; typename std::vector<VpTree<T, distance>::HeapItem, std::allocator<VpTree<T, distance>::HeapItem> >::value_type = VpTree<DataPoint, precomputed_distance>::HeapItem]':
vptree.h:131:9:   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:472:59:   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]
             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
In file included from tsne.cpp:41:
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]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
In file included from tsne.cpp:41:
vptree.h: In instantiation of 'void VpTree<T, distance>::search(VpTree<T, distance>::Node*, const T&, int, std::priority_queue<VpTree<T, distance>::HeapItem>&) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance; typename std::vector<VpTree<T, distance>::HeapItem, std::allocator<VpTree<T, distance>::HeapItem> >::value_type = VpTree<DataPoint, euclidean_distance>::HeapItem]':
vptree.h:131:9:   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:550:59:   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]
             if(heap.size() == k) heap.pop();                 // remove furthest node from result list (if we already have k results)
In file included from tsne.cpp:41:
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]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SIMLR.dll tmp.def RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.20.0.zip
* DONE (SIMLR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SIMLR' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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:  0.1311273 
Epoch: Iteration # 200  error is:  0.08447631 
Epoch: Iteration # 300  error is:  0.05910928 
Epoch: Iteration # 400  error is:  0.05898365 
Epoch: Iteration # 500  error is:  0.05886629 
Epoch: Iteration # 600  error is:  0.05876227 
Epoch: Iteration # 700  error is:  0.05867166 
Epoch: Iteration # 800  error is:  0.05858929 
Epoch: Iteration # 900  error is:  0.05851553 
Epoch: Iteration # 1000  error is:  0.05844804 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.35954 
Epoch: Iteration # 200  error is:  0.6884659 
Epoch: Iteration # 300  error is:  0.9448275 
Epoch: Iteration # 400  error is:  0.6583809 
Epoch: Iteration # 500  error is:  0.5162709 
Epoch: Iteration # 600  error is:  0.4821856 
Epoch: Iteration # 700  error is:  0.5056056 
Epoch: Iteration # 800  error is:  0.4466873 
Epoch: Iteration # 900  error is:  0.3188446 
Epoch: Iteration # 1000  error is:  0.3065957 
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:  0.07970942 
Epoch: Iteration # 200  error is:  0.07255431 
Epoch: Iteration # 300  error is:  0.0657675 
Epoch: Iteration # 400  error is:  0.06374375 
Epoch: Iteration # 500  error is:  0.06352177 
Epoch: Iteration # 600  error is:  0.06334371 
Epoch: Iteration # 700  error is:  0.0632008 
Epoch: Iteration # 800  error is:  0.06308117 
Epoch: Iteration # 900  error is:  0.06298124 
Epoch: Iteration # 1000  error is:  0.06289702 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  12.23727 
Epoch: Iteration # 200  error is:  0.7351344 
Epoch: Iteration # 300  error is:  0.6241077 
Epoch: Iteration # 400  error is:  0.5029432 
Epoch: Iteration # 500  error is:  0.6728738 
Epoch: Iteration # 600  error is:  0.6167104 
Epoch: Iteration # 700  error is:  0.3807122 
Epoch: Iteration # 800  error is:  0.322073 
Epoch: Iteration # 900  error is:  0.1407554 
Epoch: Iteration # 1000  error is:  0.139999 
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:  0.1319537 
Epoch: Iteration # 200  error is:  0.08297851 
Epoch: Iteration # 300  error is:  0.05963012 
Epoch: Iteration # 400  error is:  0.05956346 
Epoch: Iteration # 500  error is:  0.05950619 
Epoch: Iteration # 600  error is:  0.05945345 
Epoch: Iteration # 700  error is:  0.05940402 
Epoch: Iteration # 800  error is:  0.05935821 
Epoch: Iteration # 900  error is:  0.05931587 
Epoch: Iteration # 1000  error is:  0.05927651 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.20975 
Epoch: Iteration # 200  error is:  1.250742 
Epoch: Iteration # 300  error is:  0.5373852 
Epoch: Iteration # 400  error is:  0.4808992 
Epoch: Iteration # 500  error is:  0.4727013 
Epoch: Iteration # 600  error is:  0.4021521 
Epoch: Iteration # 700  error is:  0.3314536 
Epoch: Iteration # 800  error is:  0.3081624 
Epoch: Iteration # 900  error is:  0.2952463 
Epoch: Iteration # 1000  error is:  0.240361 
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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 
 127.35    5.90  142.28


