| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-07 12:08 -0400 (Thu, 07 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
| 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 1430/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netZooR 1.13.14 (landing page) Marouen Ben Guebila
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the netZooR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netZooR.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. |
| Package: netZooR |
| Version: 1.13.14 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netZooR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netZooR_1.13.14.tar.gz |
| StartedAt: 2025-08-06 22:52:53 -0400 (Wed, 06 Aug 2025) |
| EndedAt: 2025-08-06 23:02:11 -0400 (Wed, 06 Aug 2025) |
| EllapsedTime: 557.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: netZooR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netZooR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netZooR_1.13.14.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.13.14’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘netZooR’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 1.7Mb
extdata 2.8Mb
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘cmdstanr’
* 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 ... WARNING
Missing link(s) in Rd file 'normalizeTissueAware.Rd':
‘limma::qsmooth’ ‘limma::normalizeQuantiles’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
bladder.Rd: ExpressionSet-class
normalizeTissueAware.Rd: limma::qsmooth, limma::normalizeQuantiles
skin.Rd: ExpressionSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data with usage in Rd file 'bladder.Rd' but not in code:
‘bladder’
Data with usage in Rd file 'skin.Rd' but not in code:
‘skin’
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Output for data("bladder", package = "netZooR"):
No dataset created in 'envir'
Warning message:
In utils::data(list = fileName, package = pkgname, envir = dataEnv) :
data set ‘bladder’ not found
Output for data("skin", package = "netZooR"):
No dataset created in 'envir'
Warning message:
In utils::data(list = fileName, package = pkgname, envir = dataEnv) :
data set ‘skin’ not found
* 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 ‘netZooR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotateFromBiomart
> ### Title: Annotate your Expression Set with biomaRt
> ### Aliases: annotateFromBiomart
>
> ### ** Examples
>
> u <- 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/'
> bladder <- paste0(u, 'yarn/bladder.rdata')
> skin <- paste0(u, 'yarn/skin.rdata')
> data_folder <- "data"
> dest_file_bladder <- file.path(data_folder, "bladder.rdata")
> dest_file_skin <- file.path(data_folder, "skin.rdata")
> download.file(bladder, destfile=dest_file_bladder)
Warning in download.file(bladder, destfile = dest_file_bladder) :
URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/bladder.rdata: cannot open destfile 'data/bladder.rdata', reason 'No such file or directory'
Warning in download.file(bladder, destfile = dest_file_bladder) :
download had nonzero exit status
> download.file(skin, destfile=dest_file_skin)
Warning in download.file(skin, destfile = dest_file_skin) :
URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/skin.rdata: cannot open destfile 'data/skin.rdata', reason 'No such file or directory'
Warning in download.file(skin, destfile = dest_file_skin) :
download had nonzero exit status
> data(skin)
Warning in data(skin) : data set ‘skin’ not found
> # subsetting and changing column name just for a silly example
> skin <- skin[1:10,]
Error in skin[1:10, ] : incorrect number of dimensions
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck/00check.log’
for details.
netZooR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netZooR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘netZooR’ ...
** this is package ‘netZooR’ version ‘1.13.14’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
--2025-08-06 15:43:27-- https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/skin.rdata
Resolving netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)... 52.219.228.146, 3.5.132.190, 3.5.133.137, ...
Connecting to netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)|52.219.228.146|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1596768 (1.5M) [binary/octet-stream]
Saving to: ‘skin.rdata’
0K .......... .......... .......... .......... .......... 3% 1.72M 1s
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1550K ......... 100% 47.8M=0.2s
2025-08-06 15:43:27 (8.83 MB/s) - ‘skin.rdata’ saved [1596768/1596768]
--2025-08-06 15:43:27-- https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/bladder.rdata
Resolving netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)... 3.5.133.198, 3.5.132.190, 3.5.133.137, ...
