| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:28 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 212/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNERO 1.10.0 (landing page) Fabricio Almeida-Silva
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the BioNERO package: - 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 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: BioNERO |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BioNERO_1.10.0.tar.gz |
| StartedAt: 2023-11-02 08:47:46 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 08:55:32 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 465.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BioNERO.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BioNERO_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BioNERO.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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
* using option ‘--no-vignettes’
* checking for file ‘BioNERO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNERO’ version ‘1.10.0’
* 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 ‘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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BioNERO-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: module_stability
> ### Title: Perform module stability analysis
> ### Aliases: module_stability
>
> ### ** Examples
>
> data(filt.se)
> filt <- filt.se[1:100, ] # reducing even further for testing purposes
> # The SFT fit was previously calculated and the optimal power was 16
> gcn <- exp2gcn(filt, SFTpower = 16, cor_method = "pearson")
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> # For simplicity, only 2 runs
> module_stability(exp = filt, net = gcn, nRuns = 2)
...working on run 1 ..
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 444011 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
..there is nothing to merge.
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.
* 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: 2 ERRORs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/BioNERO.Rcheck/00check.log’
for details.
BioNERO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BioNERO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-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.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.
> library(testthat)
> library(BioNERO)
>
> test_check("BioNERO")
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
mergeCloseModules: less than two proper modules.
..color levels are blue, grey
..there is nothing to merge.
[2023-11-02 08:54:43 UTC] Validating user input...
[2023-11-02 08:54:44 UTC] Checking matrices for problems...
[2023-11-02 08:54:45 UTC] Input ok!
[2023-11-02 08:54:45 UTC] Calculating preservation of network subsets from
dataset "osa" in dataset "zma".
[2023-11-02 08:54:45 UTC] Pre-computing network properties in dataset
"osa"...
[2023-11-02 08:54:47 UTC] Calculating observed test statistics...
[2023-11-02 08:54:47 UTC] Generating null distributions from 2 permutations
using 1 thread...
0% completed.
100% completed.
[2023-11-02 08:54:48 UTC] Calculating P-values...
[2023-11-02 08:54:48 UTC] Collating results...
[2023-11-02 08:54:51 UTC] Done!
2 modules in osa were preserved in zma:
NA, NA
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.00534 -0.621 0.1080 11.10 12.50 21.1
2 6 0.07230 -2.480 -0.0676 10.50 10.80 20.5
3 7 0.01870 -0.777 -0.0918 10.00 9.51 19.9
