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CHECK report for SIMLR on tokay1

This page was generated on 2020-04-15 12:27:20 -0400 (Wed, 15 Apr 2020).

Package 1600/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.12.0
Luca De Sano
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SIMLR
Branch: RELEASE_3_10
Last Commit: 2fa414e
Last Changed Date: 2019-10-29 13:10:07 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SIMLR
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SIMLR_1.12.0.tar.gz
StartedAt: 2020-04-15 06:41:12 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:53:15 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 722.7 seconds
RetCode: 0
Status:  OK  
CheckDir: SIMLR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SIMLR_1.12.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SIMLR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.12.0'
* 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  6.3Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    libs   1.6Mb
* 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 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-3.10-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-3.10-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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
SIMLR_Feature_Ranking             100.61   5.44  106.05
SIMLR                              25.02   0.57   28.20
SIMLR_Estimate_Number_of_Clusters   3.89   0.29    6.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             84.03   5.89   89.92
SIMLR                             25.23   0.35   29.41
SIMLR_Estimate_Number_of_Clusters  3.48   0.20    6.46
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/SIMLR.Rcheck/00check.log'
for details.

Installation output

SIMLR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SIMLR_1.12.0.tar.gz && rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMLR.buildbin-libdir SIMLR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SIMLR_1.12.0.zip && rm SIMLR_1.12.0.tar.gz SIMLR_1.12.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3397k  100 3397k    0     0  35.7M      0 --:--:-- --:--:-- --:--:-- 37.2M

install for i386

* installing *source* package 'SIMLR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c projsplx_R.c -o projsplx_R.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c sptree.cpp -o sptree.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
   if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) {
                                                ^
In file included from tsne.cpp:41:0:
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:131:38:   required from 'void VpTree<T, distance>::search(const T&, int, std::vector<_RealType>*, 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 between signed and unsigned integer expressions [-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:41:0:
vptree.h:239:28: warning: comparison between signed and unsigned integer expressions [-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:41:0:
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:131:38:   required from 'void VpTree<T, distance>::search(const T&, int, std::vector<_RealType>*, 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 between signed and unsigned integer expressions [-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:41:0:
vptree.h:239:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
                            ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SIMLR.dll tmp.def RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/SIMLR.buildbin-libdir/00LOCK-SIMLR/00new/SIMLR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** 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:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c projsplx_R.c -o projsplx_R.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c sptree.cpp -o sptree.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
   if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) {
                                                ^
In file included from tsne.cpp:41:0:
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:131:38:   required from 'void VpTree<T, distance>::search(const T&, int, std::vector<_RealType>*, 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 between signed and unsigned integer expressions [-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:41:0:
vptree.h:239:28: warning: comparison between signed and unsigned integer expressions [-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:41:0:
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:131:38:   required from 'void VpTree<T, distance>::search(const T&, int, std::vector<_RealType>*, 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 between signed and unsigned integer expressions [-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:41:0:
vptree.h:239:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(heap.size() == k) _tau = heap.top().dist;     // update value of tau (farthest point in result list)
                            ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SIMLR.dll tmp.def RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.12.0.zip
* DONE (SIMLR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SIMLR' successfully unpacked and MD5 sums checked