Connecting to netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)|3.5.133.198|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1155612 (1.1M) [binary/octet-stream]
Saving to: ‘bladder.rdata’
0K .......... .......... .......... .......... .......... 4% 1.72M 1s
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2025-08-06 15:43:28 (7.44 MB/s) - ‘bladder.rdata’ saved [1155612/1155612]
** help
*** installing help indices
** 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 (netZooR)
netZooR.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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(netZooR)
Loading required package: igraph
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: reticulate
Loading required package: pandaR
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:igraph':
components, union
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:igraph':
normalize, path
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> #download test data
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt','testthat/ppi_medium.txt')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt'
Content type 'text/plain' length 3674311 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData','testthat/testDataset.RData')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData'
Content type 'binary/octet-stream' length 15200389 bytes (14.5 MB)
==================================================
downloaded 14.5 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv','testthat/dragon_test_get_shrunken_covariance.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_test_get_shrunken_covariance.csv'
Content type 'text/csv' length 114 bytes
==================================================
downloaded 114 bytes
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv','testthat/dragon_layer1.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer1.csv'
Content type 'text/csv' length 2549985 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv','testthat/dragon_layer2.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_layer2.csv'
Content type 'text/csv' length 12749793 bytes (12.2 MB)
==================================================
downloaded 12.2 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv','testthat/dragon_python_cov.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_cov.csv'
Content type 'text/csv' length 9179450 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv','testthat/dragon_python_prec.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_prec.csv'
Content type 'text/csv' length 9179450 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv','testthat/dragon_python_parcor.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/dragon_python_parcor.csv'
Content type 'text/csv' length 9179576 bytes (8.8 MB)
==================================================
downloaded 8.8 MB
> download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv','testthat/risk_grid_netzoopy.csv')
trying URL 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/dragon/risk_grid_netzoopy.csv'
Content type 'text/csv' length 255025 bytes (249 KB)
==================================================
downloaded 249 KB
>
> test_check("netZooR")
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.0210526315789479"
[1] "Q = 0.0263157894736842"
[1] "Q = 0.0263157894736842"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 100 communities"
[1] 1
[1] 2
[1] 3
[1] "Merging 2 communities"
[1] 1
[1] "Computing node scores..."
[1] 1
[1] 2
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0"
[1] "Q = 0"
[1] "Q = 0.132231404958678"
[1] "Q = 0.148760330578512"
[1] "Q = 0.148760330578512"
[1] 0.231405 0.231405
[1] "Q = 0.198347107438017"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "Q = 0.140495867768595"
[1] "Q = 0.140495867768595"
[1] "modularity of projected graph 0.227272727272727"
[1] "Q = 0.231404958677686"
[1] "Q = 0.231404958677686"
[1] "modularity of projected graph 0.525346928655047"
[1] "Q = 0.52666696475026"
[1] "Q = 0.52666696475026"
[1] 0.79 0.00
final value 375.120000
converged
[1] 0.31 0.29
final value 36.897493
converged
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100 578 100 578 0 0 4275 0 --:--:-- --:--:-- --:--:-- 4281
[1] "Initializing and validating"
[1] "Verified sufficient samples"
[1] "Normalizing networks..."
[1] "Learning Network..."
[1] "Using tanimoto similarity"
[1] "Initializing and validating"
[1] "Verified sufficient samples"
[1] "Normalizing networks..."
[1] "Learning Network..."
[1] "Using tanimoto similarity"
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 27822 100 27822 0 0 127k 0 --:--:-- --:--:-- --:--:-- 128k
[1] "Computing network for sample 1"
[1] "Computing network for sample 2"
[1] "Computing network for sample 3"
[1] "Computing network for sample 4"
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 1085k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1085k 100 1085k 0 0 3499k 0 --:--:-- --:--:-- --:--:-- 3500k
Time difference of 1.597404e-05 secs
Time difference of 1.993622 secs
Time difference of 0.758121 secs
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MONSTER object
2555 genes
20 baseline samples
20 final samples
Transition driven by 53 transcription factors
Run with 10 randomized permutations.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
62 27822 62 17493 0 0 123k 0 --:--:-- --:--:-- --:--:-- 122k
100 27822 100 27822 0 0 194k 0 --:--:-- --:--:-- --:--:-- 194k
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/netZooR/extdata/panda.py:278: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
norm_col = zscore(x, axis=0)
Loading motif data ...
Elapsed time: 0.01 sec.
Loading expression data ...
Elapsed time: 0.01 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.08 sec.
Calculating coexpression network ...
Elapsed time: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.06 sec.
intersection /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt True False True
Normalizing networks ...
Elapsed time: 0.00 sec.
Clearing motif and ppi data, unique tfs, and gene names for speed
Running PANDA algorithm ...
