Daniele Ramazzotti
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/SIMLR |
| Branch: RELEASE_3_7 |
| Last Commit: cc9b4e7 |
| Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:42:56 -0400 (Wed, 17 Oct 2018).
| Package 1377/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIMLR 1.6.0 Daniele Ramazzotti
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SIMLR |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SIMLR_1.6.0.tar.gz |
| StartedAt: 2018-10-17 04:53:23 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:06:57 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 814.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SIMLR_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SIMLR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.0'
* 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 4.5Mb
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
* 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-3.7-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)
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 89.02 1.90 90.92
CIMLR 24.22 0.10 32.57
SIMLR 22.65 0.52 25.67
CIMLR_Estimate_Number_of_Clusters 4.36 0.01 12.89
SIMLR_Estimate_Number_of_Clusters 3.55 0.30 7.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SIMLR_Feature_Ranking 72.79 2.79 75.64
SIMLR 27.33 0.42 30.69
CIMLR 26.86 0.06 37.42
CIMLR_Estimate_Number_of_Clusters 5.78 0.00 16.68
SIMLR_Estimate_Number_of_Clusters 4.49 0.13 8.36
* 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-3.7-bioc/meat/SIMLR.Rcheck/00check.log'
for details.
SIMLR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SIMLR_1.6.0.tar.gz && rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMLR.buildbin-libdir SIMLR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SIMLR_1.6.0.zip && rm SIMLR_1.6.0.tar.gz SIMLR_1.6.0.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 3448k 100 3448k 0 0 30.9M 0 --:--:-- --:--:-- --:--:-- 33.0M
install for i386
* installing *source* package 'SIMLR' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sptree.cpp -o sptree.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/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˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/SIMLR.buildbin-libdir/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
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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sptree.cpp -o sptree.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/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˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.6.0.zip
* DONE (SIMLR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'SIMLR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
SIMLR.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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: 11.09399
Epoch: Iteration # 200 error is: 0.5571124
Epoch: Iteration # 300 error is: 0.3197054
Epoch: Iteration # 400 error is: 0.1871681
Epoch: Iteration # 500 error is: 0.1279777
Epoch: Iteration # 600 error is: 0.08698457
Epoch: Iteration # 700 error is: 0.08577178
Epoch: Iteration # 800 error is: 0.08576902
Epoch: Iteration # 900 error is: 0.08583172
Epoch: Iteration # 1000 error is: 0.08576388
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: 12.34004
Epoch: Iteration # 200 error is: 0.8758327
Epoch: Iteration # 300 error is: 0.5945691
Epoch: Iteration # 400 error is: 0.3699569
Epoch: Iteration # 500 error is: 0.1806262
Epoch: Iteration # 600 error is: 0.1438023
Epoch: Iteration # 700 error is: 0.1431537
Epoch: Iteration # 800 error is: 0.1424609
Epoch: Iteration # 900 error is: 0.1417677
Epoch: Iteration # 1000 error is: 0.1412692
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: 11.83943
Epoch: Iteration # 200 error is: 1.055273
Epoch: Iteration # 300 error is: 0.4409981
Epoch: Iteration # 400 error is: 0.3557743
Epoch: Iteration # 500 error is: 0.3636351
Epoch: Iteration # 600 error is: 0.3475981
Epoch: Iteration # 700 error is: 0.2961238
Epoch: Iteration # 800 error is: 0.2849695
Epoch: Iteration # 900 error is: 0.2691947
Epoch: Iteration # 1000 error is: 0.1350778
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: 24.38552
Epoch: Iteration # 200 error is: 2.757676
Epoch: Iteration # 300 error is: 1.587886
Epoch: Iteration # 400 error is: 0.4669777
Epoch: Iteration # 500 error is: 0.3319992
Epoch: Iteration # 600 error is: 0.7822632
Epoch: Iteration # 700 error is: 0.6005358
Epoch: Iteration # 800 error is: 0.3362378
Epoch: Iteration # 900 error is: 0.2430515
Epoch: Iteration # 1000 error is: 0.5506252
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== testthat results ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
191.62 7.31 216.39
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SIMLR.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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: 10.83891
Epoch: Iteration # 200 error is: 0.6603084
Epoch: Iteration # 300 error is: 0.5266831
Epoch: Iteration # 400 error is: 0.6178116
Epoch: Iteration # 500 error is: 0.4521063
Epoch: Iteration # 600 error is: 0.6685031
Epoch: Iteration # 700 error is: 0.411884
Epoch: Iteration # 800 error is: 0.4017758
Epoch: Iteration # 900 error is: 0.3232486
Epoch: Iteration # 1000 error is: 0.3008195
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: 12.03026
Epoch: Iteration # 200 error is: 0.7020764
Epoch: Iteration # 300 error is: 0.661211
Epoch: Iteration # 400 error is: 0.5493373
Epoch: Iteration # 500 error is: 0.7403069
Epoch: Iteration # 600 error is: 0.4280995
Epoch: Iteration # 700 error is: 0.3474601
Epoch: Iteration # 800 error is: 0.3102808
Epoch: Iteration # 900 error is: 0.1623621
Epoch: Iteration # 1000 error is: 0.1508138
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: 10.42948
Epoch: Iteration # 200 error is: 0.6924197
Epoch: Iteration # 300 error is: 0.506191
Epoch: Iteration # 400 error is: 0.526117
Epoch: Iteration # 500 error is: 0.9814832
Epoch: Iteration # 600 error is: 0.6133556
Epoch: Iteration # 700 error is: 0.3582829
Epoch: Iteration # 800 error is: 0.314946
Epoch: Iteration # 900 error is: 0.2963401
Epoch: Iteration # 1000 error is: 0.2846765
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: 25.53085
Epoch: Iteration # 200 error is: 4.522355
Epoch: Iteration # 300 error is: 1.372012
Epoch: Iteration # 400 error is: 0.6212966
Epoch: Iteration # 500 error is: 0.6200734
Epoch: Iteration # 600 error is: 0.5662201
Epoch: Iteration # 700 error is: 0.7751892
Epoch: Iteration # 800 error is: 0.5956016
Epoch: Iteration # 900 error is: 5.131498
Epoch: Iteration # 1000 error is: 1.663777
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== testthat results ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
144.25 5.62 167.89
|
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SIMLR.Rcheck/examples_i386/SIMLR-Ex.timings
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SIMLR.Rcheck/examples_x64/SIMLR-Ex.timings
|