Tests output

SIMLR.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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:  0.08740277 
Epoch: Iteration # 200  error is:  0.06109835 
Epoch: Iteration # 300  error is:  0.06055804 
Epoch: Iteration # 400  error is:  0.06016488 
Epoch: Iteration # 500  error is:  0.05986345 
Epoch: Iteration # 600  error is:  0.05962175 
Epoch: Iteration # 700  error is:  0.05942497 
Epoch: Iteration # 800  error is:  0.05926368 
Epoch: Iteration # 900  error is:  0.05912282 
Epoch: Iteration # 1000  error is:  0.05900041 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.2169 
Epoch: Iteration # 200  error is:  0.7613668 
Epoch: Iteration # 300  error is:  0.5542765 
Epoch: Iteration # 400  error is:  0.6832031 
Epoch: Iteration # 500  error is:  0.3517567 
Epoch: Iteration # 600  error is:  0.3451582 
Epoch: Iteration # 700  error is:  0.3321427 
Epoch: Iteration # 800  error is:  0.2625442 
Epoch: Iteration # 900  error is:  0.1304586 
Epoch: Iteration # 1000  error is:  0.09468753 
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:  0.08761389 
Epoch: Iteration # 200  error is:  0.08028096 
Epoch: Iteration # 300  error is:  0.07380264 
Epoch: Iteration # 400  error is:  0.07001242 
Epoch: Iteration # 500  error is:  0.06980527 
Epoch: Iteration # 600  error is:  0.06965419 
Epoch: Iteration # 700  error is:  0.06952878 
Epoch: Iteration # 800  error is:  0.06942423 
Epoch: Iteration # 900  error is:  0.06933381 
Epoch: Iteration # 1000  error is:  0.06925543 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.99689 
Epoch: Iteration # 200  error is:  0.7984223 
Epoch: Iteration # 300  error is:  0.7793225 
Epoch: Iteration # 400  error is:  0.4546246 
Epoch: Iteration # 500  error is:  0.4146881 
Epoch: Iteration # 600  error is:  0.9846425 
Epoch: Iteration # 700  error is:  0.4989076 
Epoch: Iteration # 800  error is:  0.4132507 
Epoch: Iteration # 900  error is:  0.6557123 
Epoch: Iteration # 1000  error is:  0.4032582 
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:  0.0844205 
Epoch: Iteration # 200  error is:  0.06261698 
Epoch: Iteration # 300  error is:  0.06200857 
Epoch: Iteration # 400  error is:  0.06155497 
Epoch: Iteration # 500  error is:  0.06121478 
Epoch: Iteration # 600  error is:  0.06095032 
Epoch: Iteration # 700  error is:  0.06073815 
Epoch: Iteration # 800  error is:  0.06055936 
Epoch: Iteration # 900  error is:  0.06040826 
Epoch: Iteration # 1000  error is:  0.06027554 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.60094 
Epoch: Iteration # 200  error is:  0.6942095 
Epoch: Iteration # 300  error is:  0.6565934 
Epoch: Iteration # 400  error is:  0.5052138 
Epoch: Iteration # 500  error is:  0.6263851 
Epoch: Iteration # 600  error is:  0.5414368 
Epoch: Iteration # 700  error is:  0.4581948 
Epoch: Iteration # 800  error is:  0.3266533 
Epoch: Iteration # 900  error is:  0.2929087 
Epoch: Iteration # 1000  error is:  0.2648147 
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== testthat results  ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 167.01    6.07  182.51

SIMLR.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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:  11.28017 
Epoch: Iteration # 200  error is:  0.729827 
Epoch: Iteration # 300  error is:  0.9088172 
Epoch: Iteration # 400  error is:  0.4559953 
Epoch: Iteration # 500  error is:  0.5825769 
Epoch: Iteration # 600  error is:  0.3406144 
Epoch: Iteration # 700  error is:  0.3131891 
Epoch: Iteration # 800  error is:  0.2942295 
Epoch: Iteration # 900  error is:  0.281205 
Epoch: Iteration # 1000  error is:  0.2657714 
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:  11.63858 
Epoch: Iteration # 200  error is:  1.193234 
Epoch: Iteration # 300  error is:  1.239251 
Epoch: Iteration # 400  error is:  0.6845041 
Epoch: Iteration # 500  error is:  0.558852 
Epoch: Iteration # 600  error is:  0.5737316 
Epoch: Iteration # 700  error is:  0.5332911 
Epoch: Iteration # 800  error is:  0.5984756 
Epoch: Iteration # 900  error is:  0.5798302 
Epoch: Iteration # 1000  error is:  0.8933595 
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:  10.73551 
Epoch: Iteration # 200  error is:  0.5596449 
Epoch: Iteration # 300  error is:  0.5932937 
Epoch: Iteration # 400  error is:  0.3616173 
Epoch: Iteration # 500  error is:  0.2851981 
Epoch: Iteration # 600  error is:  0.2637433 
Epoch: Iteration # 700  error is:  0.1524155 
Epoch: Iteration # 800  error is:  0.1161524 
Epoch: Iteration # 900  error is:  0.09289502 
Epoch: Iteration # 1000  error is:  0.08616725 
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== testthat results  ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 161.10    5.53  177.51

Example timings

SIMLR.Rcheck/examples_i386/SIMLR-Ex.timings

nameusersystemelapsed
SIMLR25.02 0.5728.20
SIMLR_Estimate_Number_of_Clusters3.890.296.44
SIMLR_Feature_Ranking100.61 5.44106.05
SIMLR_Large_Scale0.090.000.09

SIMLR.Rcheck/examples_x64/SIMLR-Ex.timings

nameusersystemelapsed
SIMLR25.23 0.3529.41
SIMLR_Estimate_Number_of_Clusters3.480.206.46
SIMLR_Feature_Ranking84.03 5.8989.92
SIMLR_Large_Scale0.110.000.11