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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BiocSet.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings BiocSet_1.17.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocSet.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSet/DESCRIPTION’ ... OK
* this is package ‘BiocSet’ version ‘1.17.1’
* 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 ‘BiocSet’ 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BiocSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiocSet-methods
> ### Title: BiocSet methods
> ### Aliases: BiocSet-methods es_activate filter.BiocSet select.BiocSet
> ###   mutate.BiocSet summarise.BiocSet arrange.BiocSet
> ###   .tbl_nongroup_vars.BiocSet group_by.BiocSet left_join.BiocSet
> ###   as.list.BiocSet union.BiocSet intersect.BiocSet
> ### Keywords: internal
> 
> ### ** Examples
> 
> es <- BiocSet(set1 = letters, set2 = LETTERS)
> es_activate(es, element)
class: BiocSet

es_element() <active>:
# A tibble: 52 × 1
  element
  <chr>  
1 a      
2 b      
3 c      
# ℹ 49 more rows

es_set():
# A tibble: 2 × 1
  set  
  <chr>
1 set1 
2 set2 

es_elementset():
# A tibble: 52 × 2
  element set  
  <chr>   <chr>
1 a       set1 
2 b       set1 
3 c       set1 
# ℹ 49 more rows
> 
> es %>% es_activate(element) %>% filter(element == "a")
class: BiocSet

es_element() <active>:
# A tibble: 1 × 1
  element
  <chr>  
1 a      

es_set():
# A tibble: 2 × 1
  set  
  <chr>
1 set1 
2 set2 

es_elementset():
# A tibble: 1 × 2
  element set  
  <chr>   <chr>
1 a       set1 
> 
> es %>% select(element)
class: BiocSet

es_element():
# A tibble: 52 × 1
  element
  <chr>  
1 a      
2 b      
3 c      
# ℹ 49 more rows

es_set():
# A tibble: 2 × 1
  set  
  <chr>
1 set1 
2 set2 

es_elementset() <active>:
# A tibble: 52 × 2
  element set  
  <chr>   <chr>
1 a       set1 
2 b       set1 
3 c       set1 
# ℹ 49 more rows
> 
> es %>% es_activate(set) %>% mutate(pval = rnorm(1:2))
class: BiocSet

es_element():
# A tibble: 52 × 1
  element
  <chr>  
1 a      
2 b      
3 c      
# ℹ 49 more rows

es_set() <active>:
# A tibble: 2 × 2
  set     pval
  <chr>  <dbl>
1 set1  -0.626
2 set2   0.184

es_elementset():
# A tibble: 52 × 2
  element set  
  <chr>   <chr>
1 a       set1 
2 b       set1 
3 c       set1 
# ℹ 49 more rows
> 
> es %>% es_activate(set) %>% summarise(n = n())
# A tibble: 1 × 1
      n
  <int>
1     2
> 
> es %>% es_activate(element) %>% arrange(desc(element))
class: BiocSet

es_element() <active>:
# A tibble: 52 × 1
  element
  <chr>  
1 z      
2 y      
3 x      
# ℹ 49 more rows

es_set():
# A tibble: 2 × 1
  set  
  <chr>
1 set1 
2 set2 

es_elementset():
# A tibble: 52 × 2
  element set  
  <chr>   <chr>
1 a       set1 
2 b       set1 
3 c       set1 
# ℹ 49 more rows
> 
> es %>% mutate(pval = rnorm(1:52)) %>% es_elementset() %>%
+     BiocSet:::.tbl_nongroup_vars()
[1] "element" "set"     "pval"   
> 
> es %>% group_by(element, set)
Warning: The `add` argument of `group_by()` is deprecated as of dplyr 1.0.0.
ℹ Please use the `.add` argument instead.
ℹ The deprecated feature was likely used in the dplyr package.
  Please report the issue at <https://github.com/tidyverse/dplyr/issues>.
# A tibble: 52 × 2
# Groups:   element, set [52]
   element set  
   <chr>   <chr>
 1 a       set1 
 2 b       set1 
 3 c       set1 
 4 d       set1 
 5 e       set1 
 6 f       set1 
 7 g       set1 
 8 h       set1 
 9 i       set1 
10 j       set1 
# ℹ 42 more rows
> 
> es <- BiocSet(set1 = letters[1:5], set2 = LETTERS[1:5])
> tbl <- tibble(x = 1:10, y = c(letters[1:5], LETTERS[1:5]))
> es %>% left_join(tbl, by = c(element = "y"))
class: BiocSet

es_element():
# A tibble: 10 × 1
  element
  <chr>  
1 a      
2 b      
3 c      
# ℹ 7 more rows

es_set():
# A tibble: 2 × 1
  set  
  <chr>
1 set1 
2 set2 

es_elementset() <active>:
# A tibble: 10 × 3
  element set       x
  <chr>   <chr> <int>
1 a       set1      1
2 b       set1      2
3 c       set1      3
# ℹ 7 more rows
> 
> library(org.Hs.eg.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:dplyr’:

    combine, intersect, setdiff, union

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:dplyr’:

    first, rename

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname


Attaching package: ‘IRanges’

The following objects are masked from ‘package:dplyr’:

    collapse, desc, slice


Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:dplyr’:

    select


> es <- go_sets(org.Hs.eg.db, "ENSEMBL")
* 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
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocSet.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL BiocSet
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘BiocSet’ ...
** using staged installation
** R
** 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 (BiocSet)

R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 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(BiocSet)
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> test_check("BiocSet")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 573 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 573 ]
> 
> proc.time()
   user  system elapsed 
 96.455  14.552 176.911