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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:fishpond.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings fishpond_2.17.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/fishpond.Rcheck’
* using R Under development (unstable) (2025-12-18 r89199)
* 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 ‘fishpond/DESCRIPTION’ ... OK
* this is package ‘fishpond’ version ‘2.17.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Michael Love <michaelisaiahlove@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Title field starts with the package name.
The Title field should be in title case. Current version is:
  ‘Fishpond: downstream methods and tools for expression data’
In title case that is:
  ‘Fishpond: Downstream Methods and Tools for Expression Data’

The Description field should not start with the package name,
  'This package' or similar.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘alevinEC.Rd’:
    https://doi.org/10.1186/s13059-019-1670-y
  File ‘computeInfRV.Rd’:
    https://doi.org/10.1093/nar/gkz622
  File ‘fishpond-package.Rd’:
    https://doi.org/10.1093/nar/gkz622
    https://doi.org/10.1101/2020.07.06.189639
  File ‘importAllelicCounts.Rd’:
    https://doi.org/10.1101/2022.08.12.503785
  File ‘loadFry.Rd’:
    https://doi.org/10.1038/s41592-022-01408-3
  File ‘makeInfReps.Rd’:
    https://doi.org/10.1101/2020.07.06.189639
  File ‘plotAllelicGene.Rd’:
    https://doi.org/10.1101/2022.08.12.503785
    https://doi.org/10.1007/978-1-4939-3578-9_16
  File ‘plotAllelicHeatmap.Rd’:
    https://doi.org/10.1101/2022.08.12.503785
  File ‘salmonEC.Rd’:
    https://doi.org/10.1038/nmeth.4197
  File ‘splitSwish.Rd’:
    https://doi.org/10.1101/2020.07.06.189639
    https://doi.org/10.1093/bioinformatics/bts480
  File ‘swish.Rd’:
    https://doi.org/10.1093/nar/gkz622
    https://doi.org/10.1177/0962280211428386
* 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 ‘fishpond’ 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'samr:::localfdr' 'samr:::predictlocalfdr' 'samr:::qvalue.func'
  'samr:::samr.compute.delta.table.seq'
  See the note in ?`:::` about the use of this operator.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/fishpond.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL fishpond
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘fishpond’ ...
** this is package ‘fishpond’ version ‘2.17.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (fishpond)

R Under development (unstable) (2025-12-18 r89199) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(fishpond)
> 
> test_check("fishpond")
Progress: 1 on 2  Progress: 2 on 2  [ FAIL 0 | WARN 0 | SKIP 6 | PASS 43 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (6): 'test_allelic.R:5:1', 'test_compress.R:5:1',
  'test_correlation.R:5:1', 'test_swish.R:120:1', 'test_swish.R:129:1',
  'test_swish.R:154:1'

[ FAIL 0 | WARN 0 | SKIP 6 | PASS 43 ]
> 
> proc.time()
   user  system elapsed 
 38.411   0.826  39.640