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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SIMLR_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/SIMLR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SIMLR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    libs   1.9Mb
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
SIMLR_Feature_Ranking             85.58  0.676  86.410
SIMLR                             23.40  0.264  26.924
SIMLR_Estimate_Number_of_Clusters  3.84  0.140   7.858
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/SIMLR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL SIMLR
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Rtsne.cpp -o Rtsne.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c package_init.c -o package_init.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c projsplx_R.c -o projsplx_R.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sptree.cpp -o sptree.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) {
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
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:131:15:   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:131:15:   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)
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-SIMLR/00new/SIMLR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SIMLR)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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:  0.1326426 
Epoch: Iteration # 200  error is:  0.08721104 
Epoch: Iteration # 300  error is:  0.05808032 
Epoch: Iteration # 400  error is:  0.05713627 
Epoch: Iteration # 500  error is:  0.0570977 
Epoch: Iteration # 600  error is:  0.0570602 
Epoch: Iteration # 700  error is:  0.05702496 
Epoch: Iteration # 800  error is:  0.05699161 
Epoch: Iteration # 900  error is:  0.05696026 
Epoch: Iteration # 1000  error is:  0.05693017 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.26561 
Epoch: Iteration # 200  error is:  0.7396534 
Epoch: Iteration # 300  error is:  0.4116925 
Epoch: Iteration # 400  error is:  0.5374765 
Epoch: Iteration # 500  error is:  0.416797 
Epoch: Iteration # 600  error is:  0.3764571 
Epoch: Iteration # 700  error is:  0.4031923 
Epoch: Iteration # 800  error is:  0.4658629 
Epoch: Iteration # 900  error is:  0.5429834 
Epoch: Iteration # 1000  error is:  0.7786782 
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:  0.07916304 
Epoch: Iteration # 200  error is:  0.07265125 
Epoch: Iteration # 300  error is:  0.06588937 
Epoch: Iteration # 400  error is:  0.06431247 
Epoch: Iteration # 500  error is:  0.06408182 
Epoch: Iteration # 600  error is:  0.06389943 
Epoch: Iteration # 700  error is:  0.06375158 
Epoch: Iteration # 800  error is:  0.06362855 
Epoch: Iteration # 900  error is:  0.06352469 
Epoch: Iteration # 1000  error is:  0.06343539 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  10.90448 
Epoch: Iteration # 200  error is:  1.12194 
Epoch: Iteration # 300  error is:  0.9263245 
Epoch: Iteration # 400  error is:  0.6190663 
Epoch: Iteration # 500  error is:  0.4292005 
Epoch: Iteration # 600  error is:  0.372235 
Epoch: Iteration # 700  error is:  0.1507011 
Epoch: Iteration # 800  error is:  0.1493127 
Epoch: Iteration # 900  error is:  0.1488297 
Epoch: Iteration # 1000  error is:  0.1484048 
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:  0.1188644 
Epoch: Iteration # 200  error is:  0.06789612 
Epoch: Iteration # 300  error is:  0.05787332 
Epoch: Iteration # 400  error is:  0.05782322 
Epoch: Iteration # 500  error is:  0.05777752 
Epoch: Iteration # 600  error is:  0.05773384 
Epoch: Iteration # 700  error is:  0.05769336 
Epoch: Iteration # 800  error is:  0.05765563 
Epoch: Iteration # 900  error is:  0.05761978 
Epoch: Iteration # 1000  error is:  0.0575862 
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100  error is:  11.29595 
Epoch: Iteration # 200  error is:  0.6271535 
Epoch: Iteration # 300  error is:  0.5892638 
Epoch: Iteration # 400  error is:  0.439202 
Epoch: Iteration # 500  error is:  0.7205718 
Epoch: Iteration # 600  error is:  0.4206356 
Epoch: Iteration # 700  error is:  0.3308785 
Epoch: Iteration # 800  error is:  0.3098221 
Epoch: Iteration # 900  error is:  0.2966871 
Epoch: Iteration # 1000  error is:  0.2831221 
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
164.968   1.188 176.585