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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sparrow_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sparrow.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ 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 ‘sparrow’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.map_ids_orthogene: no visible binding for global variable ‘gspecies’
.map_ids_orthogene: no visible binding for global variable ‘species’
.map_ids_orthogene: no visible binding for global variable ‘input_ensg’
.map_ids_orthogene: no visible binding for global variable
  ‘ortholog_ensg’
.map_ids_orthogene: no visible binding for global variable
  ‘ortholog_gene’
.map_ids_orthogene: no visible binding for global variable ‘symbol’
.map_ids_orthogene: no visible binding for global variable ‘input_id’
.map_ids_orthogene: no visible global function definition for
  ‘starts_with’
.map_ids_orthogene: no visible global function definition for
  ‘last_col’
.map_ids_orthogene: no visible binding for global variable ‘rm_na’
geneSetsStats: no visible binding for global variable ‘direction’
getMSigGeneSetDb: no visible binding for global variable ‘ncbi_gene’
getMSigGeneSetDb: no visible binding for global variable ‘db_species’
getMSigGeneSetDb: no visible binding for global variable
  ‘msigdb_collection’
getMSigGeneSetDb: no visible binding for global variable ‘gene_symbol’
getMSigGeneSetDb: no visible binding for global variable
  ‘gs_collection_name’
getMSigGeneSetDb: no visible binding for global variable ‘gs_url’
convertIdentifiers,GeneSetDb: no visible binding for global variable
  ‘.convert_ids_with_babelgene’
convertIdentifiers,GeneSetDb: no visible global function definition for
  ‘.map_ids_babelgene’
Undefined global functions or variables:
  .convert_ids_with_babelgene .map_ids_babelgene db_species direction
  gene_symbol gs_collection_name gs_url gspecies input_ensg input_id
  last_col msigdb_collection ncbi_gene ortholog_ensg ortholog_gene
  rm_na species starts_with symbol
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'GeneSetDb-class.Rd':
  ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’

Non-topic package-anchored link(s) in Rd file 'calculateIndividualLogFC.Rd':
  ‘[limma:ebayes]{limma::eBayes()}’

Non-topic package-anchored link(s) in Rd file 'collectionMetadata.Rd':
  ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’

Non-topic package-anchored link(s) in Rd file 'seas.Rd':
  ‘[limma:toptable]{limma::topTable()}’
  ‘[limma:dupcor]{limma::duplicateCorrelation()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  seas.Rd: BiocParallel
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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘sparrow-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iplot
> ### Title: Visualize gene level behavior of genes within a geneset across a
> ###   contrast.
> ### Aliases: iplot
> 
> ### ** Examples
> 
> mgr <- exampleSparrowResult()
> iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
+       value = c("t-statistic" = "t"),
+       type = "density")
> iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
+       value = c("log2FC" = "logFC"),
+       type = "boxplot")
Error in pm[[2]] : subscript out of bounds
Calls: iplot ... withCallingHandlers -> ggplotly -> ggplotly.ggplot -> gg2list
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
goseq                     9.917  0.211  10.945
eigenWeightedMean         6.824  0.080   8.405
annotateGeneSetMembership 5.966  0.216   6.565
geneSetsStats             5.153  0.080   5.452
SparrowResult-utilities   4.777  0.112   5.578
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/sparrow.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sparrow
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘sparrow’ ...
** this is package ‘sparrow’ version ‘1.14.0’
** 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 (sparrow)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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("sparrow")
> library("testthat")
> library("data.table")
> library("dplyr")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following object is masked from 'package:testthat':

    matches

The following object is masked from 'package:sparrow':

    combine

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("sparrow")

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

[ FAIL 0 | WARN 0 | SKIP 6 | PASS 1475 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-MultiGSEAResult.R:3:1'
• {misgdbdf} is not installed (5): 'test-get-msigdb.R:6:3',
  'test-get-msigdb.R:14:3', 'test-get-msigdb.R:27:3', 'test-get-msigdb.R:65:3',
  'test-get-msigdb.R:99:3'

[ FAIL 0 | WARN 0 | SKIP 6 | PASS 1475 ]
> 
> ## Remove temporary files that were generated
> test.dir <- system.file('tests', package = "sparrow")
> pdfs <- dir(test.dir, "\\.pdf$", full.names=TRUE)
> if (length(pdfs)) {
+   unlink(pdfs)
+ }
> 
> 
> proc.time()
   user  system elapsed 
344.241   8.975 383.828