step: 0, hamming: 0.6788049340248108
step: 1, hamming: 0.4237635135650635
step: 2, hamming: 0.37942326068878174
step: 3, hamming: 0.3818596303462982
step: 4, hamming: 0.38526612520217896
step: 5, hamming: 0.3832989037036896
step: 6, hamming: 0.36915773153305054
step: 7, hamming: 0.34574776887893677
step: 8, hamming: 0.3152081370353699
step: 9, hamming: 0.2818054258823395
step: 10, hamming: 0.24849660694599152
step: 11, hamming: 0.21666744351387024
step: 12, hamming: 0.18729539215564728
step: 13, hamming: 0.16079428791999817
step: 14, hamming: 0.13726867735385895
step: 15, hamming: 0.11666569113731384
step: 16, hamming: 0.09877122193574905
step: 17, hamming: 0.08336563408374786
step: 18, hamming: 0.07016084343194962
step: 19, hamming: 0.0588911771774292
step: 20, hamming: 0.04931585118174553
step: 21, hamming: 0.041211165487766266
step: 22, hamming: 0.03437765687704086
step: 23, hamming: 0.02863147482275963
step: 24, hamming: 0.023808928206562996
step: 25, hamming: 0.01977088674902916
step: 26, hamming: 0.016396764665842056
step: 27, hamming: 0.013582728803157806
step: 28, hamming: 0.011239760555326939
step: 29, hamming: 0.009291945025324821
step: 30, hamming: 0.00767497019842267
step: 31, hamming: 0.006334253121167421
step: 32, hamming: 0.005223960615694523
step: 33, hamming: 0.004305404145270586
step: 34, hamming: 0.003546181134879589
step: 35, hamming: 0.002919197781011462
step: 36, hamming: 0.002401866717264056
step: 37, hamming: 0.001975313061848283
step: 38, hamming: 0.0016238006064668298
step: 39, hamming: 0.001334363128989935
step: 40, hamming: 0.0010961104417219758
step: 41, hamming: 0.0009001354337669909
Running panda took: 0.02 seconds!
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/netZooR/extdata/panda.py:278: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
norm_col = zscore(x, axis=0)
Loading motif data ...
Elapsed time: 0.00 sec.
Loading expression data ...
Elapsed time: 0.00 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.07 sec.
Calculating coexpression network ...
Elapsed time: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.06 sec.
legacy /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False False False
Normalizing networks ...
Elapsed time: 0.01 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.5867745269558597
step: 1, hamming: 0.47709480696171536
step: 2, hamming: 0.46956168666614617
step: 3, hamming: 0.45425003629838684
step: 4, hamming: 0.4187427725151872
step: 5, hamming: 0.36797241244238343
step: 6, hamming: 0.31337190961143313
step: 7, hamming: 0.2640386174641925
step: 8, hamming: 0.2239999232789824
step: 9, hamming: 0.19253176059893798
step: 10, hamming: 0.1676553667649102
step: 11, hamming: 0.14730006142326466
step: 12, hamming: 0.12982159089839332
step: 13, hamming: 0.11459157116297604
step: 14, hamming: 0.10108821391424125
step: 15, hamming: 0.08890364507467007
step: 16, hamming: 0.07787244456478047
step: 17, hamming: 0.06785464923123906
step: 18, hamming: 0.05878796471238135
step: 19, hamming: 0.05062155744809771
step: 20, hamming: 0.04333239380925903
step: 21, hamming: 0.036892574940160516
step: 22, hamming: 0.03126206012121671
step: 23, hamming: 0.026384280403921743
step: 24, hamming: 0.02219096174091557
step: 25, hamming: 0.01860922988517212
step: 26, hamming: 0.015566652188260116
step: 27, hamming: 0.012993283312056427
step: 28, hamming: 0.010824919177296213
step: 29, hamming: 0.009003507268894196
step: 30, hamming: 0.007477552910889816
step: 31, hamming: 0.006202062894110505
step: 32, hamming: 0.005138069423501655
step: 33, hamming: 0.004252085993537945
step: 34, hamming: 0.0035154788596479794
step: 35, hamming: 0.0029039267439058677
step: 36, hamming: 0.0023968521367998463
step: 37, hamming: 0.0019768786344578106
step: 38, hamming: 0.0016294013136896753
step: 39, hamming: 0.0013421799963357426
step: 40, hamming: 0.0011049738470584863
step: 41, hamming: 0.0009092279973180559
Running panda took: 0.06 seconds!
Loading motif data ...
Elapsed time: 0.00 sec.
Loading expression data ...
Elapsed time: 0.00 sec.
Loading PPI data ...
Number of PPIs: 100019
Elapsed time: 0.07 sec.
Remove expression not in motif:
166 rows removed from the initial 200
Remove motif not in expression data:
467 rows removed from the initial 506
Remove ppi not in motif:
100017 rows removed from the initial 100019
new case
Calculating coexpression network ...
Elapsed time: 0.00 sec.
Creating motif network ...
Elapsed time: 0.00 sec.
Creating PPI network ...
Elapsed time: 0.00 sec.
legacy /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/netZooR/extdata/chip_medium.txt ./expr4_200_L.txt ./ppi_medium.txt False True False
Normalizing networks ...
Elapsed time: 0.00 sec.
Saving expression matrix and normalized networks ...
Elapsed time: 0.00 sec.
