Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for SIMLR on tokay2

This page was generated on 2020-10-17 11:57:49 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SIMLR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1667/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.14.0
Luca De Sano
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SIMLR
Branch: RELEASE_3_11
Last Commit: 5ed9270
Last Changed Date: 2020-04-27 15:02:08 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SIMLR
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SIMLR_1.14.0.tar.gz
StartedAt: 2020-10-17 08:21:32 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:33:06 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 694.2 seconds
RetCode: 0
Status:  OK  
CheckDir: SIMLR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SIMLR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SIMLR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.14.0'
* 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  6.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    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-3.11-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-3.11-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 (user + system) or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             78.92   4.47   83.39
SIMLR                             21.56   0.83   25.22
SIMLR_Estimate_Number_of_Clusters  3.10   0.25    7.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             71.66   4.48   76.14
SIMLR                             22.61   0.42   26.51
SIMLR_Estimate_Number_of_Clusters  3.65   0.15    8.08
* 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-3.11-bioc/meat/SIMLR.Rcheck/00check.log'
for details.



Installation output

SIMLR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SIMLR_1.14.0.tar.gz && rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMLR.buildbin-libdir SIMLR_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SIMLR_1.14.0.zip && rm SIMLR_1.14.0.tar.gz SIMLR_1.14.0.zip
###
##############################################################################
##############################################################################


  % 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 3394k  100 3394k    0     0  30.4M      0 --:--:-- --:--:-- --:--:-- 32.1M

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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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 projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-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 projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.14.0.zip
* DONE (SIMLR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SIMLR' successfully unpacked and MD5 sums checked

Tests output

SIMLR.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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:  0.1311273 
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:  10.88041 
Epoch: Iteration # 200  error is:  0.8521355 
Epoch: Iteration # 300  error is:  0.5724507 
Epoch: Iteration # 400  error is:  0.4258744 
Epoch: Iteration # 500  error is:  0.341483 
Epoch: Iteration # 600  error is:  0.3202915 
Epoch: Iteration # 700  error is:  0.3017287 
Epoch: Iteration # 800  error is:  0.275941 
Epoch: Iteration # 900  error is:  0.1424166 
Epoch: Iteration # 1000  error is:  0.1095229 
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:  11.1425 
Epoch: Iteration # 200  error is:  0.7244486 
Epoch: Iteration # 300  error is:  0.4858046 
Epoch: Iteration # 400  error is:  0.4434364 
Epoch: Iteration # 500  error is:  0.2506075 
Epoch: Iteration # 600  error is:  0.1335137 
Epoch: Iteration # 700  error is:  0.1320724 
Epoch: Iteration # 800  error is:  0.1303744 
Epoch: Iteration # 900  error is:  0.1284217 
Epoch: Iteration # 1000  error is:  0.1261027 
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:  10.95575 
Epoch: Iteration # 200  error is:  0.8198897 
Epoch: Iteration # 300  error is:  0.5294874 
Epoch: Iteration # 400  error is:  0.6056302 
Epoch: Iteration # 500  error is:  0.4615676 
Epoch: Iteration # 600  error is:  0.4479364 
Epoch: Iteration # 700  error is:  0.5138178 
Epoch: Iteration # 800  error is:  0.463686 
Epoch: Iteration # 900  error is:  0.3632868 
Epoch: Iteration # 1000  error is:  0.322364 
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 
== testthat results  ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 142.62    6.81  157.93 

SIMLR.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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:  11.40656 
Epoch: Iteration # 200  error is:  0.7105595 
Epoch: Iteration # 300  error is:  0.5135811 
Epoch: Iteration # 400  error is:  0.4881752 
Epoch: Iteration # 500  error is:  0.3295515 
Epoch: Iteration # 600  error is:  0.2982699 
Epoch: Iteration # 700  error is:  0.2875464 
Epoch: Iteration # 800  error is:  0.2731632 
Epoch: Iteration # 900  error is:  0.1565793 
Epoch: Iteration # 1000  error is:  0.1135492 
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:  11.56453 
Epoch: Iteration # 200  error is:  0.7185407 
Epoch: Iteration # 300  error is:  0.5519615 
Epoch: Iteration # 400  error is:  0.4246319 
Epoch: Iteration # 500  error is:  0.3611967 
Epoch: Iteration # 600  error is:  0.1406989 
Epoch: Iteration # 700  error is:  0.138621 
Epoch: Iteration # 800  error is:  0.1376401 
Epoch: Iteration # 900  error is:  0.1365045 
Epoch: Iteration # 1000  error is:  0.1354006 
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:  10.87543 
Epoch: Iteration # 200  error is:  0.8507639 
Epoch: Iteration # 300  error is:  0.6276289 
Epoch: Iteration # 400  error is:  0.3394408 
Epoch: Iteration # 500  error is:  0.3003384 
Epoch: Iteration # 600  error is:  0.2674544 
Epoch: Iteration # 700  error is:  0.1423747 
Epoch: Iteration # 800  error is:  0.1050858 
Epoch: Iteration # 900  error is:  0.1105361 
Epoch: Iteration # 1000  error is:  0.09116955 
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 
== testthat results  ===========================================================
[ OK: 4 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 165.48    6.28  181.95 

Example timings

SIMLR.Rcheck/examples_i386/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR000
CIMLR_Estimate_Number_of_Clusters000
SIMLR21.56 0.8325.22
SIMLR_Estimate_Number_of_Clusters3.100.257.25
SIMLR_Feature_Ranking78.92 4.4783.39
SIMLR_Large_Scale0.060.000.07

SIMLR.Rcheck/examples_x64/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR000
CIMLR_Estimate_Number_of_Clusters000
SIMLR22.61 0.4226.51
SIMLR_Estimate_Number_of_Clusters3.650.158.08
SIMLR_Feature_Ranking71.66 4.4876.14
SIMLR_Large_Scale0.060.000.07