Daniele Ramazzotti
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/SIMLR |
| Branch: RELEASE_3_6 |
| Last Commit: 1fe35a0 |
| Last Changed Date: 2018-03-24 09:14:20 -0400 (Sat, 24 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:28:46 -0400 (Thu, 12 Apr 2018).
| Package 1301/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIMLR 1.4.1 Daniele Ramazzotti
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: SIMLR |
| Version: 1.4.1 |
| Command: rm -rf SIMLR.buildbin-libdir SIMLR.Rcheck && mkdir SIMLR.buildbin-libdir SIMLR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SIMLR.buildbin-libdir SIMLR_1.4.1.tar.gz >SIMLR.Rcheck\00install.out 2>&1 && cp SIMLR.Rcheck\00install.out SIMLR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SIMLR.buildbin-libdir --install="check:SIMLR-install.out" --force-multiarch --no-vignettes --timings SIMLR_1.4.1.tar.gz |
| StartedAt: 2018-04-12 03:14:09 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:28:35 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 865.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### rm -rf SIMLR.buildbin-libdir SIMLR.Rcheck && mkdir SIMLR.buildbin-libdir SIMLR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SIMLR.buildbin-libdir SIMLR_1.4.1.tar.gz >SIMLR.Rcheck\00install.out 2>&1 && cp SIMLR.Rcheck\00install.out SIMLR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SIMLR.buildbin-libdir --install="check:SIMLR-install.out" --force-multiarch --no-vignettes --timings SIMLR_1.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SIMLR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.4.1'
* 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 6.5Mb
sub-directories of 1Mb or more:
data 4.5Mb
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
** checking loading without being on the library search path ... 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 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 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-3.6-bioc/meat/SIMLR.buildbin-libdir/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)
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 installed files from 'inst/doc' ... OK
* 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 110.78 3.18 113.97
CIMLR 30.98 0.04 40.08
SIMLR 24.74 0.64 28.27
CIMLR_Estimate_Number_of_Clusters 4.05 0.01 11.73
SIMLR_Estimate_Number_of_Clusters 3.53 0.28 6.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SIMLR_Feature_Ranking 84.44 5.36 89.79
CIMLR 23.72 0.04 33.83
SIMLR 20.99 0.30 24.98
CIMLR_Estimate_Number_of_Clusters 5.83 0.03 16.44
SIMLR_Estimate_Number_of_Clusters 2.95 0.09 7.41
* 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-3.6-bioc/meat/SIMLR.Rcheck/00check.log'
for details.
SIMLR.Rcheck/00install.out
install for i386
* installing *source* package 'SIMLR' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c projsplx_R.c -o projsplx_R.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c sptree.cpp -o sptree.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c tsne.cpp -o tsne.o
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<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 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<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 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++ -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˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
GliomasReduced 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
In R CMD INSTALL
install for x64
* installing *source* package 'SIMLR' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c projsplx_R.c -o projsplx_R.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c sptree.cpp -o sptree.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c tsne.cpp -o tsne.o
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<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 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<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 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++ -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˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.4.1.zip
* DONE (SIMLR)
In R CMD INSTALL
In R CMD INSTALL
|
SIMLR.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 11.27251
Epoch: Iteration # 200 error is: 1.062771
Epoch: Iteration # 300 error is: 0.4736484
Epoch: Iteration # 400 error is: 0.4512871
Epoch: Iteration # 500 error is: 0.2940488
Epoch: Iteration # 600 error is: 0.2257851
Epoch: Iteration # 700 error is: 0.1307382
Epoch: Iteration # 800 error is: 0.08965238
Epoch: Iteration # 900 error is: 0.08866443
Epoch: Iteration # 1000 error is: 0.08893276
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: 11.51391
Epoch: Iteration # 200 error is: 0.7761078
Epoch: Iteration # 300 error is: 0.6171518
Epoch: Iteration # 400 error is: 0.4921703
Epoch: Iteration # 500 error is: 0.598387
Epoch: Iteration # 600 error is: 0.5480543
Epoch: Iteration # 700 error is: 0.4557189
Epoch: Iteration # 800 error is: 0.3924478
Epoch: Iteration # 900 error is: 0.5321621
Epoch: Iteration # 1000 error is: 0.3718931
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: 10.94211
Epoch: Iteration # 200 error is: 0.4626488
Epoch: Iteration # 300 error is: 0.1627829
Epoch: Iteration # 400 error is: 0.1008859
Epoch: Iteration # 500 error is: 0.08965958
Epoch: Iteration # 600 error is: 0.08964323
Epoch: Iteration # 700 error is: 0.08962987
Epoch: Iteration # 800 error is: 0.08961683
Epoch: Iteration # 900 error is: 0.08981224
Epoch: Iteration # 1000 error is: 0.08959328
Computing the multiple Kernels.
