Luca De Sano
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/SIMLR |
| Branch: RELEASE_3_11 |
| Last Commit: 5ed9270 |
| Last Changed Date: 2020-04-27 15:02:08 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:46 -0400 (Sat, 17 Oct 2020).
| 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 1667/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIMLR 1.14.0 Luca De Sano
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: SIMLR |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SIMLR_1.14.0.tar.gz |
| StartedAt: 2020-10-17 05:33:02 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:38:55 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 352.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SIMLR_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SIMLR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.0’
* 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 6.6Mb
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 79.924 0.619 80.560
SIMLR 24.302 0.234 27.889
SIMLR_Estimate_Number_of_Clusters 3.168 0.124 6.754
* 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-3.11-bioc/meat/SIMLR.Rcheck/00check.log’
for details.
SIMLR.Rcheck/00install.out
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###
### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SIMLR
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c Rtsne.cpp -o Rtsne.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-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)
SIMLR.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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: 10.76474
Epoch: Iteration # 200 error is: 0.7216043
Epoch: Iteration # 300 error is: 0.4862485
Epoch: Iteration # 400 error is: 0.36464
Epoch: Iteration # 500 error is: 0.3406427
Epoch: Iteration # 600 error is: 0.1694211
Epoch: Iteration # 700 error is: 0.1473943
Epoch: Iteration # 800 error is: 0.1069471
Epoch: Iteration # 900 error is: 0.09382392
Epoch: Iteration # 1000 error is: 0.09381111
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: 12.79467
Epoch: Iteration # 200 error is: 1.001361
Epoch: Iteration # 300 error is: 0.7795016
Epoch: Iteration # 400 error is: 0.6429233
Epoch: Iteration # 500 error is: 0.4830962
Epoch: Iteration # 600 error is: 0.5427652
Epoch: Iteration # 700 error is: 0.3767644
Epoch: Iteration # 800 error is: 0.3392701
Epoch: Iteration # 900 error is: 0.1526477
Epoch: Iteration # 1000 error is: 0.1473267
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: 11.1754
Epoch: Iteration # 200 error is: 0.5914209
Epoch: Iteration # 300 error is: 0.405185
Epoch: Iteration # 400 error is: 0.3017797
Epoch: Iteration # 500 error is: 0.2683896
Epoch: Iteration # 600 error is: 0.1445389
Epoch: Iteration # 700 error is: 0.1229764
Epoch: Iteration # 800 error is: 0.08812063
Epoch: Iteration # 900 error is: 0.08800135
Epoch: Iteration # 1000 error is: 0.08799902
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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
152.917 1.215 164.538
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| CIMLR | 0.000 | 0.000 | 0.001 | |
| CIMLR_Estimate_Number_of_Clusters | 0 | 0 | 0 | |
| SIMLR | 24.302 | 0.234 | 27.889 | |
| SIMLR_Estimate_Number_of_Clusters | 3.168 | 0.124 | 6.754 | |
| SIMLR_Feature_Ranking | 79.924 | 0.619 | 80.560 | |
| SIMLR_Large_Scale | 0.049 | 0.000 | 0.049 | |