Marouen Ben Guebila
| Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/netZooR |
| git_branch: devel |
| git_last_commit: fcf288f |
| git_last_commit_date: 2024-10-29 11:07:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-28 11:47 -0500 (Tue, 28 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4659 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
| 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 1412/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netZooR 1.11.0 (landing page) Marouen Ben Guebila
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: netZooR |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings netZooR_1.11.0.tar.gz |
| StartedAt: 2025-01-28 13:17:39 -0000 (Tue, 28 Jan 2025) |
| EndedAt: 2025-01-28 13:37:55 -0000 (Tue, 28 Jan 2025) |
| EllapsedTime: 1215.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: netZooR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:netZooR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings netZooR_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/netZooR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netZooR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netZooR’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/netZooR.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 1.5Mb
extdata 2.9Mb
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
Package in Depends field not imported from: ‘matrixcalc’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
estimatePenaltyParameters: no visible global function definition for
‘matrix.trace’
runEgret: no visible binding for global variable ‘NA12878’
show,panda: no visible global function definition for ‘print.panda’
Undefined global functions or variables:
NA12878 matrix.trace print.panda
* checking Rd files ... NOTE
checkRd: (-1) condorCluster.Rd:39: Lost braces; missing escapes or markup?
39 | in the modularity for each iteration. Default is min(10^{-4},1/(number of edges)),
| ^
checkRd: (-1) dragon.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dragon.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
monsterMonsterNI 43.238 0.034 58.598
lioness 7.063 0.096 9.874
monsterTransformationMatrix 6.402 0.004 9.136
monsterBereFull 5.072 0.035 7.901
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-panda.R:29:4'): panda function works ───────────────────────────
<python.builtin.ModuleNotFoundError/python.builtin.ImportError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_run_file_impl(file, local, convert)`: ModuleNotFoundError: No module named 'pandas'
Run `reticulate::py_last_error()` for details.
Backtrace:
▆
1. └─netZooR::pandaPy(...) at test-panda.R:29:4
2. └─reticulate::source_python(pandapath, convert = TRUE)
3. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
4. └─reticulate:::py_run_file_impl(file, local, convert)
[ FAIL 1 | WARN 9 | SKIP 1 | PASS 48 ]
Error: Test failures
Execution halted
* 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, 5 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/netZooR.Rcheck/00check.log’
for details.
netZooR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL netZooR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘netZooR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (netZooR)
netZooR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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")'.
Loading required package: yarn
Warning: program compiled against libxml 212 using older 211
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: matrixcalc
Attaching package: 'matrixcalc'
The following object is masked from 'package:igraph':
%s%
>
> #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 0.0223684210526324"
[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
% 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 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 355 100 355 0 0 190 0 0:00:01 0:00:01 --:--:-- 190
100 355 100 355 0 0 190 0 0:00:01 0:00:01 --:--:-- 190
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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100 569 100 569 0 0 777 0 --:--:-- --:--:-- --:--:-- 777
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 840 100 840 0 0 962 0 --:--:-- --:--:-- --:--:-- 962
