Multiple platform build/check report for BioC 3.22 - CHECK results for netZooR on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4810
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4528
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4493
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*

CHECK results for netZooR on taishan

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.

raw results

Summary

Package: netZooR

Version: 1.13.4

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_1.13.4.tar.gz

StartedAt: 2025-06-17 10:00:03 -0000 (Tue, 17 Jun 2025)

EndedAt: 2025-06-17 10:12:58 -0000 (Tue, 17 Jun 2025)

EllapsedTime: 774.2 seconds

RetCode: 1

Status: ERROR

CheckDir: netZooR.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.13.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘1.13.4’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    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 ... 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bladder.Rd: ExpressionSet-class
  normalizeTissueAware.Rd: 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')
> download.file(bladder, destfile='netZooR/data/bladder.rdata')
Warning in download.file(bladder, destfile = "netZooR/data/bladder.rdata") :
  URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/bladder.rdata: cannot open destfile 'netZooR/data/bladder.rdata', reason 'No such file or directory'
Warning in download.file(bladder, destfile = "netZooR/data/bladder.rdata") :
  download had nonzero exit status
> download.file(skin, destfile='netZooR/data/skin.rdata')
Warning in download.file(skin, destfile = "netZooR/data/skin.rdata") :
  URL https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/yarn/skin.rdata: cannot open destfile 'netZooR/data/skin.rdata', reason 'No such file or directory'
Warning in download.file(skin, destfile = "netZooR/data/skin.rdata") :
  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’
 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 1 | SKIP 1 | PASS 98 ]
  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: 2 ERRORs, 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/netZooR.Rcheck/00check.log’
for details.

Installation output

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/site-library’
* installing *source* package ‘netZooR’ ...
** this is package ‘netZooR’ version ‘1.13.4’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
--2025-06-16 21:04:36--  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)... 3.5.132.170, 52.219.229.98, 52.219.232.234, ...
Connecting to netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)|3.5.132.170|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1596768 (1.5M) [binary/octet-stream]
Saving to: ‘skin.rdata’

     0K .......... .......... .......... .......... ..........  3%  222K 7s
    50K .......... .......... .......... .......... ..........  6%  222K 7s
   100K .......... .......... .......... .......... ..........  9%  201M 4s
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  1550K .........                                             100% 17.4T=1.1s

2025-06-16 21:04:38 (1.35 MB/s) - ‘skin.rdata’ saved [1596768/1596768]

--2025-06-16 21:04:38--  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)... 52.219.99.66, 52.219.94.178, 52.219.142.74, ...
Connecting to netzoo.s3.us-east-2.amazonaws.com (netzoo.s3.us-east-2.amazonaws.com)|52.219.99.66|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1155612 (1.1M) [binary/octet-stream]
Saving to: ‘bladder.rdata’

     0K .......... .......... .......... .......... ..........  4% 53.5K 20s
    50K .......... .......... .......... .......... ..........  8% 56.6K 19s
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  1100K .......... .......... ........                        100%  168K=6.0s

2025-06-16 21:04:45 (189 KB/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)

Tests output

netZooR.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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")'.



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 0.0250000000000011"
[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  3242  100  3242    0     0   4500      0 --:--:-- --:--:-- --:--:--  4496
  % 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   410  100   410    0     0    494      0 --:--:-- --:--:-- --:--:--   494
100   410  100   410    0     0    494      0 --:--:-- --:--:-- --:--:--   494
  % 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   222  100   222    0     0    284      0 --:--:-- --:--:-- --:--:--   284
100   222  100   222    0     0    284      0 --:--:-- --:--:-- --:--:--   284
  % 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 1438k    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  4 1438k    4 69181    0     0  32491      0  0:00:45  0:00:02  0:00:43 32494
  8 1438k    8  118k    0     0  40093      0  0:00:36  0:00:03  0:00:33 40107
 15 1438k   15  220k    0     0  54373      0  0:00:27  0:00:04  0:00:23 54383
 27 1438k   27  390k    0     0  79189      0  0:00:18  0:00:05  0:00:13 79194
 42 1438k   42  611k    0     0   102k      0  0:00:13  0:00:05  0:00:08  123k
 85 1438k   85 1223k    0     0   172k      0  0:00:08  0:00:07  0:00:01  233k
100 1438k  100 1438k    0     0   197k      0  0:00:07  0:00:07 --:--:--  309k
  % 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   578  100   578    0     0    800      0 --:--:-- --:--:-- --:--:--   800
100   578  100   578    0     0    800      0 --:--:-- --:--:-- --:--:--   800
[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 27822    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 27822  100 27822    0     0  27723      0  0:00:01  0:00:01 --:--:-- 27738
[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
  1 1079k    1 16936    0     0  20439      0  0:00:54 --:--:--  0:00:54 20429
 43 1079k   43  468k    0     0   263k      0  0:00:04  0:00:01  0:00:03  263k
100 1079k  100 1079k    0     0   533k      0  0:00:02  0:00:02 --:--:--  533k
Time difference of 2.408028e-05 secs
Time difference of 42.17371 secs
Time difference of 1.759736 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 27822    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 27822  100 27822    0     0  21554      0  0:00:01  0:00:01 --:--:-- 21567
[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..."
[1] 1
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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 1 | SKIP 1 | PASS 98 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-lioness.R:45:1'

══ 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 1 | SKIP 1 | PASS 98 ]
Error: Test failures
Execution halted

Example timings

netZooR.Rcheck/netZooR-Ex.timings

name	user	system	elapsed
alpaca	0.751	0.008	0.763
alpacaCommunityStructureRotation	0	0	0
alpacaComputeDWBMmatmScale	0	0	0
alpacaComputeWBMmat	0	0	0
alpacaCrane	0	0	0
alpacaDeltaZAnalysis	0.000	0.000	0.001
alpacaDeltaZAnalysisLouvain	0	0	0
alpacaExtractTopGenes	0.421	0.008	0.430
alpacaGOtabtogenes	0	0	0
alpacaGenLouvain	0.000	0.000	0.001
alpacaGoToGenes	0	0	0
alpacaListToGo	0	0	0
alpacaMetaNetwork	0.000	0.000	0.001
alpacaNodeToGene	0	0	0
alpacaRotationAnalysis	0	0	0
alpacaRotationAnalysisLouvain	0.000	0.000	0.001
alpacaSimulateNetwork	0	0	0
alpacaTestNodeRank	0	0	0
alpacaTidyConfig	0.001	0.000	0.000
alpacaTopEnsembltoTopSym	0	0	0
alpacaWBMlouvain	0	0	0