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This page was generated on 2021-11-26 15:05:43 -0500 (Fri, 26 Nov 2021).

CHECK results for BioNERO on machv2

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.

raw results

Package 187/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNERO 1.2.0  (landing page)
Fabricio Almeida-Silva
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/BioNERO
git_branch: RELEASE_3_14
git_last_commit: c11998f
git_last_commit_date: 2021-10-26 13:08:05 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioNERO
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNERO_1.2.0.tar.gz
StartedAt: 2021-11-25 14:21:27 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 14:29:10 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 462.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNERO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNERO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNERO_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BioNERO.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.2.0’
* 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 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 24.051  0.053  24.119
* 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


Installation output

BioNERO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNERO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

BioNERO.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
[2021-11-25 14:28:06 EST] Validating user input...
[2021-11-25 14:28:06 EST]   Checking matrices for problems...
[2021-11-25 14:28:07 EST] Input ok!
[2021-11-25 14:28:07 EST] Calculating preservation of network subsets from
                          dataset "osa" in dataset "zma".
[2021-11-25 14:28:07 EST]   Pre-computing network properties in dataset
                            "osa"...
[2021-11-25 14:28:08 EST]   Calculating observed test statistics...
[2021-11-25 14:28:08 EST]   Generating null distributions from 2 permutations
                            using 1 thread...


    0% completed.
  100% completed.

[2021-11-25 14:28:09 EST]   Calculating P-values...
[2021-11-25 14:28:09 EST]   Collating results...
[2021-11-25 14:28:11 EST] 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:0.999999729526025
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 
 81.152   1.981  84.395 

Example timings

BioNERO.Rcheck/BioNERO-Ex.timings

nameusersystemelapsed
PC_correction2.5280.0492.580
SFT_fit1.8100.0471.859
ZKfiltering0.2020.0040.205
check_SFT1.2060.1121.318
consensus_SFT_fit3.3590.0753.440
consensus_modules2.7750.0422.820
consensus_trait_cor2.8520.0422.897
cormat_to_edgelist0.1480.0290.177
detect_communities0.1310.0130.145
dfs2one0.0340.0030.036
enrichment_analysis000
exp2gcn0.9800.0251.004
exp2grn0.9980.0321.030
exp_genes2orthogroups0.0010.0010.000
exp_preprocess3.1950.1043.301
filt.se0.0080.0010.009
filter_by_variance0.560.010.57
gene_significance0.1610.0100.172
get_HK0.4290.0110.440
get_edge_list1.1410.0361.178
get_hubs_gcn1.0500.0191.070
get_hubs_grn1.0860.0181.105
get_neighbors1.0290.0321.060
grn_average_rank0.6140.0350.648
grn_combined0.7100.0160.727
grn_filter1.6450.0251.672
grn_infer0.6650.0300.696
is_singleton0.0530.0030.055
modPres_WGCNA000
modPres_netrep0.0000.0000.001
module_enrichment000
module_preservation000
module_stability24.051 0.05324.119
module_trait_cor1.0400.0221.064
net_stats0.0010.0000.000
og.zma.osa0.0650.0010.066
osa.se0.1020.0020.104
parse_orthofinder0.0280.0020.029
plot_PCA0.5150.0050.520
plot_dendro_and_colors1.0360.0271.064
plot_dendro_and_cons_colors2.7210.0212.744
plot_eigengene_network1.0320.0131.046
plot_expression_profile1.0210.0121.034
plot_gcn1.1020.0191.123
plot_grn1.0760.0141.091
plot_heatmap0.0000.0010.000
plot_ngenes_per_module1.3120.0141.327
plot_ppi0.0560.0000.057
q_normalize0.3060.0060.312
remove_nonexp0.2130.0030.216
replace_na0.2080.0160.224
zma.interpro0.0580.0020.060
zma.se0.1530.0030.156
zma.tfs0.0010.0010.003