| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:42 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1899/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SIMLR 1.27.1 (landing page) Luca De Sano
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: SIMLR |
| Version: 1.27.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SIMLR_1.27.1.tar.gz |
| StartedAt: 2023-06-06 07:00:59 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 07:18:55 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 1075.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SIMLR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:SIMLR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings SIMLR_1.27.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SIMLR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘SIMLR/DESCRIPTION’ ... OK
* this is package ‘SIMLR’ version ‘1.27.1’
* 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: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
data 3.3Mb
libs 2.5Mb
* 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 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 269.687 0.260 270.487
SIMLR 32.052 0.149 35.383
SIMLR_Estimate_Number_of_Clusters 4.605 0.025 7.684
* 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 ...
‘v1_introduction.Rmd’ using ‘UTF-8’... OK
‘v2_running_SIMLR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/SIMLR.Rcheck/00check.log’
for details.
SIMLR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL SIMLR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘SIMLR’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c Rtsne.cpp -o Rtsne.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/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-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/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-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c sptree.cpp -o sptree.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c tsne.cpp -o tsne.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o SIMLR.so RcppExports.o Rtsne.o package_init.o projsplx_R.o sptree.o tsne.o -llapack -lblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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: 0.125773
Epoch: Iteration # 200 error is: 0.07288419
Epoch: Iteration # 300 error is: 0.05820779
Epoch: Iteration # 400 error is: 0.0581354
Epoch: Iteration # 500 error is: 0.05808696
Epoch: Iteration # 600 error is: 0.05804318
Epoch: Iteration # 700 error is: 0.05800252
Epoch: Iteration # 800 error is: 0.05796352
Epoch: Iteration # 900 error is: 0.05792691
Epoch: Iteration # 1000 error is: 0.05789231
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.11449
Epoch: Iteration # 200 error is: 0.7646582
Epoch: Iteration # 300 error is: 0.5079967
Epoch: Iteration # 400 error is: 0.6897691
Epoch: Iteration # 500 error is: 0.4314475
Epoch: Iteration # 600 error is: 0.3667167
Epoch: Iteration # 700 error is: 0.5275262
Epoch: Iteration # 800 error is: 0.5281594
Epoch: Iteration # 900 error is: 0.4221967
Epoch: Iteration # 1000 error is: 0.3124382
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: 0.07877011
Epoch: Iteration # 200 error is: 0.07230809
Epoch: Iteration # 300 error is: 0.06545191
Epoch: Iteration # 400 error is: 0.06398822
Epoch: Iteration # 500 error is: 0.0637717
Epoch: Iteration # 600 error is: 0.06359895
Epoch: Iteration # 700 error is: 0.0634564
Epoch: Iteration # 800 error is: 0.06333717
Epoch: Iteration # 900 error is: 0.06323729
Epoch: Iteration # 1000 error is: 0.06315039
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 15.99458
Epoch: Iteration # 200 error is: 1.605406
Epoch: Iteration # 300 error is: 0.8692489
Epoch: Iteration # 400 error is: 0.7372846
Epoch: Iteration # 500 error is: 0.550561
Epoch: Iteration # 600 error is: 0.4992398
Epoch: Iteration # 700 error is: 0.42913
Epoch: Iteration # 800 error is: 0.5471447
Epoch: Iteration # 900 error is: 0.4700958
Epoch: Iteration # 1000 error is: 0.5129453
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: 0.115207
Epoch: Iteration # 200 error is: 0.05926174
Epoch: Iteration # 300 error is: 0.05826744
Epoch: Iteration # 400 error is: 0.05820007
Epoch: Iteration # 500 error is: 0.05813742
Epoch: Iteration # 600 error is: 0.05808124
Epoch: Iteration # 700 error is: 0.05802915
Epoch: Iteration # 800 error is: 0.05798035
Epoch: Iteration # 900 error is: 0.05793462
Epoch: Iteration # 1000 error is: 0.05789233
Performing Kmeans.
Performing t-SNE.
Epoch: Iteration # 100 error is: 11.51279
Epoch: Iteration # 200 error is: 0.5974999
Epoch: Iteration # 300 error is: 0.4053609
Epoch: Iteration # 400 error is: 0.298952
Epoch: Iteration # 500 error is: 0.1546419
Epoch: Iteration # 600 error is: 0.1308436
Epoch: Iteration # 700 error is: 0.09064797
Epoch: Iteration # 800 error is: 0.08616984
Epoch: Iteration # 900 error is: 0.08616485
Epoch: Iteration # 1000 error is: 0.08616518
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
378.083 1.454 389.284
SIMLR.Rcheck/SIMLR-Ex.timings
| name | user | system | elapsed | |
| SIMLR | 32.052 | 0.149 | 35.383 | |
| SIMLR_Estimate_Number_of_Clusters | 4.605 | 0.025 | 7.684 | |
| SIMLR_Feature_Ranking | 269.687 | 0.260 | 270.487 | |
| SIMLR_Large_Scale | 0.046 | 0.000 | 0.046 | |