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
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0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 3242 100 3242 0 0 625 0 0:00:05 0:00:05 --:--:-- 625
100 3242 100 3242 0 0 625 0 0:00:05 0:00:05 --:--:-- 805
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
100 410 100 410 0 0 132 0 0:00:03 0:00:03 --:--:-- 132
100 410 100 410 0 0 132 0 0:00:03 0:00:03 --:--:-- 132
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 222 100 222 0 0 308 0 --:--:-- --:--:-- --:--:-- 308
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
1 1438k 1 16945 0 0 22226 0 0:01:06 --:--:-- 0:01:06 22208
40 1438k 40 579k 0 0 349k 0 0:00:04 0:00:01 0:00:03 349k
100 1438k 100 1438k 0 0 761k 0 0:00:01 0:00:01 --:--:-- 761k
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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100 578 100 578 0 0 314 0 0:00:01 0:00:01 --:--:-- 314
100 578 100 578 0 0 314 0 0:00:01 0:00:01 --:--:-- 314
[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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 27822 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
62 27822 62 17493 0 0 5018 0 0:00:05 0:00:03 0:00:02 5018
100 27822 100 27822 0 0 7159 0 0:00:03 0:00:03 --:--:-- 7159
[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 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
4 1079k 4 53482 0 0 21711 0 0:00:50 0:00:02 0:00:48 21705
6 1079k 6 70890 0 0 23108 0 0:00:47 0:00:03 0:00:44 23106
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45 1079k 45 494k 0 0 24724 0 0:00:44 0:00:20 0:00:24 13680
47 1079k 47 510k 0 0 24822 0 0:00:44 0:00:21 0:00:23 15266
50 1079k 50 545k 0 0 25132 0 0:00:43 0:00:22 0:00:21 17245
50 1079k 50 545k 0 0 24046 0 0:00:45 0:00:23 0:00:22 17245
50 1079k 50 545k 0 0 23072 0 0:00:47 0:00:24 0:00:23 14061
50 1079k 50 545k 0 0 21978 0 0:00:50 0:00:25 0:00:25 10584
52 1079k 52 562k 0 0 21730 0 0:00:50 0:00:26 0:00:24 9781
55 1079k 55 596k 0 0 22166 0 0:00:49 0:00:27 0:00:22 9799
56 1079k 56 613k 0 0 22312 0 0:00:49 0:00:28 0:00:21 14138
61 1079k 61 664k 0 0 23171 0 0:00:47 0:00:29 0:00:18 23638
61 1079k 61 664k 0 0 22407 0 0:00:49 0:00:30 0:00:19 24607
64 1079k 64 698k 0 0 22973 0 0:00:48 0:00:31 0:00:17 30085
66 1079k 66 715k 0 0 22681 0 0:00:48 0:00:32 0:00:16 25670
67 1079k 67 732k 0 0 22399 0 0:00:49 0:00:33 0:00:16 22858
69 1079k 69 749k 0 0 22515 0 0:00:49 0:00:34 0:00:15 18432
69 1079k 69 749k 0 0 21777 0 0:00:50 0:00:35 0:00:15 17850
70 1079k 70 766k 0 0 21544 0 0:00:51 0:00:36 0:00:15 13150
74 1079k 74 800k 0 0 21815 0 0:00:50 0:00:37 0:00:13 16509
75 1079k 75 817k 0 0 21983 0 0:00:50 0:00:38 0:00:12 18950
77 1079k 77 834k 0 0 21759 0 0:00:50 0:00:39 0:00:11 16790
82 1079k 82 885k 0 0 22422 0 0:00:49 0:00:40 0:00:09 26796
86 1079k 86 936k 0 0 23370 0 0:00:47 0:00:41 0:00:06 37802
89 1079k 89 969k 0 0 23301 0 0:00:47 0:00:42 0:00:05 34397
93 1079k 93 1004k 0 0 23585 0 0:00:46 0:00:43 0:00:03 34614
96 1079k 96 1038k 0 0 24051 0 0:00:45 0:00:44 0:00:01 42243
97 1079k 97 1055k 0 0 23637 0 0:00:46 0:00:45 0:00:01 32938
99 1079k 99 1072k 0 0 23714 0 0:00:46 0:00:46 --:--:-- 26390
100 1079k 100 1079k 0 0 23864 0 0:00:46 0:00:46 --:--:-- 30306
Time difference of 2.026558e-05 secs
Time difference of 55.34757 secs
Time difference of 0.5409088 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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 27822 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 27822 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 27822 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 27822 100 27822 0 0 4925 0 0:00:05 0:00:05 --:--:-- 5514
100 27822 100 27822 0 0 4925 0 0:00:05 0:00:05 --:--:-- 7960
[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 1 | WARN 9 | SKIP 1 | PASS 48 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-lioness.R:44:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-panda.R:29:4'): panda function works ───────────────────────────
<python.builtin.ModuleNotFoundError/python.builtin.ImportError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_run_file_impl(file, local, convert)`: ModuleNotFoundError: No module named 'pandas'
Run `reticulate::py_last_error()` for details.
