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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sSNAPPY.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sSNAPPY_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sSNAPPY.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 ‘sSNAPPY/DESCRIPTION’ ... OK
* this is package ‘sSNAPPY’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sSNAPPY’ 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 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 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-compute_ssFC.Rd':
  ‘factor’ ‘control’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 ... ERROR
Running examples in ‘sSNAPPY-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pathway_pert
> ### Title: Compute Single-sample Pathway-level Perturbation Score
> ### Aliases: pathway_pert
> 
> ### ** Examples
> 
> #compute weighted single sample logFCs
> data(metadata_example)
> data(logCPM_example)
> metadata_example <- dplyr::mutate(metadata_example, treatment = factor(
+    treatment, levels = c("Vehicle", "E2+R5020", "R5020")))
> ls <- weight_ss_fc(logCPM_example, metadata = metadata_example,
+ groupBy = "patient", treatColumn = "treatment", sampleColumn = "sample")
> # extract all the KEGG pathways
> gsTopology <- retrieve_topology(database = "kegg", species = "hsapiens")
Warning: Local storage of pathway data using format v1 was deprecated in graphite
1.55.1.
✔ graphite will automatically migrate to and use format v2 going forward.
ℹ If you no longer need compatibility with older graphite versions, run
  purgeCacheV1() to reclaim disk space.
ℹ The deprecated feature was likely used in the sSNAPPY package.
  Please report the issue at <https://github.com/Wenjun-Liu/sSNAPPY/issues>.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Resolving timed out after 10001 milliseconds
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?
Calls: retrieve_topology ... pathways -> loadData -> withArchiveDir -> func -> fetchRemote
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. └─sSNAPPY::retrieve_topology(...) at test-pathwayTopology.R:9:5
   2.   └─sSNAPPY:::.retrieveTopology(database, species, keyword)
   3.     └─base::lapply(database, function(x) pathways(species, x))
   4.       └─sSNAPPY (local) FUN(X[[i]], ...)
   5.         └─graphite::pathways(species, x)
   6.           └─graphite:::loadData(paste(species, database, sep = "-"))
   7.             └─graphite:::withArchiveDir(...)
   8.               └─graphite (local) func(path)
   9.                 └─graphite:::fetchRemote(name, path)
  
  [ FAIL 1 | WARN 20 | SKIP 0 | PASS 99 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/sSNAPPY.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sSNAPPY
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘sSNAPPY’ ...
** this is package ‘sSNAPPY’ version ‘1.14.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (sSNAPPY)

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.191   0.046   0.396 

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(sSNAPPY)
Loading required package: ggplot2

> 
> test_check("sSNAPPY")
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Resolving timed out after 10001 milliseconds
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Timeout was reached [graphiteweb.bio.unipd.it]:
Resolving timed out after 10001 milliseconds
Column names of the perturbation score matrix must match
                the sample column of the annotation_df. Annotation df ignored.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
Gene fold-changes were not provided as a named vector. All genes will be colored identically.
[ FAIL 1 | WARN 20 | SKIP 0 | PASS 99 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pathwayTopology.R:9:5'): retrieve_topology returns expected output ──
Error in `fetchRemote(name, path)`: cannot download pathway data: are you offline?
Backtrace:
    ▆
 1. └─sSNAPPY::retrieve_topology(...) at test-pathwayTopology.R:9:5
 2.   └─sSNAPPY:::.retrieveTopology(database, species, keyword)
 3.     └─base::lapply(database, function(x) pathways(species, x))
 4.       └─sSNAPPY (local) FUN(X[[i]], ...)
 5.         └─graphite::pathways(species, x)
 6.           └─graphite:::loadData(paste(species, database, sep = "-"))
 7.             └─graphite:::withArchiveDir(...)
 8.               └─graphite (local) func(path)
 9.                 └─graphite:::fetchRemote(name, path)

[ FAIL 1 | WARN 20 | SKIP 0 | PASS 99 ]
Error: Test failures
Execution halted