Daniele Ramazzotti
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/SIMLR |
| Branch: RELEASE_3_6 |
| Last Commit: 1fe35a0 |
| Last Changed Date: 2018-03-24 09:14:20 -0400 (Sat, 24 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:28 -0400 (Thu, 12 Apr 2018).
| Package 1301/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIMLR 1.4.1 Daniele Ramazzotti
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: SIMLR |
| Version: 1.4.1 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SIMLR_1.4.1.tar.gz |
| StartedAt: 2018-04-12 02:58:32 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:04:44 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 372.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SIMLR_1.4.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SIMLR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.1’
* 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 6.4Mb
sub-directories of 1Mb or more:
data 4.5Mb
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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SIMLR_Feature_Ranking 69.308 0.816 70.172
CIMLR 19.396 0.096 27.829
SIMLR 17.260 0.148 20.382
CIMLR_Estimate_Number_of_Clusters 4.712 0.108 13.349
SIMLR_Estimate_Number_of_Clusters 2.648 0.104 5.375
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/SIMLR.Rcheck/00check.log’
for details.
SIMLR.Rcheck/00install.out
* installing *source* package ‘SIMLR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c Rtsne.cpp -o Rtsne.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c projsplx_R.c -o projsplx_R.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c sptree.cpp -o sptree.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -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:131:15: 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)
^
tsne.cpp: In member function ‘bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)’:
tsne.cpp:938:29: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(n, sizeof(int), 1, h); // number of datapoints
^
tsne.cpp:939:29: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(d, sizeof(int), 1, h); // original dimensionality
^
tsne.cpp:940:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(theta, sizeof(double), 1, h); // gradient accuracy
^
tsne.cpp:941:41: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(perplexity, sizeof(double), 1, h); // perplexity
^
tsne.cpp:942:36: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(no_dims, sizeof(int), 1, h); // output dimensionality
^
tsne.cpp:945:45: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
fread(*data, sizeof(double), *n * *d, h); // the data
^
tsne.cpp:946:50: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
if(!feof(h)) fread(rand_seed, sizeof(int), 1, h); // random seed
^
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/SIMLR.Rcheck/SIMLR/libs
** 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
* DONE (SIMLR)
SIMLR.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 11.78908
Epoch: Iteration # 200 error is: 0.7079761
Epoch: Iteration # 300 error is: 0.512032
Epoch: Iteration # 400 error is: 0.6009774
Epoch: Iteration # 500 error is: 0.3636438
Epoch: Iteration # 600 error is: 0.3009944
Epoch: Iteration # 700 error is: 0.2812429
Epoch: Iteration # 800 error is: 0.267533
Epoch: Iteration # 900 error is: 0.1601832
Epoch: Iteration # 1000 error is: 0.1214188
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: 15.11473
Epoch: Iteration # 200 error is: 1.566407
Epoch: Iteration # 300 error is: 0.8852822
Epoch: Iteration # 400 error is: 0.593069
Epoch: Iteration # 500 error is: 0.469659
Epoch: Iteration # 600 error is: 0.792341
Epoch: Iteration # 700 error is: 0.4968921
Epoch: Iteration # 800 error is: 0.770514
Epoch: Iteration # 900 error is: 0.5251297
Epoch: Iteration # 1000 error is: 0.974118
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: 11.28532
Epoch: Iteration # 200 error is: 0.7066455
Epoch: Iteration # 300 error is: 0.568004
Epoch: Iteration # 400 error is: 0.5332019
Epoch: Iteration # 500 error is: 0.486104
Epoch: Iteration # 600 error is: 0.3944789
Epoch: Iteration # 700 error is: 0.3097391
Epoch: Iteration # 800 error is: 0.2987659
Epoch: Iteration # 900 error is: 0.2871239
Epoch: Iteration # 1000 error is: 0.2527763
Computing the multiple Kernels.
Performing network diffusion.
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: 0.1871698
Epoch: Iteration # 200 error is: 0.09894385
Epoch: Iteration # 300 error is: 0.09686709
Epoch: Iteration # 400 error is: 0.09643462
Epoch: Iteration # 500 error is: 0.1065708
Epoch: Iteration # 600 error is: 0.09599006
Epoch: Iteration # 700 error is: 0.4685521
Epoch: Iteration # 800 error is: 0.09790608
Epoch: Iteration # 900 error is: 0.09616597
Epoch: Iteration # 1000 error is: 0.09567124
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 22.81257
Epoch: Iteration # 200 error is: 1.476039
Epoch: Iteration # 300 error is: 5.737254
Epoch: Iteration # 400 error is: 1.151689
Epoch: Iteration # 500 error is: 0.5234374
Epoch: Iteration # 600 error is: 1.025298
Epoch: Iteration # 700 error is: 0.9642921
Epoch: Iteration # 800 error is: 1.826024
Epoch: Iteration # 900 error is: 0.7731801
Epoch: Iteration # 1000 error is: 0.2646443
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══ testthat results ═══════════════════════════════════════════════════════════
OK: 8 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
146.072 1.432 164.100
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| CIMLR | 19.396 | 0.096 | 27.829 | |
| CIMLR_Estimate_Number_of_Clusters | 4.712 | 0.108 | 13.349 | |
| SIMLR | 17.260 | 0.148 | 20.382 | |
| SIMLR_Estimate_Number_of_Clusters | 2.648 | 0.104 | 5.375 | |
| SIMLR_Feature_Ranking | 69.308 | 0.816 | 70.172 | |
| SIMLR_Large_Scale | 0.048 | 0.000 | 0.049 | |