Luca De Sano
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/SIMLR |
| Branch: master |
| Last Commit: 443a70b |
| Last Changed Date: 2019-10-29 13:42:07 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:46:15 -0500 (Thu, 16 Jan 2020).
| Package 1596/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SIMLR 1.13.0 Luca De Sano
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SIMLR |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIMLR_1.13.0.tar.gz |
| StartedAt: 2020-01-16 08:58:42 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 09:08:31 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 589.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIMLR_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SIMLR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.13.0’
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SIMLR_Feature_Ranking 98.262 1.737 100.005
SIMLR 39.602 20.055 66.155
SIMLR_Estimate_Number_of_Clusters 5.490 2.180 12.989
* 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
‘/Users/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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIMLR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SIMLR’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Rtsne.cpp -o Rtsne.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c projsplx_R.c -o projsplx_R.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c sptree.cpp -o sptree.o
In file included from sptree.cpp:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
inline void warning(const std::string& message) { // #nocov start
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c tsne.cpp -o tsne.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 0.1140084
Epoch: Iteration # 200 error is: 0.06181848
Epoch: Iteration # 300 error is: 0.05932105
Epoch: Iteration # 400 error is: 0.05923113
Epoch: Iteration # 500 error is: 0.05914954
Epoch: Iteration # 600 error is: 0.05907505
Epoch: Iteration # 700 error is: 0.05900841
Epoch: Iteration # 800 error is: 0.05894696
Epoch: Iteration # 900 error is: 0.05889082
Epoch: Iteration # 1000 error is: 0.0588387
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.06134
Epoch: Iteration # 200 error is: 0.5629555
Epoch: Iteration # 300 error is: 0.364128
Epoch: Iteration # 400 error is: 0.2352786
Epoch: Iteration # 500 error is: 0.1219153
Epoch: Iteration # 600 error is: 0.09245907
Epoch: Iteration # 700 error is: 0.09084255
Epoch: Iteration # 800 error is: 0.08707661
Epoch: Iteration # 900 error is: 0.08706578
Epoch: Iteration # 1000 error is: 0.08711182
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: 0.08442679
Epoch: Iteration # 200 error is: 0.07563968
Epoch: Iteration # 300 error is: 0.0686836
Epoch: Iteration # 400 error is: 0.06687578
Epoch: Iteration # 500 error is: 0.06663136
Epoch: Iteration # 600 error is: 0.06645222
Epoch: Iteration # 700 error is: 0.06630663
Epoch: Iteration # 800 error is: 0.06618637
Epoch: Iteration # 900 error is: 0.06608476
Epoch: Iteration # 1000 error is: 0.0659978
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 15.52812
Epoch: Iteration # 200 error is: 1.714605
Epoch: Iteration # 300 error is: 1.059885
Epoch: Iteration # 400 error is: 0.8344297
Epoch: Iteration # 500 error is: 0.7312595
Epoch: Iteration # 600 error is: 0.6613094
Epoch: Iteration # 700 error is: 0.4670909
Epoch: Iteration # 800 error is: 0.3242695
Epoch: Iteration # 900 error is: 0.1311762
Epoch: Iteration # 1000 error is: 0.1295416
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: 0.1302831
Epoch: Iteration # 200 error is: 0.08219885
Epoch: Iteration # 300 error is: 0.0587416
Epoch: Iteration # 400 error is: 0.05864968
Epoch: Iteration # 500 error is: 0.05856638
Epoch: Iteration # 600 error is: 0.05849335
Epoch: Iteration # 700 error is: 0.05842535
Epoch: Iteration # 800 error is: 0.05836222
Epoch: Iteration # 900 error is: 0.05830468
Epoch: Iteration # 1000 error is: 0.05825144
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.30135
Epoch: Iteration # 200 error is: 0.5960109
Epoch: Iteration # 300 error is: 0.3803661
Epoch: Iteration # 400 error is: 0.3046971
Epoch: Iteration # 500 error is: 0.1818794
Epoch: Iteration # 600 error is: 0.1055357
Epoch: Iteration # 700 error is: 0.08532411
Epoch: Iteration # 800 error is: 0.08531052
Epoch: Iteration # 900 error is: 0.08533731
Epoch: Iteration # 1000 error is: 0.08539889
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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 4 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
218.586 66.022 300.357
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| SIMLR | 39.602 | 20.055 | 66.155 | |
| SIMLR_Estimate_Number_of_Clusters | 5.490 | 2.180 | 12.989 | |
| SIMLR_Feature_Ranking | 98.262 | 1.737 | 100.005 | |
| SIMLR_Large_Scale | 0.086 | 0.047 | 0.134 | |