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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings seqsetvis_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.30.0’
* 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 ‘seqsetvis’ 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘seqsetvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ssvSignalHeatmap
> ### Title: heatmap style representation of membership table. instead of
> ###   clustering, each column is sorted starting from the left.
> ### Aliases: ssvSignalHeatmap
> 
> ### ** Examples
> 
> data(CTCF_in_10a_profiles_gr)
> 
> #the simplest use
> ssvSignalHeatmap(CTCF_in_10a_profiles_gr)
clustering...
making plot...
> ssvSignalHeatmap(CTCF_in_10a_profiles_gr, show_cluster_bars = FALSE)
clustering...
making plot...
> 
> #clustering can be done manually beforehand
> clust_dt = ssvSignalClustering(CTCF_in_10a_profiles_gr, nclust = 3)
clustering...
> ssvSignalHeatmap(clust_dt)
making plot...
> 
> ssvSignalHeatmap(clust_dt, max_rows = 20, max_cols = 7)
7 columns were discarded according to max_cols: 7
80 rows were discarded according to max_rows: 20
making plot...
Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
ℹ Consider using `geom_tile()` instead.
> 
> # aggregation, when facet_ is shared by multiple samples
> prof_gr = CTCF_in_10a_profiles_gr
> prof_gr$mark = "CTCF"
> clust_gr = ssvSignalClustering(
+   prof_gr,
+   facet_ = "mark",
+   fun.aggregate = function(x)as.numeric(x > 10)
+ )
clustering...
Error: Aggregating functions should take a vector as input and return a single value (length=1), but they do not, so the result is undefined. Please fix by modifying your function so that a single value is always returned.
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
ssvFeatureBinaryHeatmap  7.245  0.270   7.516
ssvFetchBam              5.737  0.035   5.720
ssvSignalBandedQuantiles 4.872  0.141   4.818
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/seqsetvis.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL seqsetvis
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘seqsetvis’ ...
** this is package ‘seqsetvis’ version ‘1.30.0’
** 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 (seqsetvis)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> 
> ## load dependencies
> library(testthat)
> library(seqsetvis)
Loading required package: ggplot2
> library(data.table)
> 
> ## test package
> test_check(package = "seqsetvis")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1291 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1291 ]
> 
> proc.time()
   user  system elapsed 
266.733   1.582 263.648