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CHECK report for SIMLR on tokay1

This page was generated on 2021-04-17 12:09:52 -0400 (Sat, 17 Apr 2021).

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 1718/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.16.0  (landing page)
Luca De Sano
Snapshot Date: 2021-04-16 14:50:12 -0400 (Fri, 16 Apr 2021)
URL: https://git.bioconductor.org/packages/SIMLR
Branch: RELEASE_3_12
Last Commit: 596a86f
Last Changed Date: 2020-10-27 11:17:59 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SIMLR
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SIMLR_1.16.0.tar.gz
StartedAt: 2021-04-17 05:41:43 -0400 (Sat, 17 Apr 2021)
EndedAt: 2021-04-17 05:53:05 -0400 (Sat, 17 Apr 2021)
EllapsedTime: 682.1 seconds
RetCode: 0
Status:   OK   
CheckDir: SIMLR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIMLR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SIMLR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SIMLR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.16.0'
* 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-3.12-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-3.12-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             90.93   3.37   94.32
SIMLR                             26.32   0.63   30.89
SIMLR_Estimate_Number_of_Clusters  3.57   0.20    6.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             88.31   6.20   94.53
SIMLR                             23.08   0.36   26.23
SIMLR_Estimate_Number_of_Clusters  3.06   0.21    6.08
* 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-3.12-bioc/meat/SIMLR.Rcheck/00check.log'
for details.



Installation output

SIMLR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SIMLR_1.16.0.tar.gz && rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIMLR.buildbin-libdir SIMLR_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SIMLR_1.16.0.zip && rm SIMLR_1.16.0.tar.gz SIMLR_1.16.0.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
  2 3396k    2 78595    0     0   192k      0  0:00:17 --:--:--  0:00:17  192k
100 3396k  100 3396k    0     0  7140k      0 --:--:-- --:--:-- --:--:-- 7135k

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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c package_init.c -o package_init.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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 package_init.o projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c package_init.c -o package_init.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-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 package_init.o projsplx_R.o sptree.o tsne.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.16.0.zip
* DONE (SIMLR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SIMLR' successfully unpacked and MD5 sums checked

Tests output

SIMLR.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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:  10.59875 
Epoch: Iteration # 200  error is:  0.9619874 
Epoch: Iteration # 300  error is:  0.5665638 
Epoch: Iteration # 400  error is:  0.6779151 
Epoch: Iteration # 500  error is:  0.3848024 
Epoch: Iteration # 600  error is:  0.3211689 
Epoch: Iteration # 700  error is:  0.3082795 
Epoch: Iteration # 800  error is:  0.2982666 
Epoch: Iteration # 900  error is:  0.2860989 
Epoch: Iteration # 1000  error is:  0.1781301 
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:  12.1877 
Epoch: Iteration # 200  error is:  0.9197569 
Epoch: Iteration # 300  error is:  0.6924188 
Epoch: Iteration # 400  error is:  0.8906617 
Epoch: Iteration # 500  error is:  0.7017097 
Epoch: Iteration # 600  error is:  0.630142 
Epoch: Iteration # 700  error is:  0.76244 
Epoch: Iteration # 800  error is:  0.5355426 
Epoch: Iteration # 900  error is:  0.4439679 
Epoch: Iteration # 1000  error is:  0.5284193 
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:  11.35145 
Epoch: Iteration # 200  error is:  0.7002961 
Epoch: Iteration # 300  error is:  0.6021221 
Epoch: Iteration # 400  error is:  0.4040208 
Epoch: Iteration # 500  error is:  0.3848705 
Epoch: Iteration # 600  error is:  0.3070025 
Epoch: Iteration # 700  error is:  0.2958764 
Epoch: Iteration # 800  error is:  0.2829787 
Epoch: Iteration # 900  error is:  0.425713 
Epoch: Iteration # 1000  error is:  0.2913335 
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 142.17    5.48  159.78 

SIMLR.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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:  10.92751 
Epoch: Iteration # 200  error is:  0.7210359 
Epoch: Iteration # 300  error is:  0.5104007 
Epoch: Iteration # 400  error is:  0.3313284 
Epoch: Iteration # 500  error is:  0.289371 
Epoch: Iteration # 600  error is:  0.174851 
Epoch: Iteration # 700  error is:  0.1495089 
Epoch: Iteration # 800  error is:  0.108155 
Epoch: Iteration # 900  error is:  0.1092274 
Epoch: Iteration # 1000  error is:  0.09952299 
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:  11.35152 
Epoch: Iteration # 200  error is:  0.6705065 
Epoch: Iteration # 300  error is:  0.5956412 
Epoch: Iteration # 400  error is:  0.4155148 
Epoch: Iteration # 500  error is:  0.152056 
Epoch: Iteration # 600  error is:  0.134689 
Epoch: Iteration # 700  error is:  0.1307356 
Epoch: Iteration # 800  error is:  0.1284252 
Epoch: Iteration # 900  error is:  0.125692 
Epoch: Iteration # 1000  error is:  0.1217373 
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:  10.85675 
Epoch: Iteration # 200  error is:  0.6320118 
Epoch: Iteration # 300  error is:  0.3543777 
Epoch: Iteration # 400  error is:  0.2897542 
Epoch: Iteration # 500  error is:  0.1632009 
Epoch: Iteration # 600  error is:  0.1368882 
Epoch: Iteration # 700  error is:  0.09562749 
Epoch: Iteration # 800  error is:  0.09214039 
Epoch: Iteration # 900  error is:  0.09213624 
Epoch: Iteration # 1000  error is:  0.09215991 
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 138.87    4.96  156.14 

Example timings

SIMLR.Rcheck/examples_i386/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR0.020.000.01
CIMLR_Estimate_Number_of_Clusters000
SIMLR26.32 0.6330.89
SIMLR_Estimate_Number_of_Clusters3.570.206.77
SIMLR_Feature_Ranking90.93 3.3794.32
SIMLR_Large_Scale0.090.000.10

SIMLR.Rcheck/examples_x64/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR000
CIMLR_Estimate_Number_of_Clusters000
SIMLR23.08 0.3626.23
SIMLR_Estimate_Number_of_Clusters3.060.216.08
SIMLR_Feature_Ranking88.31 6.2094.53
SIMLR_Large_Scale0.050.030.08