BioC 3.5: CHECK report for SIMLR on tokay2

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###
### Running command:
###
###   rm -rf SIMLR.buildbin-libdir SIMLR.Rcheck && mkdir SIMLR.buildbin-libdir SIMLR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SIMLR.buildbin-libdir SIMLR_1.2.3.tar.gz >SIMLR.Rcheck\00install.out 2>&1 && cp SIMLR.Rcheck\00install.out SIMLR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SIMLR.buildbin-libdir --install="check:SIMLR-install.out" --force-multiarch --no-vignettes --timings SIMLR_1.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SIMLR.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.2.3'
* 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
** 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-3.5-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 the system RNG.
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' ... ERROR
Running examples in 'SIMLR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SIMLR_Large_Scale
> ### Title: SIMLR Large Scale
> ### Aliases: SIMLR_Large_Scale
> 
> ### ** Examples
> 
> SIMLR_Large_Scale(X = ZeiselAmit$in_X, c = ZeiselAmit$n_clust, k = 5, kk = 5)
Performing fast PCA.
Performing k-nearest neighbour search.
Computing the multiple Kernels.
Performing the iterative procedure  5  times.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Performing Kmeans.
Performing t-SNE.
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
SIMLR_Feature_Ranking 81.05   3.98   85.03
SIMLR                 36.14   1.07   40.98
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla  "testthat.R" "testthat.Rout"' had status 5 
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
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  Performing fast PCA.
  Performing k-nearest neighbour search.
  Computing the multiple Kernels.
  Performing the iterative procedure  5  times.
  Iteration:  1 
  Iteration:  2 
  Iteration:  3 
  Iteration:  4 
  Iteration:  5 
  Performing Kmeans.
  Performing t-SNE.
** 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 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/SIMLR.Rcheck/00check.log'
for details.


R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 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:  10.66328 
Epoch: Iteration # 200  error is:  0.641005 
Epoch: Iteration # 300  error is:  0.667622 
Epoch: Iteration # 400  error is:  0.3981987 
Epoch: Iteration # 500  error is:  0.5879284 
Epoch: Iteration # 600  error is:  0.3850756 
Epoch: Iteration # 700  error is:  0.4332917 
Epoch: Iteration # 800  error is:  0.6046907 
Epoch: Iteration # 900  error is:  0.4231447 
Epoch: Iteration # 1000  error is:  0.3311644 
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:  15.68627 
Epoch: Iteration # 200  error is:  1.77144 
Epoch: Iteration # 300  error is:  1.225507 
Epoch: Iteration # 400  error is:  0.8085878 
Epoch: Iteration # 500  error is:  0.7076275 
Epoch: Iteration # 600  error is:  0.4931554 
Epoch: Iteration # 700  error is:  0.3910218 
Epoch: Iteration # 800  error is:  0.3889046 
Epoch: Iteration # 900  error is:  0.4454889 
Epoch: Iteration # 1000  error is:  0.4761313 
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:  11.80124 
Epoch: Iteration # 200  error is:  0.7481161 
Epoch: Iteration # 300  error is:  0.525638 
Epoch: Iteration # 400  error is:  0.6685444 
Epoch: Iteration # 500  error is:  0.480298 
Epoch: Iteration # 600  error is:  0.3920087 
Epoch: Iteration # 700  error is:  0.3446316 
Epoch: Iteration # 800  error is:  0.340509 
Epoch: Iteration # 900  error is:  0.3376508 
Epoch: Iteration # 1000  error is:  0.3346658 
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Performing fast PCA.
Performing k-nearest neighbour search.
Computing the multiple Kernels.
Performing the iterative procedure  5  times.
Iteration:  1 
Iteration:  2 
Iteration:  3 
Iteration:  4 
Iteration:  5 
Performing Kmeans.
Performing t-SNE.


install for i386

* installing *source* package 'SIMLR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c projsplx_R.c -o projsplx_R.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sptree.cpp -o sptree.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SIMLR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Rtsne.cpp -o Rtsne.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c projsplx_R.c -o projsplx_R.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sptree.cpp -o sptree.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -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˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIMLR' as SIMLR_1.2.3.zip
* DONE (SIMLR)

BioC 3.5: CHECK report for SIMLR on tokay2

Summary

Command output

name	user	system	elapsed
SIMLR	24.25	0.80	28.94
SIMLR_Feature_Ranking	87.51	3.80	91.32