Luca De Sano
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SIMLR |
| git_branch: devel |
| git_last_commit: d51d195 |
| git_last_commit_date: 2025-10-03 12:54:57 -0400 (Fri, 03 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:05 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2022/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIMLR 1.35.1 (landing page) Luca De Sano
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the SIMLR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SIMLR |
| Version: 1.35.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIMLR_1.35.1.tar.gz |
| StartedAt: 2025-10-24 00:14:22 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 00:19:53 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 331.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIMLR_1.35.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SIMLR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.35.1’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 code 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 76.206 1.571 78.159
SIMLR 18.584 2.665 24.137
SIMLR_Estimate_Number_of_Clusters 2.441 0.267 5.467
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.22-bioc/meat/SIMLR.Rcheck/00check.log’
for details.
SIMLR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIMLR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘SIMLR’ ... ** this is package ‘SIMLR’ version ‘1.35.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rtsne.cpp -o Rtsne.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c package_init.c -o package_init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c projsplx_R.c -o projsplx_R.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sptree.cpp -o sptree.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tsne.cpp -o tsne.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-SIMLR/00new/SIMLR/libs ** R ** data ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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: 0.1229518
Epoch: Iteration # 200 error is: 0.07312843
Epoch: Iteration # 300 error is: 0.05759931
Epoch: Iteration # 400 error is: 0.05753535
Epoch: Iteration # 500 error is: 0.05747493
Epoch: Iteration # 600 error is: 0.05741953
Epoch: Iteration # 700 error is: 0.05736816
Epoch: Iteration # 800 error is: 0.05732153
Epoch: Iteration # 900 error is: 0.05727754
Epoch: Iteration # 1000 error is: 0.05723597
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 10.97291
Epoch: Iteration # 200 error is: 0.7272309
Epoch: Iteration # 300 error is: 0.6249083
Epoch: Iteration # 400 error is: 0.5576059
Epoch: Iteration # 500 error is: 0.5591361
Epoch: Iteration # 600 error is: 0.3558293
Epoch: Iteration # 700 error is: 0.3064292
Epoch: Iteration # 800 error is: 0.2934235
Epoch: Iteration # 900 error is: 0.2814463
Epoch: Iteration # 1000 error is: 0.2531454
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: 0.08098743
Epoch: Iteration # 200 error is: 0.07527675
Epoch: Iteration # 300 error is: 0.06842219
Epoch: Iteration # 400 error is: 0.06588471
Epoch: Iteration # 500 error is: 0.06569059
Epoch: Iteration # 600 error is: 0.06552502
Epoch: Iteration # 700 error is: 0.06538976
Epoch: Iteration # 800 error is: 0.06527794
Epoch: Iteration # 900 error is: 0.06517972
Epoch: Iteration # 1000 error is: 0.06509532
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.55185
Epoch: Iteration # 200 error is: 0.8064129
Epoch: Iteration # 300 error is: 0.6080224
Epoch: Iteration # 400 error is: 0.5999544
Epoch: Iteration # 500 error is: 0.3745553
Epoch: Iteration # 600 error is: 0.2292517
Epoch: Iteration # 700 error is: 0.1394939
Epoch: Iteration # 800 error is: 0.1382918
Epoch: Iteration # 900 error is: 0.1370003
Epoch: Iteration # 1000 error is: 0.1356662
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: 0.1173198
Epoch: Iteration # 200 error is: 0.05977255
Epoch: Iteration # 300 error is: 0.05807182
Epoch: Iteration # 400 error is: 0.05797701
Epoch: Iteration # 500 error is: 0.05789108
Epoch: Iteration # 600 error is: 0.05781275
Epoch: Iteration # 700 error is: 0.05774361
Epoch: Iteration # 800 error is: 0.05768104
Epoch: Iteration # 900 error is: 0.05762174
Epoch: Iteration # 1000 error is: 0.0575677
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.06096
Epoch: Iteration # 200 error is: 0.7185216
Epoch: Iteration # 300 error is: 0.939583
Epoch: Iteration # 400 error is: 0.4668489
Epoch: Iteration # 500 error is: 0.3872058
Epoch: Iteration # 600 error is: 0.5686431
Epoch: Iteration # 700 error is: 0.3811623
Epoch: Iteration # 800 error is: 0.4262217
Epoch: Iteration # 900 error is: 0.3605678
Epoch: Iteration # 1000 error is: 0.3474171
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[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
132.949 10.683 152.655
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| SIMLR | 18.584 | 2.665 | 24.137 | |
| SIMLR_Estimate_Number_of_Clusters | 2.441 | 0.267 | 5.467 | |
| SIMLR_Feature_Ranking | 76.206 | 1.571 | 78.159 | |
| SIMLR_Large_Scale | 0.036 | 0.002 | 0.039 | |