4 8 0.02070 -0.788 -0.1050 9.55 8.43 19.4
5 9 0.06560 -1.360 -0.1890 9.15 7.54 19.0
6 10 0.03530 -1.310 -0.1230 8.80 6.80 18.6
7 11 0.00722 -0.433 -0.0709 8.48 6.18 18.2
8 12 0.24400 -0.449 0.3850 8.19 5.65 17.8
9 13 0.04590 -1.130 -0.1740 7.92 5.29 17.5
10 14 0.04890 -1.140 -0.1780 7.68 5.00 17.2
11 15 0.25400 -0.442 0.3110 7.45 4.74 16.9
12 16 0.26300 -0.463 0.2150 7.24 4.51 16.6
13 17 0.02240 -0.739 -0.1300 7.04 4.30 16.3
14 18 0.02370 -0.760 -0.1380 6.85 4.12 16.0
15 19 0.02300 -0.792 -0.1280 6.68 3.95 15.8
16 20 0.02500 -0.819 -0.1280 6.51 3.79 15.6
No power reached R-squared cut-off, now choosing max R-squared based power
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.053700 -2.630 0.30600 11.90 16.50 22.4
2 6 0.017700 -1.330 0.25400 11.30 15.10 21.8
3 7 0.023200 -1.470 0.22400 10.80 13.90 21.2
4 8 0.005780 -0.636 0.15100 10.40 12.80 20.7
5 9 0.006220 -0.638 0.13800 9.98 11.80 20.2
6 10 0.007630 -0.691 0.11800 9.62 10.90 19.8
7 11 0.008810 -0.730 0.11400 9.30 10.20 19.3
8 12 0.002260 0.370 0.19400 9.00 9.47 19.0
9 13 0.004820 -0.614 0.08500 8.72 8.84 18.6
10 14 0.006750 -0.714 0.06110 8.47 8.28 18.3
11 15 0.001410 0.278 0.16100 8.23 7.77 18.0
12 16 0.000813 0.209 0.16400 8.00 7.30 17.7
13 17 0.000846 0.158 -0.00154 7.79 6.88 17.4
14 18 0.005320 -0.524 -0.01290 7.59 6.50 17.1
15 19 0.006440 -0.573 -0.02410 7.41 6.15 16.9
16 20 0.007590 -0.620 -0.03410 7.23 5.83 16.6
No power reached R-squared cut-off, now choosing max R-squared based power
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.012500 -0.655 -0.06640 12.30 15.20 21.9
2 6 0.039300 -1.430 -0.14300 11.00 13.20 20.4
3 7 0.000461 -0.120 0.02030 9.99 11.60 19.0
4 8 0.001340 0.257 0.17800 9.14 10.20 17.9
5 9 0.010800 -0.675 -0.06680 8.41 9.05 16.9
6 10 0.002830 0.270 0.09540 7.78 8.06 16.0
7 11 0.052300 1.580 0.25900 7.23 7.21 15.2
8 12 0.009940 0.761 0.27100 6.73 6.47 14.5
9 13 0.001370 0.236 -0.00272 6.29 5.83 13.9
10 14 0.000390 0.122 -0.01540 5.89 5.27 13.2
11 15 0.017200 0.585 0.07480 5.53 4.77 12.7
12 16 0.013800 0.508 0.06910 5.21 4.34 12.1
13 17 0.004920 0.393 0.19900 4.91 3.96 11.6
14 18 0.000553 0.128 0.11200 4.63 3.62 11.2
15 19 0.020800 -0.579 -0.11900 4.38 3.31 10.7
16 20 0.189000 -0.287 0.65200 4.14 3.10 10.3
No power reached R-squared cut-off, now choosing max R-squared based power
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.042000 -1.180 -0.2040 15.10 20.60 24.9
2 6 0.015800 -0.126 0.6970 13.60 18.60 23.4
3 7 0.024500 -0.909 -0.1420 12.40 16.90 22.1
4 8 0.025900 -0.899 -0.1370 11.30 15.40 20.9
5 9 0.011600 -0.567 -0.0690 10.50 14.00 19.9
6 10 0.008510 -0.509 -0.0515 9.71 12.90 18.9
7 11 0.010400 -0.527 -0.0564 9.04 11.80 18.1
8 12 0.005750 -0.537 0.0953 8.45 10.90 17.3
9 13 0.000810 -0.149 0.0368 7.92 9.99 16.5
10 14 0.000519 -0.120 0.0417 7.44 9.21 15.9
11 15 0.002240 0.326 0.2360 7.01 8.50 15.3
12 16 0.000815 0.189 0.2190 6.61 7.86 14.7
13 17 0.001540 0.265 0.2080 6.24 7.27 14.1
14 18 0.000705 0.173 0.1970 5.91 6.73 13.6
15 19 0.001480 0.181 0.0535 5.60 6.23 13.2
16 20 0.000709 0.121 0.0521 5.31 5.78 12.7
No power reached R-squared cut-off, now choosing max R-squared based power
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.0788 -0.225 0.274 9.01 9.20 17.30
2 6 0.0813 -0.238 0.238 7.98 8.19 15.70
3 7 0.1150 -0.272 0.448 7.18 7.43 14.50
4 8 0.1000 -0.285 0.374 6.54 6.83 13.50
5 9 0.0952 -0.275 0.376 6.01 6.18 12.60
6 10 0.1270 -0.270 0.351 5.57 5.61 12.00
7 11 0.1340 -0.293 0.372 5.20 5.11 11.50
8 12 0.1090 -0.276 0.340 4.87 4.67 11.00
