Luca De Sano
| Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SIMLR |
| git_branch: devel |
| git_last_commit: c71cdab |
| git_last_commit_date: 2025-10-29 10:34:34 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 1992/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIMLR 1.37.0 (landing page) Luca De Sano
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
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: 1.37.0 |
| 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_1.37.0.tar.gz |
| StartedAt: 2025-11-12 20:24:05 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 20:25:28 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 83.1 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_1.37.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SIMLR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.37.0’
* 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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 ... INFO
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 6.506 1.723 10.030
SIMLR_Feature_Ranking 5.614 0.239 6.031
* 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: OK
SIMLR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIMLR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘SIMLR’ ... ** this is package ‘SIMLR’ version ‘1.37.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rtsne.cpp -o Rtsne.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c package_init.c -o package_init.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c projsplx_R.c -o projsplx_R.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sptree.cpp -o sptree.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tsne.cpp -o tsne.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-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/4.6-arm64/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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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: 0.1259277
Epoch: Iteration # 200 error is: 0.07210802
Epoch: Iteration # 300 error is: 0.05685978
Epoch: Iteration # 400 error is: 0.05680295
Epoch: Iteration # 500 error is: 0.05675019
Epoch: Iteration # 600 error is: 0.05670144
Epoch: Iteration # 700 error is: 0.05665626
Epoch: Iteration # 800 error is: 0.05661447
Epoch: Iteration # 900 error is: 0.05657567
Epoch: Iteration # 1000 error is: 0.05653806
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.48727
Epoch: Iteration # 200 error is: 0.6659356
Epoch: Iteration # 300 error is: 0.9877796
Epoch: Iteration # 400 error is: 0.4753637
Epoch: Iteration # 500 error is: 0.4349385
Epoch: Iteration # 600 error is: 0.4494219
Epoch: Iteration # 700 error is: 0.3338565
Epoch: Iteration # 800 error is: 0.3212187
Epoch: Iteration # 900 error is: 0.3096333
Epoch: Iteration # 1000 error is: 0.2971573
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: 0.08759611
Epoch: Iteration # 200 error is: 0.07740588
Epoch: Iteration # 300 error is: 0.07069018
Epoch: Iteration # 400 error is: 0.06738164
Epoch: Iteration # 500 error is: 0.06716357
Epoch: Iteration # 600 error is: 0.06698192
Epoch: Iteration # 700 error is: 0.06683599
Epoch: Iteration # 800 error is: 0.06671643
Epoch: Iteration # 900 error is: 0.0666142
Epoch: Iteration # 1000 error is: 0.0665278
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.62822
Epoch: Iteration # 200 error is: 0.8924103
Epoch: Iteration # 300 error is: 0.5482815
Epoch: Iteration # 400 error is: 0.4410494
Epoch: Iteration # 500 error is: 0.4619603
Epoch: Iteration # 600 error is: 0.4580351
Epoch: Iteration # 700 error is: 0.4404129
Epoch: Iteration # 800 error is: 0.3397917
Epoch: Iteration # 900 error is: 0.2166422
Epoch: Iteration # 1000 error is: 0.1510207
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: 0.09360971
Epoch: Iteration # 200 error is: 0.06261791
Epoch: Iteration # 300 error is: 0.0623342
Epoch: Iteration # 400 error is: 0.06209626
Epoch: Iteration # 500 error is: 0.06190268
Epoch: Iteration # 600 error is: 0.0617429
Epoch: Iteration # 700 error is: 0.06160663
Epoch: Iteration # 800 error is: 0.06148643
Epoch: Iteration # 900 error is: 0.06138284
Epoch: Iteration # 1000 error is: 0.06128984
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.27708
Epoch: Iteration # 200 error is: 0.6839249
Epoch: Iteration # 300 error is: 0.5336491
Epoch: Iteration # 400 error is: 0.4627225
Epoch: Iteration # 500 error is: 0.4958128
Epoch: Iteration # 600 error is: 0.4669063
Epoch: Iteration # 700 error is: 0.8247911
Epoch: Iteration # 800 error is: 0.5578106
Epoch: Iteration # 900 error is: 0.3804679
Epoch: Iteration # 1000 error is: 0.3966902
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
25.241 5.620 35.575
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| SIMLR | 6.506 | 1.723 | 10.030 | |
| SIMLR_Estimate_Number_of_Clusters | 0.829 | 0.173 | 2.173 | |
| SIMLR_Feature_Ranking | 5.614 | 0.239 | 6.031 | |
| SIMLR_Large_Scale | 0.021 | 0.001 | 0.023 | |