| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the BioNERO package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNERO.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 185/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNERO 1.0.4 (landing page) Fabricio Almeida-Silva
| 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: BioNERO |
| Version: 1.0.4 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BioNERO_1.0.4.tar.gz |
| StartedAt: 2021-10-14 09:03:02 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:08:50 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 347.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNERO.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BioNERO_1.0.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BioNERO.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNERO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNERO’ version ‘1.0.4’
* 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 ‘BioNERO’ 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
module_stability 26.88 0.232 27.113
* 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: OK
BioNERO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BioNERO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘BioNERO’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BioNERO)
BioNERO.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-pc-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.
> library(testthat)
> library(BioNERO)
>
> test_check("BioNERO")
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[2021-10-14 09:07:44 EDT] Validating user input...
[2021-10-14 09:07:44 EDT] Checking matrices for problems...
[2021-10-14 09:07:45 EDT] Input ok!
[2021-10-14 09:07:45 EDT] Calculating preservation of network subsets from
dataset "osa" in dataset "zma".
[2021-10-14 09:07:45 EDT] Pre-computing network properties in dataset
"osa"...
[2021-10-14 09:07:46 EDT] Calculating observed test statistics...
[2021-10-14 09:07:46 EDT] Generating null distributions from 2 permutations
using 1 thread...
0% completed.
100% completed.
[2021-10-14 09:07:47 EDT] Calculating P-values...
[2021-10-14 09:07:47 EDT] Collating results...
[2021-10-14 09:07:50 EDT] Done!
None of the modules in osa were preserved in zma.
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.162 -0.241 0.0679 49.8 39.10 120.0
2 6 0.317 -0.353 0.1980 42.9 31.60 109.0
3 7 0.504 -0.441 0.4200 37.7 26.10 101.0
4 8 0.653 -0.529 0.5950 33.5 22.50 93.7
5 9 0.720 -0.598 0.6690 30.2 19.90 87.5
6 10 0.731 -0.656 0.6590 27.4 18.80 82.1
7 11 0.872 -0.686 0.8430 25.1 17.20 77.4
8 12 0.826 -0.721 0.7800 23.1 15.40 73.1
9 13 0.832 -0.739 0.7850 21.4 13.70 69.3
10 14 0.903 -0.737 0.8780 19.9 12.80 65.8
11 15 0.875 -0.756 0.8420 18.6 11.70 62.7
12 16 0.894 -0.764 0.8680 17.4 10.90 59.8
13 17 0.908 -0.756 0.8860 16.4 10.10 57.2
14 18 0.930 -0.761 0.9180 15.4 9.36 54.7
15 19 0.941 -0.762 0.9300 14.6 8.73 52.4
16 20 0.944 -0.764 0.9340 13.8 8.20 50.3
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.0693 -0.178 -0.154 59.7 44.3 137.0
2 6 0.1920 -0.282 0.026 51.9 37.8 127.0
3 7 0.3530 -0.378 0.226 45.8 33.3 119.0
4 8 0.4680 -0.453 0.335 40.9 28.6 111.0
5 9 0.6020 -0.530 0.505 36.9 25.6 105.0
6 10 0.6560 -0.596 0.564 33.6 22.3 98.9
7 11 0.7400 -0.664 0.667 30.8 20.1 93.8
8 12 0.7690 -0.699 0.704 28.3 19.1 89.1
9 13 0.8040 -0.747 0.749 26.2 17.5 84.9
10 14 0.8060 -0.781 0.750 24.4 16.1 81.1
11 15 0.8250 -0.792 0.776 22.7 14.8 77.5
12 16 0.8510 -0.822 0.811 21.3 13.6 74.3
13 17 0.8630 -0.816 0.824 20.0 12.5 71.4
14 18 0.8360 -0.847 0.789 18.8 11.5 68.7
15 19 0.8470 -0.867 0.804 17.7 11.0 66.1
16 20 0.8720 -0.884 0.836 16.8 10.2 63.8
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..done.
multiSetMEs: Calculating module MEs.
Working on set 1 ...
Working on set 2 ...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..done.
multiSetMEs: Calculating module MEs.
Working on set 1 ...
Working on set 2 ...
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..done.
multiSetMEs: Calculating module MEs.
Working on set 1 ...
Working on set 2 ...
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
Number of removed samples: 1
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 3 0.3340 1.0300 0.18900 145.0 149.0 222.0
2 4 0.2060 0.5420 0.05910 116.0 114.0 195.0
3 5 0.1460 0.3930 -0.00703 96.8 91.3 176.0
4 6 0.0556 0.1930 -0.07170 83.6 74.2 162.0
5 7 0.0209 0.1050 -0.07690 73.7 61.8 151.0
6 8 0.0015 -0.0255 -0.12100 66.0 51.9 142.0
7 9 0.0443 -0.1400 -0.16000 59.8 46.5 134.0
8 10 0.1470 -0.2570 -0.08480 54.7 43.2 127.0
9 11 0.2570 -0.3460 0.04810 50.4 39.7 121.0
10 12 0.3320 -0.3770 0.14800 46.7 36.6 116.0
11 13 0.4520 -0.4400 0.29700 43.5 32.8 111.0
12 14 0.5470 -0.4910 0.41800 40.8 30.1 107.0
13 15 0.5880 -0.5240 0.47300 38.3 27.6 103.0
14 16 0.6870 -0.5470 0.59800 36.1 24.8 99.5
15 17 0.7570 -0.5730 0.68900 34.1 22.9 96.1
16 18 0.8060 -0.5880 0.75100 32.3 21.4 93.0
17 19 0.8350 -0.6170 0.78800 30.7 20.1 90.1
18 20 0.8770 -0.6480 0.84100 29.2 19.3 87.4
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
...working on run 1 ..