Running PANDA algorithm ...
step: 0, hamming: 0.6201117836163109
step: 1, hamming: 0.48938385169250487
step: 2, hamming: 0.49937220814370303
step: 3, hamming: 0.5234998024292964
step: 4, hamming: 0.5316279091580729
step: 5, hamming: 0.5196461826284898
step: 6, hamming: 0.49096615680840516
step: 7, hamming: 0.4513686776299505
step: 8, hamming: 0.4081852233215106
step: 9, hamming: 0.363060630725845
step: 10, hamming: 0.31891232474094794
step: 11, hamming: 0.27733895854371826
step: 12, hamming: 0.23925292481822666
step: 13, hamming: 0.20518316158337402
step: 14, hamming: 0.17501658473943318
step: 15, hamming: 0.14854288648840214
step: 16, hamming: 0.12553582999076407
step: 17, hamming: 0.10573284427875865
step: 18, hamming: 0.08878386418920353
step: 19, hamming: 0.0743688270511516
step: 20, hamming: 0.062172412390917475
step: 21, hamming: 0.05188071541370959
step: 22, hamming: 0.0432203223195204
step: 23, hamming: 0.03594946787636905
step: 24, hamming: 0.0298598954759094
step: 25, hamming: 0.024770938396293206
step: 26, hamming: 0.020525756048994263
step: 27, hamming: 0.016990787588434902
step: 28, hamming: 0.01405117127516721
step: 29, hamming: 0.011609873894851032
step: 30, hamming: 0.009584973156032739
step: 31, hamming: 0.007907374279360037
step: 32, hamming: 0.006518966440957099
step: 33, hamming: 0.005370999156869476
step: 34, hamming: 0.004422666090211268
step: 35, hamming: 0.0036398792478184367
step: 36, hamming: 0.0029942146499029876
step: 37, hamming: 0.002462010284380602
step: 38, hamming: 0.0020235978467206695
step: 39, hamming: 0.001662650998788413
step: 40, hamming: 0.00136563438767126
step: 41, hamming: 0.0011213392761822388
step: 42, hamming: 0.0009204932425645715
Running panda took: 0.01 seconds!
[1] "Detecting communities in control network..."
[1] "modularity of projected graph 0.471004488691679"
[1] "Q = 0.471024100010188"
[1] "Q = 0.471024100010188"
[1] "Computing differential modularity matrix..."
[1] "Computing differential modules..."
[1] "Merging 386 communities"
[1] 1
[1] 2
[1] "Merging 201 communities"
[1] 1
[1] "Computing node scores..."
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Read 7424 items
WARNING: Score threshold is not specified. We will be using medium stringency cut-off of 400.
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.0/83332.protein.aliases.v11.0.txt.gz'
Content type 'application/octet-stream' length 614783 bytes (600 KB)
==================================================
downloaded 600 KB
trying URL 'https://stringdb-downloads.org/download/protein.info.v11.0/83332.protein.info.v11.0.txt.gz'
Content type 'application/octet-stream' length 442274 bytes (431 KB)
==================================================
downloaded 431 KB
trying URL 'https://stringdb-downloads.org/download/protein.links.v11.0/83332.protein.links.v11.0.txt.gz'
Content type 'application/octet-stream' length 7455726 bytes (7.1 MB)
==================================================
downloaded 7.1 MB
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 115 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-lioness.R:45:1'
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 115 ]
>
> proc.time()
user system elapsed
58.114 4.913 83.667
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.450 | 0.031 | 0.486 | |
| alpacaCommunityStructureRotation | 0 | 0 | 0 | |
| alpacaComputeDWBMmatmScale | 0.000 | 0.000 | 0.001 | |
| alpacaComputeWBMmat | 0 | 0 | 0 | |
| alpacaCrane | 0.000 | 0.000 | 0.001 | |
| alpacaDeltaZAnalysis | 0.000 | 0.000 | 0.001 | |
| alpacaDeltaZAnalysisLouvain | 0.000 | 0.000 | 0.001 | |
| alpacaExtractTopGenes | 0.289 | 0.039 | 0.330 | |
| alpacaGOtabtogenes | 0 | 0 | 0 | |
| alpacaGenLouvain | 0.001 | 0.000 | 0.000 | |
| alpacaGoToGenes | 0 | 0 | 0 | |
| alpacaListToGo | 0 | 0 | 0 | |
| alpacaMetaNetwork | 0 | 0 | 0 | |
| alpacaNodeToGene | 0 | 0 | 0 | |
| alpacaRotationAnalysis | 0 | 0 | 0 | |
| alpacaRotationAnalysisLouvain | 0.000 | 0.000 | 0.001 | |
| alpacaSimulateNetwork | 0 | 0 | 0 | |
| alpacaTestNodeRank | 0 | 0 | 0 | |
| alpacaTidyConfig | 0 | 0 | 0 | |
| alpacaTopEnsembltoTopSym | 0 | 0 | 0 | |
| alpacaWBMlouvain | 0 | 0 | 0 | |