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CHECK report for SIMLR on malbec1

This page was generated on 2021-04-17 12:07:46 -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: /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
StartedAt: 2021-04-17 05:12:38 -0400 (Sat, 17 Apr 2021)
EndedAt: 2021-04-17 05:18:45 -0400 (Sat, 17 Apr 2021)
EllapsedTime: 366.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SIMLR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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             87.252  0.716  88.130
SIMLR                             25.016  0.236  28.464
SIMLR_Estimate_Number_of_Clusters  3.652  0.148   7.122
* 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.



Installation output

SIMLR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /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)

Tests output

SIMLR.Rcheck/tests/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-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:  11.16506 
Epoch: Iteration # 200  error is:  0.7866167 
Epoch: Iteration # 300  error is:  0.5305779 
Epoch: Iteration # 400  error is:  0.4934085 
Epoch: Iteration # 500  error is:  0.4658882 
Epoch: Iteration # 600  error is:  0.4056047 
Epoch: Iteration # 700  error is:  0.30896 
Epoch: Iteration # 800  error is:  0.2967416 
Epoch: Iteration # 900  error is:  0.2839588 
Epoch: Iteration # 1000  error is:  0.2651477 
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:  16.25715 
Epoch: Iteration # 200  error is:  2.209165 
Epoch: Iteration # 300  error is:  1.3092 
Epoch: Iteration # 400  error is:  0.5572943 
Epoch: Iteration # 500  error is:  0.570856 
Epoch: Iteration # 600  error is:  0.4976744 
Epoch: Iteration # 700  error is:  0.3912271 
Epoch: Iteration # 800  error is:  0.3796709 
Epoch: Iteration # 900  error is:  0.337547 
Epoch: Iteration # 1000  error is:  0.1737488 
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:  11.12705 
Epoch: Iteration # 200  error is:  1.029333 
Epoch: Iteration # 300  error is:  1.079088 
Epoch: Iteration # 400  error is:  0.7155709 
Epoch: Iteration # 500  error is:  0.6190219 
Epoch: Iteration # 600  error is:  0.4396076 
Epoch: Iteration # 700  error is:  0.3239738 
Epoch: Iteration # 800  error is:  0.3034358 
Epoch: Iteration # 900  error is:  0.2930345 
Epoch: Iteration # 1000  error is:  0.2834659 
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
162.728   1.932 175.033 

Example timings

SIMLR.Rcheck/SIMLR-Ex.timings

nameusersystemelapsed
CIMLR000
CIMLR_Estimate_Number_of_Clusters000
SIMLR25.016 0.23628.464
SIMLR_Estimate_Number_of_Clusters3.6520.1487.122
SIMLR_Feature_Ranking87.252 0.71688.130
SIMLR_Large_Scale0.0840.0040.085