Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-30 13:54:45 -0500 (Tue, 30 Nov 2021).

CHECK results for BioNERO on riesling1

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 184/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioNERO 1.3.0  (landing page)
Fabricio Almeida-Silva
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/BioNERO
git_branch: master
git_last_commit: 47d4c2a
git_last_commit_date: 2021-10-26 13:08:05 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioNERO
Version: 1.3.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNERO.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioNERO_1.3.0.tar.gz
StartedAt: 2021-11-30 00:55:25 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 01:00:15 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 290.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BioNERO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioNERO.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BioNERO_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BioNERO.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioNERO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNERO' version '1.3.0'
* 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 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 17.49   0.02    17.5
* 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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/BioNERO_1.3.0.tar.gz && rm -rf BioNERO.buildbin-libdir && mkdir BioNERO.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioNERO.buildbin-libdir BioNERO_1.3.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BioNERO_1.3.0.zip && rm BioNERO_1.3.0.tar.gz BioNERO_1.3.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 32 2496k   32  804k    0     0  2400k      0  0:00:01 --:--:--  0:00:01 2393k
100 2496k  100 2496k    0     0  3263k      0 --:--:-- --:--:-- --:--:-- 3263k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'BioNERO' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioNERO'
    finding HTML links ... done
    PC_correction                           html  
    SFT_fit                                 html  
    ZKfiltering                             html  
    check_SFT                               html  
    consensus_SFT_fit                       html  
    consensus_modules                       html  
    consensus_trait_cor                     html  
    cormat_to_edgelist                      html  
    detect_communities                      html  
    dfs2one                                 html  
    enrichment_analysis                     html  
    exp2gcn                                 html  
    exp2grn                                 html  
    exp_genes2orthogroups                   html  
    exp_preprocess                          html  
    filt.se                                 html  
    filter_by_variance                      html  
    gene_significance                       html  
    get_HK                                  html  
    get_edge_list                           html  
    get_hubs_gcn                            html  
    get_hubs_grn                            html  
    get_neighbors                           html  
    grn_average_rank                        html  
    grn_combined                            html  
    grn_filter                              html  
    grn_infer                               html  
    is_singleton                            html  
    modPres_WGCNA                           html  
    modPres_netrep                          html  
    module_enrichment                       html  
    module_preservation                     html  
    module_stability                        html  
    module_trait_cor                        html  
    net_stats                               html  
    og.zma.osa                              html  
    osa.se                                  html  
    parse_orthofinder                       html  
    plot_PCA                                html  
    plot_dendro_and_colors                  html  
    plot_dendro_and_cons_colors             html  
    plot_eigengene_network                  html  
    plot_expression_profile                 html  
    plot_gcn                                html  
    plot_grn                                html  
    plot_heatmap                            html  
    plot_ngenes_per_module                  html  
    plot_ppi                                html  
    q_normalize                             html  
    remove_nonexp                           html  
    replace_na                              html  
    zma.interpro                            html  
    zma.se                                  html  
    zma.tfs                                 html  
*** 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
* MD5 sums
packaged installation of 'BioNERO' as BioNERO_1.3.0.zip
* DONE (BioNERO)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'BioNERO' successfully unpacked and MD5 sums checked

Tests output

BioNERO.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
[2021-11-30 00:58:46 EST] Validating user input...
[2021-11-30 00:58:46 EST]   Checking matrices for problems...
[2021-11-30 00:58:46 EST] Input ok!
[2021-11-30 00:58:46 EST] Calculating preservation of network subsets from
                          dataset "osa" in dataset "zma".
[2021-11-30 00:58:46 EST]   Pre-computing network properties in dataset
                            "osa"...
[2021-11-30 00:58:47 EST]   Calculating observed test statistics...
[2021-11-30 00:58:47 EST]   Generating null distributions from 2 permutations
                            using 1 thread...


    0% completed.
  100% completed.

[2021-11-30 00:58:48 EST]   Calculating P-values...
[2021-11-30 00:58:48 EST]   Collating results...
[2021-11-30 00:58:50 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 272
The top number of edges that best fits the scale-free topology is 272
The top number of edges that best fits the scale-free topology is 269
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
The top number of edges that best fits the scale-free topology is 243
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
  44.89    2.10   48.00 

Example timings

BioNERO.Rcheck/BioNERO-Ex.timings

nameusersystemelapsed
PC_correction1.200.031.23
SFT_fit1.230.061.30
ZKfiltering0.130.020.14
check_SFT0.890.060.95
consensus_SFT_fit2.090.082.17
consensus_modules1.460.051.50
consensus_trait_cor1.450.121.60
cormat_to_edgelist0.090.000.09
detect_communities0.100.020.11
dfs2one0.030.000.03
enrichment_analysis000
exp2gcn0.650.010.67
exp2grn0.500.070.57
exp_genes2orthogroups000
exp_preprocess1.160.091.25
filt.se0.000.020.01
filter_by_variance0.240.010.25
gene_significance0.030.030.08
get_HK0.120.050.17
get_edge_list0.660.030.69
get_hubs_gcn0.70.00.7
get_hubs_grn0.500.050.55
get_neighbors0.740.030.76
grn_average_rank0.350.050.41
grn_combined0.350.030.38
grn_filter0.450.030.51
grn_infer0.350.000.34
is_singleton0.010.030.05
modPres_WGCNA000
modPres_netrep000
module_enrichment000
module_preservation000
module_stability17.49 0.0217.50
module_trait_cor0.680.000.70
net_stats000
og.zma.osa0.020.010.04
osa.se0.060.000.06
parse_orthofinder0.020.000.01
plot_PCA0.250.030.29
plot_dendro_and_colors0.680.020.70
plot_dendro_and_cons_colors1.600.001.59
plot_eigengene_network0.720.000.72
plot_expression_profile0.470.000.47
plot_gcn0.730.000.73
plot_grn0.520.000.52
plot_heatmap000
plot_ngenes_per_module0.840.010.86
plot_ppi0.030.000.03
q_normalize0.140.020.16
remove_nonexp0.110.000.11
replace_na0.110.000.11
zma.interpro0.030.000.03
zma.se0.080.000.08
zma.tfs0.010.000.02