Luca De Sano
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SIMLR |
| Branch: master |
| Last Commit: fcb4351 |
| Last Changed Date: 2019-01-04 13:17:49 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:27:20 -0400 (Tue, 09 Apr 2019).
| Package 1497/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIMLR 1.9.1 Luca De Sano
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: SIMLR |
| Version: 1.9.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SIMLR_1.9.1.tar.gz |
| StartedAt: 2019-04-09 05:59:53 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:11:04 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 671.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SIMLR_1.9.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SIMLR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.9.1'
* 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 6.3Mb
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-3.9-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-3.9-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 70.61 3.90 74.53
SIMLR 21.34 0.59 24.25
SIMLR_Estimate_Number_of_Clusters 3.05 0.29 6.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SIMLR_Feature_Ranking 77.99 5.28 83.27
SIMLR 25.03 0.44 28.69
SIMLR_Estimate_Number_of_Clusters 3.55 0.15 6.49
* 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-3.9-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/3.9/bioc/src/contrib/SIMLR_1.9.1.tar.gz && rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMLR.buildbin-libdir SIMLR_1.9.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SIMLR_1.9.1.zip && rm SIMLR_1.9.1.tar.gz SIMLR_1.9.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
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100 3394k 100 3394k 0 0 22.2M 0 --:--:-- --:--:-- --:--:-- 23.1M
install for i386
* installing *source* package 'SIMLR' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.9.1.zip
* DONE (SIMLR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SIMLR' successfully unpacked and MD5 sums checked
|
SIMLR.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 11.18104
Epoch: Iteration # 200 error is: 0.4060685
Epoch: Iteration # 300 error is: 0.3114011
Epoch: Iteration # 400 error is: 0.1192762
Epoch: Iteration # 500 error is: 0.08464071
Epoch: Iteration # 600 error is: 0.08446789
Epoch: Iteration # 700 error is: 0.0844437
Epoch: Iteration # 800 error is: 0.0844258
Epoch: Iteration # 900 error is: 0.0850738
Epoch: Iteration # 1000 error is: 0.08438791
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: 17.64345
Epoch: Iteration # 200 error is: 1.960739
Epoch: Iteration # 300 error is: 1.424987
Epoch: Iteration # 400 error is: 0.8779441
Epoch: Iteration # 500 error is: 0.4875093
Epoch: Iteration # 600 error is: 0.3702732
Epoch: Iteration # 700 error is: 0.3488799
Epoch: Iteration # 800 error is: 0.1401622
Epoch: Iteration # 900 error is: 0.1392329
Epoch: Iteration # 1000 error is: 0.1384884
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: 11.07578
Epoch: Iteration # 200 error is: 1.378578
Epoch: Iteration # 300 error is: 1.055422
Epoch: Iteration # 400 error is: 0.606604
Epoch: Iteration # 500 error is: 0.6289526
Epoch: Iteration # 600 error is: 0.3893473
Epoch: Iteration # 700 error is: 0.3092045
Epoch: Iteration # 800 error is: 0.2803128
Epoch: Iteration # 900 error is: 0.1822032
Epoch: Iteration # 1000 error is: 0.1327397
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== testthat results ===========================================================
OK: 7 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
181.51 7.06 197.12
|
SIMLR.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 10.98224
Epoch: Iteration # 200 error is: 0.6360427
Epoch: Iteration # 300 error is: 0.3582133
Epoch: Iteration # 400 error is: 0.3223337
Epoch: Iteration # 500 error is: 0.2435822
Epoch: Iteration # 600 error is: 0.1253733
Epoch: Iteration # 700 error is: 0.08811818
Epoch: Iteration # 800 error is: 0.08517532
Epoch: Iteration # 900 error is: 0.08387783
Epoch: Iteration # 1000 error is: 0.08395212
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: 11.79281
Epoch: Iteration # 200 error is: 1.036511
Epoch: Iteration # 300 error is: 0.5807686
Epoch: Iteration # 400 error is: 0.7118712
Epoch: Iteration # 500 error is: 0.5498773
Epoch: Iteration # 600 error is: 0.5106477
Epoch: Iteration # 700 error is: 0.5427104
Epoch: Iteration # 800 error is: 0.7105668
Epoch: Iteration # 900 error is: 0.7734808
Epoch: Iteration # 1000 error is: 1.049789
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: 11.65457
Epoch: Iteration # 200 error is: 0.8189088
Epoch: Iteration # 300 error is: 0.4188216
Epoch: Iteration # 400 error is: 0.6338034
Epoch: Iteration # 500 error is: 0.4357441
Epoch: Iteration # 600 error is: 0.4091913
Epoch: Iteration # 700 error is: 1.289636
Epoch: Iteration # 800 error is: 0.5405964
Epoch: Iteration # 900 error is: 0.4573122
Epoch: Iteration # 1000 error is: 0.4443251
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== testthat results ===========================================================
OK: 7 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
134.76 5.03 149.75
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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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