Backtrace:
▆
1. └─netZooR::pandaPy(...) at test-panda.R:29:4
2. └─reticulate::source_python(pandapath, convert = TRUE)
3. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
4. └─reticulate:::py_run_file_impl(file, local, convert)
[ FAIL 1 | WARN 9 | SKIP 1 | PASS 48 ]
Error: Test failures
Execution halted
netZooR.Rcheck/netZooR-Ex.timings
| name | user | system | elapsed | |
| alpaca | 0.590 | 0.024 | 1.233 | |
| alpacaCommunityStructureRotation | 0.000 | 0.000 | 0.001 | |
| alpacaComputeDWBMmatmScale | 0.001 | 0.000 | 0.000 | |
| alpacaComputeWBMmat | 0 | 0 | 0 | |
| alpacaCrane | 0 | 0 | 0 | |
| alpacaDeltaZAnalysis | 0 | 0 | 0 | |
| alpacaDeltaZAnalysisLouvain | 0 | 0 | 0 | |
| alpacaExtractTopGenes | 0.398 | 0.060 | 0.459 | |
| alpacaGOtabtogenes | 0 | 0 | 0 | |
| alpacaGenLouvain | 0 | 0 | 0 | |
| alpacaGoToGenes | 0 | 0 | 0 | |
| alpacaListToGo | 0 | 0 | 0 | |
| alpacaMetaNetwork | 0 | 0 | 0 | |
| alpacaNodeToGene | 0 | 0 | 0 | |
| alpacaRotationAnalysis | 0 | 0 | 0 | |
| alpacaRotationAnalysisLouvain | 0 | 0 | 0 | |
| alpacaSimulateNetwork | 0 | 0 | 0 | |
| alpacaTestNodeRank | 0.000 | 0.001 | 0.000 | |
| alpacaTidyConfig | 0 | 0 | 0 | |
| alpacaTopEnsembltoTopSym | 0 | 0 | 0 | |
| alpacaWBMlouvain | 0.000 | 0.001 | 0.000 | |
| condorCluster | 1.464 | 0.058 | 1.973 | |
| condorCoreEnrich | 2.540 | 0.008 | 3.470 | |
| condorMatrixModularity | 0.013 | 0.004 | 0.018 | |
| condorModularityMax | 0.031 | 0.004 | 0.035 | |
| condorPlotCommunities | 1.461 | 0.008 | 1.969 | |
| condorPlotHeatmap | 0.206 | 0.012 | 0.219 | |
| condorQscore | 1.423 | 0.035 | 2.279 | |
| craneBipartite | 0 | 0 | 0 | |
| createCondorObject | 0.007 | 0.000 | 0.008 | |
| createPandaStyle | 0 | 0 | 0 | |
| lioness | 7.063 | 0.096 | 9.874 | |
| lionessPy | 0.004 | 0.000 | 0.004 | |
| monster | 0.034 | 0.000 | 0.034 | |
| monsterBereFull | 5.072 | 0.035 | 7.901 | |
| monsterCalculateTmPValues | 0.016 | 0.004 | 0.020 | |
| monsterCheckDataType | 0.131 | 0.084 | 0.216 | |
| monsterGetTm | 0.000 | 0.004 | 0.004 | |
| monsterHclHeatmapPlot | 0.761 | 0.027 | 0.877 | |
| monsterMonsterNI | 43.238 | 0.034 | 58.598 | |
| monsterPlotMonsterAnalysis | 0.033 | 0.000 | 0.033 | |
| monsterPrintMonsterAnalysis | 0.033 | 0.000 | 0.033 | |
| monsterTransformationMatrix | 6.402 | 0.004 | 9.136 | |
| monsterTransitionNetworkPlot | 0.354 | 0.004 | 0.359 | |
| monsterTransitionPCAPlot | 0.209 | 0.000 | 0.385 | |
| monsterdTFIPlot | 0.468 | 0.004 | 0.576 | |
| otter | 0.003 | 0.000 | 0.003 | |
| pandaDiffEdges | 0.003 | 0.000 | 0.004 | |
| pandaPy | 0.004 | 0.000 | 0.003 | |
| pandaToAlpaca | 0.004 | 0.000 | 0.004 | |
| pandaToCondorObject | 0.003 | 0.000 | 0.003 | |
| runEgret | 0.020 | 0.000 | 0.059 | |
| sambar | 2.462 | 0.013 | 4.054 | |
| sourcePPI | 0.010 | 0.000 | 0.022 | |
| spider | 0.011 | 0.000 | 0.025 | |
| visPandaInCytoscape | 0 | 0 | 0 | |