The correlation threshold that best fits the scale-free topology is 0.02
Your graph fits the scale-free topology. P-value:0.999999729606805
The top number of edges that best fits the scale-free topology is 137
The top number of edges that best fits the scale-free topology is 137
The top number of edges that best fits the scale-free topology is 274
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
The top number of edges that best fits the scale-free topology is 279
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 107 ]
>
> proc.time()
user system elapsed
82.139 2.917 86.057
BioNERO.Rcheck/BioNERO-Ex.timings
| name | user | system | elapsed | |
| PC_correction | 1.707 | 0.015 | 1.723 | |
| SFT_fit | 1.609 | 0.032 | 1.641 | |
| ZKfiltering | 0.147 | 0.013 | 0.158 | |
| check_SFT | 1.920 | 0.088 | 2.008 | |
| consensus_SFT_fit | 2.812 | 0.039 | 2.852 | |
| consensus_modules | 2.345 | 0.036 | 2.381 | |
| consensus_trait_cor | 2.190 | 0.043 | 2.234 | |
| cormat_to_edgelist | 0.073 | 0.020 | 0.093 | |
| detect_communities | 0.099 | 0.017 | 0.115 | |
| dfs2one | 0.022 | 0.000 | 0.022 | |
| enrichment_analysis | 0.001 | 0.000 | 0.000 | |
| exp2gcn | 1.024 | 0.015 | 1.040 | |
| exp2grn | 0.678 | 0.004 | 0.682 | |
| exp_genes2orthogroups | 0 | 0 | 0 | |
| exp_preprocess | 1.560 | 0.048 | 1.608 | |
| filt.se | 0.008 | 0.000 | 0.008 | |
| filter_by_variance | 0.288 | 0.016 | 0.304 | |
| gene_significance | 1.390 | 0.016 | 1.410 | |
| get_HK | 0.221 | 0.008 | 0.229 | |
| get_edge_list | 1.019 | 0.016 | 1.036 | |
| get_hubs_gcn | 1.131 | 0.008 | 1.139 | |
| get_hubs_grn | 0.735 | 0.012 | 0.747 | |
| get_neighbors | 1.149 | 0.016 | 1.165 | |
| grn_average_rank | 0.532 | 0.004 | 0.537 | |
| grn_combined | 0.516 | 0.012 | 0.527 | |
| grn_filter | 0.672 | 0.000 | 0.673 | |
| grn_infer | 0.448 | 0.000 | 0.447 | |
| is_singleton | 0.051 | 0.004 | 0.055 | |
| modPres_WGCNA | 0 | 0 | 0 | |
| modPres_netrep | 0 | 0 | 0 | |
| module_enrichment | 0 | 0 | 0 | |
| module_preservation | 0 | 0 | 0 | |
| module_stability | 26.880 | 0.232 | 27.113 | |
| module_trait_cor | 1.017 | 0.012 | 1.028 | |
| net_stats | 0.001 | 0.000 | 0.000 | |
| og.zma.osa | 0.039 | 0.000 | 0.039 | |
| osa.se | 0.067 | 0.004 | 0.072 | |
| parse_orthofinder | 0.020 | 0.001 | 0.020 | |
| plot_PCA | 0.281 | 0.007 | 0.290 | |
| plot_dendro_and_colors | 0.990 | 0.036 | 1.026 | |
| plot_dendro_and_cons_colors | 2.222 | 0.028 | 2.249 | |
| plot_eigengene_network | 1.030 | 0.015 | 1.046 | |
| plot_expression_profile | 0.583 | 0.025 | 0.607 | |
| plot_gcn | 1.025 | 0.000 | 1.025 | |
| plot_grn | 0.590 | 0.015 | 0.606 | |
| plot_heatmap | 0 | 0 | 0 | |
| plot_ngenes_per_module | 1.234 | 0.012 | 1.247 | |
| plot_ppi | 0.032 | 0.000 | 0.032 | |
| q_normalize | 0.204 | 0.001 | 0.204 | |
| remove_nonexp | 0.144 | 0.008 | 0.152 | |
| replace_na | 0.143 | 0.003 | 0.147 | |
| zma.interpro | 0.037 | 0.004 | 0.041 | |
| zma.se | 0.119 | 0.000 | 0.119 | |
| zma.tfs | 0.002 | 0.000 | 0.002 | |