Luca De Sano
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/SIMLR |
| git_branch: RELEASE_3_13 |
| git_last_commit: e3f8bf7 |
| git_last_commit_date: 2021-05-19 12:23:15 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:53 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the SIMLR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIMLR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1772/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIMLR 1.18.0 (landing page) Luca De Sano
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SIMLR |
| Version: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2021-10-15 00:04:15 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:10:44 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 389.6 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SIMLR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.18.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 LazyData ... 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’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
‘vignettes/1_introduction.Rmd’
‘vignettes/2_running_SIMLR.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SIMLR_Feature_Ranking 78.193 0.623 78.898
SIMLR 28.291 3.395 35.372
SIMLR_Estimate_Number_of_Clusters 3.532 0.208 7.014
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/SIMLR.Rcheck/00check.log’
for details.
SIMLR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIMLR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘SIMLR’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rtsne.cpp -o Rtsne.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c package_init.c -o package_init.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c projsplx_R.c -o projsplx_R.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sptree.cpp -o sptree.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tsne.cpp -o tsne.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 package_init.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-darwin18/8.2.0 -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/4.1/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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 11.83198
Epoch: Iteration # 200 error is: 1.160777
Epoch: Iteration # 300 error is: 0.5094063
Epoch: Iteration # 400 error is: 0.4451492
Epoch: Iteration # 500 error is: 0.3884115
Epoch: Iteration # 600 error is: 0.3819326
Epoch: Iteration # 700 error is: 0.3117741
Epoch: Iteration # 800 error is: 0.2884803
Epoch: Iteration # 900 error is: 0.2715681
Epoch: Iteration # 1000 error is: 0.1361636
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: 11.82515
Epoch: Iteration # 200 error is: 1.154264
Epoch: Iteration # 300 error is: 0.6795842
Epoch: Iteration # 400 error is: 0.8113276
Epoch: Iteration # 500 error is: 0.5412348
Epoch: Iteration # 600 error is: 0.6298531
Epoch: Iteration # 700 error is: 0.9992023
Epoch: Iteration # 800 error is: 0.7070315
Epoch: Iteration # 900 error is: 0.624638
Epoch: Iteration # 1000 error is: 0.5186006
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: 10.85252
Epoch: Iteration # 200 error is: 0.5761315
Epoch: Iteration # 300 error is: 0.5312145
Epoch: Iteration # 400 error is: 0.3584581
Epoch: Iteration # 500 error is: 0.1712543
Epoch: Iteration # 600 error is: 0.1232919
Epoch: Iteration # 700 error is: 0.08783833
Epoch: Iteration # 800 error is: 0.08771178
Epoch: Iteration # 900 error is: 0.08770943
Epoch: Iteration # 1000 error is: 0.08770704
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
166.608 10.338 187.517
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| CIMLR | 0.000 | 0.001 | 0.001 | |
| CIMLR_Estimate_Number_of_Clusters | 0.000 | 0.001 | 0.001 | |
| SIMLR | 28.291 | 3.395 | 35.372 | |
| SIMLR_Estimate_Number_of_Clusters | 3.532 | 0.208 | 7.014 | |
| SIMLR_Feature_Ranking | 78.193 | 0.623 | 78.898 | |
| SIMLR_Large_Scale | 0.102 | 0.006 | 0.108 | |