Performing network diffusion.
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
Performing t-SNE.
Epoch: Iteration # 100 error is: 0.3170709
Epoch: Iteration # 200 error is: 0.09659138
Epoch: Iteration # 300 error is: 0.1074762
Epoch: Iteration # 400 error is: 0.1187364
Epoch: Iteration # 500 error is: 0.1051877
Epoch: Iteration # 600 error is: 0.09606742
Epoch: Iteration # 700 error is: 0.09858888
Epoch: Iteration # 800 error is: 0.1164786
Epoch: Iteration # 900 error is: 0.175918
Epoch: Iteration # 1000 error is: 0.0963613
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 22.52237
Epoch: Iteration # 200 error is: 1.466014
Epoch: Iteration # 300 error is: 1.757457
Epoch: Iteration # 400 error is: 0.9722038
Epoch: Iteration # 500 error is: 0.4307521
Epoch: Iteration # 600 error is: 0.2402635
Epoch: Iteration # 700 error is: 0.2733784
Epoch: Iteration # 800 error is: 0.540778
Epoch: Iteration # 900 error is: 0.2395337
Epoch: Iteration # 1000 error is: 0.2348548
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== testthat results ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
177.17 6.46 199.18
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SIMLR.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 10.70386
Epoch: Iteration # 200 error is: 0.4997174
Epoch: Iteration # 300 error is: 0.3400674
Epoch: Iteration # 400 error is: 0.1859793
Epoch: Iteration # 500 error is: 0.1428731
Epoch: Iteration # 600 error is: 0.1098466
Epoch: Iteration # 700 error is: 0.08338651
Epoch: Iteration # 800 error is: 0.08331506
Epoch: Iteration # 900 error is: 0.08323587
Epoch: Iteration # 1000 error is: 0.08322855
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: 14.55626
Epoch: Iteration # 200 error is: 1.617
Epoch: Iteration # 300 error is: 1.019088
Epoch: Iteration # 400 error is: 0.7004357
Epoch: Iteration # 500 error is: 0.6027189
Epoch: Iteration # 600 error is: 0.7080138
Epoch: Iteration # 700 error is: 0.7926942
Epoch: Iteration # 800 error is: 0.8285671
Epoch: Iteration # 900 error is: 0.8827093
Epoch: Iteration # 1000 error is: 0.6609599
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: 11.33151
Epoch: Iteration # 200 error is: 0.5657535
Epoch: Iteration # 300 error is: 0.7035568
Epoch: Iteration # 400 error is: 0.3997072
Epoch: Iteration # 500 error is: 0.3636334
Epoch: Iteration # 600 error is: 0.5706599
Epoch: Iteration # 700 error is: 0.398457
Epoch: Iteration # 800 error is: 0.339344
Epoch: Iteration # 900 error is: 0.6585522
Epoch: Iteration # 1000 error is: 0.5223795
Computing the multiple Kernels.
Performing network diffusion.
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: 0.1871698
Epoch: Iteration # 200 error is: 0.09894385
Epoch: Iteration # 300 error is: 0.09686709
Epoch: Iteration # 400 error is: 0.09643462
Epoch: Iteration # 500 error is: 0.1065708
Epoch: Iteration # 600 error is: 0.09599006
Epoch: Iteration # 700 error is: 0.4685521
Epoch: Iteration # 800 error is: 0.09790608
Epoch: Iteration # 900 error is: 0.09616597
Epoch: Iteration # 1000 error is: 0.09567124
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 21.82999
Epoch: Iteration # 200 error is: 4.677011
Epoch: Iteration # 300 error is: 0.8675726
Epoch: Iteration # 400 error is: 0.2411761
Epoch: Iteration # 500 error is: 0.2345582
Epoch: Iteration # 600 error is: 0.2602773
Epoch: Iteration # 700 error is: 0.4574073
Epoch: Iteration # 800 error is: 0.2328001
Epoch: Iteration # 900 error is: 0.2522098
Epoch: Iteration # 1000 error is: 0.2888645
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== testthat results ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
132.51 4.84 156.75
|
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SIMLR.Rcheck/examples_i386/SIMLR-Ex.timings
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SIMLR.Rcheck/examples_x64/SIMLR-Ex.timings
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