9 13 0.1070 -0.255 0.392 4.59 4.29 10.60
10 14 0.1770 -0.285 0.425 4.34 3.95 10.20
11 15 0.2660 -0.325 0.542 4.12 3.64 9.88
12 16 0.0187 -0.713 -0.132 3.92 3.27 9.57
13 17 0.3350 -0.359 0.385 3.74 2.94 9.29
14 18 0.3150 -0.386 0.415 3.57 2.65 9.02
15 19 0.2970 -0.388 0.393 3.42 2.46 8.78
16 20 0.2540 -0.410 0.256 3.28 2.29 8.55
No power reached R-squared cut-off, now choosing max R-squared based power
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 5 0.051100 -0.2120 0.45900 12.70 15.10 23.2
2 6 0.010000 -0.6510 -0.07510 11.50 13.30 21.9
3 7 0.009570 -0.6000 -0.06850 10.60 11.90 20.7
4 8 0.000273 -0.1010 -0.01280 9.77 10.70 19.7
5 9 0.000223 -0.0938 -0.00614 9.10 9.72 18.8
6 10 0.001810 -0.4020 0.09960 8.52 8.76 18.0
7 11 0.003510 -0.5440 0.08990 8.03 7.93 17.3
8 12 0.004520 -0.6210 0.07440 7.59 7.22 16.6
9 13 0.002930 0.3120 0.01400 7.21 6.73 16.0
10 14 0.001980 0.2530 0.00897 6.87 6.30 15.4
11 15 0.001330 -0.3040 -0.00181 6.56 5.96 14.9
12 16 0.000502 -0.1820 0.00537 6.29 5.67 14.4
13 17 0.000976 -0.2510 -0.00053 6.04 5.30 14.0
14 18 0.032800 -1.0800 -0.15100 5.81 4.96 13.7
15 19 0.168000 -0.3710 0.52600 5.59 4.62 13.4
16 20 0.241000 -0.3990 0.62500 5.40 4.31 13.1
No power reached R-squared cut-off, now choosing max R-squared based power
Calculating adjacency matrix...
Calculating topological overlap matrix (TOM)...
..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 ...
mergeCloseModules: less than two proper modules.
..color levels are blue, grey
..there is nothing to merge.
Calculating adjacency matrix...
Calculating topological overlap matrix (TOM)...
..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 ...
mergeCloseModules: less than two proper modules.
..color levels are blue, grey
..there is nothing to merge.
Calculating adjacency matrix...
Calculating topological overlap matrix (TOM)...
..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 ...
mergeCloseModules: less than two proper modules.
..color levels are blue, grey
..there is nothing to merge.
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.
BioNERO.Rcheck/BioNERO-Ex.timings
| name | user | system | elapsed | |
| PC_correction | 1.516 | 0.060 | 1.589 | |
| SFT_fit | 2.201 | 0.096 | 2.325 | |
| ZKfiltering | 0.185 | 0.008 | 0.206 | |
| check_SFT | 12.293 | 1.007 | 14.986 | |
| consensus_SFT_fit | 4.806 | 0.056 | 4.883 | |
| consensus_modules | 4.485 | 0.068 | 4.585 | |
| consensus_trait_cor | 4.494 | 0.040 | 4.546 | |
| cormat_to_edgelist | 0.462 | 0.008 | 0.471 | |
| detect_communities | 0.505 | 0.000 | 0.507 | |
| dfs2one | 0.028 | 0.004 | 0.034 | |
| enrichment_analysis | 0 | 0 | 0 | |
| exp2gcn | 2.051 | 0.056 | 2.114 | |
| exp2grn | 1.488 | 0.008 | 1.501 | |
| exp_genes2orthogroups | 0 | 0 | 0 | |
| exp_preprocess | 2.525 | 0.028 | 2.558 | |
| filt.se | 0.007 | 0.000 | 0.007 | |
| filter_by_variance | 0.455 | 0.000 | 0.456 | |
| gene_significance | 0.041 | 0.000 | 0.042 | |
| get_HK | 0.325 | 0.008 | 0.334 | |
| get_edge_list | 2.110 | 0.008 | 2.123 | |
| get_hubs_gcn | 2.048 | 0.008 | 2.060 | |
| get_hubs_grn | 1.495 | 0.008 | 1.506 | |
| get_neighbors | 2.106 | 0.044 | 2.154 | |
| grn_average_rank | 2.278 | 0.016 | 2.298 | |
| grn_combined | 1.400 | 0.004 | 1.406 | |
| grn_filter | 1.485 | 0.004 | 1.492 | |
| grn_infer | 1.364 | 0.000 | 1.370 | |
| is_singleton | 0.054 | 0.031 | 0.101 | |
| modPres_WGCNA | 0 | 0 | 0 | |
| modPres_netrep | 0 | 0 | 0 | |
| module_enrichment | 0 | 0 | 0 | |
| module_preservation | 0 | 0 | 0 | |