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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:  0.1311273 
Epoch: Iteration # 200  error is:  0.08447631 
Epoch: Iteration # 300  error is:  0.05910928 
Epoch: Iteration # 400  error is:  0.05898365 
Epoch: Iteration # 500  error is:  0.05886629 
Epoch: Iteration # 600  error is:  0.05876227 
Epoch: Iteration # 700  error is:  0.05867166 
Epoch: Iteration # 800  error is:  0.05858929 
Epoch: Iteration # 900  error is:  0.05851553 
Epoch: Iteration # 1000  error is:  0.05844804 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  14.92689 
Epoch: Iteration # 200  error is:  1.313446 
Epoch: Iteration # 300  error is:  0.5998493 
Epoch: Iteration # 400  error is:  0.3804625 
Epoch: Iteration # 500  error is:  0.33827 
Epoch: Iteration # 600  error is:  0.3126991 
Epoch: Iteration # 700  error is:  0.2829422 
Epoch: Iteration # 800  error is:  0.2627728 
Epoch: Iteration # 900  error is:  0.1345485 
Epoch: Iteration # 1000  error is:  0.09680077 
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:  0.07970942 
Epoch: Iteration # 200  error is:  0.07255431 
Epoch: Iteration # 300  error is:  0.0657675 
Epoch: Iteration # 400  error is:  0.06374375 
Epoch: Iteration # 500  error is:  0.06352177 
Epoch: Iteration # 600  error is:  0.06334371 
Epoch: Iteration # 700  error is:  0.0632008 
Epoch: Iteration # 800  error is:  0.06308117 
Epoch: Iteration # 900  error is:  0.06298124 
Epoch: Iteration # 1000  error is:  0.06289702 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  12.13945 
Epoch: Iteration # 200  error is:  0.7994889 
Epoch: Iteration # 300  error is:  0.6074577 
Epoch: Iteration # 400  error is:  0.4161036 
Epoch: Iteration # 500  error is:  0.3320566 
Epoch: Iteration # 600  error is:  0.1659079 
Epoch: Iteration # 700  error is:  0.1625233 
Epoch: Iteration # 800  error is:  0.1546702 
Epoch: Iteration # 900  error is:  0.1531655 
Epoch: Iteration # 1000  error is:  0.1512352 
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:  0.1319537 
Epoch: Iteration # 200  error is:  0.08297851 
Epoch: Iteration # 300  error is:  0.05963012 
Epoch: Iteration # 400  error is:  0.05956346 
Epoch: Iteration # 500  error is:  0.05950619 
Epoch: Iteration # 600  error is:  0.05945345 
Epoch: Iteration # 700  error is:  0.05940402 
Epoch: Iteration # 800  error is:  0.05935821 
Epoch: Iteration # 900  error is:  0.05931587 
Epoch: Iteration # 1000  error is:  0.05927651 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.86578 
Epoch: Iteration # 200  error is:  0.596972 
Epoch: Iteration # 300  error is:  0.4109633 
Epoch: Iteration # 400  error is:  0.2896662 
Epoch: Iteration # 500  error is:  0.1508158 
Epoch: Iteration # 600  error is:  0.1271 
Epoch: Iteration # 700  error is:  0.08637933 
Epoch: Iteration # 800  error is:  0.08264471 
Epoch: Iteration # 900  error is:  0.08265851 
Epoch: Iteration # 1000  error is:  0.08264892 
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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 
 126.04    4.06  138.73

name	user	system	elapsed
CIMLR	0	0	0
CIMLR_Estimate_Number_of_Clusters	0	0	0
SIMLR	20.23	0.72	23.61
SIMLR_Estimate_Number_of_Clusters	3.27	0.16	6.50
SIMLR_Feature_Ranking	58.60	2.85	61.50
SIMLR_Large_Scale	0.07	0.00	0.07

name	user	system	elapsed
CIMLR	0	0	0
CIMLR_Estimate_Number_of_Clusters	0	0	0
SIMLR	21.44	0.52	24.73
SIMLR_Estimate_Number_of_Clusters	3.48	0.15	6.74
SIMLR_Feature_Ranking	61.73	3.03	64.78
SIMLR_Large_Scale	0.07	0.00	0.06

CHECK results for SIMLR on tokay2

Summary

Command output

Installation output

Tests output

Example timings