Luca De Sano
| Snapshot Date: 2024-12-08 13:40 -0500 (Sun, 08 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/SIMLR |
| git_branch: devel |
| git_last_commit: 5ff2f17 |
| git_last_commit_date: 2024-10-29 10:14:19 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-09 11:47 -0500 (Mon, 09 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4749 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4461 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4411 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4366 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4241 |
| 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 1950/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIMLR 1.33.0 (landing page) Luca De Sano
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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 [email protected]: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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SIMLR |
| Version: 1.33.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SIMLR_1.33.0.tar.gz |
| StartedAt: 2024-12-09 10:02:55 -0000 (Mon, 09 Dec 2024) |
| EndedAt: 2024-12-09 10:07:32 -0000 (Mon, 09 Dec 2024) |
| EllapsedTime: 276.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SIMLR_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SIMLR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (conda-forge gcc 14.2.0-1) 14.2.0
GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.33.0’
* 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: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... INFO
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 3.3Mb
libs 2.0Mb
* 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 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 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 55.515 0.363 31.571
SIMLR 32.945 0.403 34.829
SIMLR_Estimate_Number_of_Clusters 3.103 0.075 5.801
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/SIMLR.Rcheck/00check.log’
for details.
SIMLR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SIMLR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘SIMLR’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c Rtsne.cpp -o Rtsne.o gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c package_init.c -o package_init.o gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c projsplx_R.c -o projsplx_R.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c sptree.cpp -o sptree.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -DR_NO_REMAP -c tsne.cpp -o tsne.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -lopenblas -L -L -lgfortran -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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: 0.1002465
Epoch: Iteration # 200 error is: 0.05982035
Epoch: Iteration # 300 error is: 0.05947052
Epoch: Iteration # 400 error is: 0.05926682
Epoch: Iteration # 500 error is: 0.05909646
Epoch: Iteration # 600 error is: 0.05895061
Epoch: Iteration # 700 error is: 0.0588265
Epoch: Iteration # 800 error is: 0.05871539
Epoch: Iteration # 900 error is: 0.05861945
Epoch: Iteration # 1000 error is: 0.05853214
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.30736
Epoch: Iteration # 200 error is: 0.8187899
Epoch: Iteration # 300 error is: 0.4808361
Epoch: Iteration # 400 error is: 0.5659874
Epoch: Iteration # 500 error is: 0.493312
Epoch: Iteration # 600 error is: 0.3656733
Epoch: Iteration # 700 error is: 0.3054119
Epoch: Iteration # 800 error is: 0.2926999
Epoch: Iteration # 900 error is: 0.2820008
Epoch: Iteration # 1000 error is: 0.2738678
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: 0.07985683
Epoch: Iteration # 200 error is: 0.07405478
Epoch: Iteration # 300 error is: 0.06712199
Epoch: Iteration # 400 error is: 0.06481996
Epoch: Iteration # 500 error is: 0.06459687
Epoch: Iteration # 600 error is: 0.0644226
Epoch: Iteration # 700 error is: 0.06427758
Epoch: Iteration # 800 error is: 0.06415905
Epoch: Iteration # 900 error is: 0.06405579
Epoch: Iteration # 1000 error is: 0.06396948
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.63175
Epoch: Iteration # 200 error is: 0.7934453
Epoch: Iteration # 300 error is: 0.8966482
Epoch: Iteration # 400 error is: 0.4827954
Epoch: Iteration # 500 error is: 0.3548003
Epoch: Iteration # 600 error is: 0.333882
Epoch: Iteration # 700 error is: 0.1609191
Epoch: Iteration # 800 error is: 0.1467918
Epoch: Iteration # 900 error is: 0.1457483
Epoch: Iteration # 1000 error is: 0.1452899
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: 0.1071239
Epoch: Iteration # 200 error is: 0.06081309
Epoch: Iteration # 300 error is: 0.06036734
Epoch: Iteration # 400 error is: 0.06020438
Epoch: Iteration # 500 error is: 0.06006716
Epoch: Iteration # 600 error is: 0.05994882
Epoch: Iteration # 700 error is: 0.05984484
Epoch: Iteration # 800 error is: 0.05975454
Epoch: Iteration # 900 error is: 0.05966999
Epoch: Iteration # 1000 error is: 0.05959479
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.03059
Epoch: Iteration # 200 error is: 0.6345634
Epoch: Iteration # 300 error is: 0.401524
Epoch: Iteration # 400 error is: 0.995778
Epoch: Iteration # 500 error is: 0.6201319
Epoch: Iteration # 600 error is: 0.3672825
Epoch: Iteration # 700 error is: 0.3214211
Epoch: Iteration # 800 error is: 0.3073427
Epoch: Iteration # 900 error is: 0.2989003
Epoch: Iteration # 1000 error is: 0.2897882
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
157.610 1.124 138.577
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| SIMLR | 32.945 | 0.403 | 34.829 | |
| SIMLR_Estimate_Number_of_Clusters | 3.103 | 0.075 | 5.801 | |
| SIMLR_Feature_Ranking | 55.515 | 0.363 | 31.571 | |
| SIMLR_Large_Scale | 0.051 | 0.004 | 0.054 | |