- using R version 4.5.1 (2025-06-13)
- using platform: x86_64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.3.1
- using session charset: UTF-8
- checking for file ‘SurprisalAnalysis/DESCRIPTION’ ... OK
- this is package ‘SurprisalAnalysis’ version ‘3.0.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... INFO
Package suggested but not available for checking: ‘org.Mm.eg.db’
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘SurprisalAnalysis’ can be installed ... [21s/25s] OK
See the install log for details.
- checking installed package size ... INFO
installed size is 8.7Mb
sub-directories of 1Mb or more:
doc 1.5Mb
extdata 4.0Mb
shiny 3.1Mb
- 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 ... [7s/8s] OK
- checking whether the package can be loaded with stated dependencies ... [7s/8s] OK
- checking whether the package can be unloaded cleanly ... [7s/8s] OK
- checking whether the namespace can be loaded with stated dependencies ... [7s/8s] OK
- checking whether the namespace can be unloaded cleanly ... [7s/8s] OK
- checking loading without being on the library search path ... [7s/8s] 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 ... [14s/17s] OK
- checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [8s/8s] ERROR
Running examples in ‘SurprisalAnalysis-Ex.R’ failed
The error most likely occurred in:
> ### Name: runSurprisalApp
> ### Title: Launch the SurprisalAnalysis Shiny App
> ### Aliases: runSurprisalApp
>
> ### ** Examples
>
>
> runSurprisalApp(port = httpuv::randomPort(), run = FALSE)
Loading required package: shiny
Attaching package: ‘shinyjs’
The following object is masked from ‘package:shiny’:
runExample
The following objects are masked from ‘package:methods’:
removeClass, show
Attaching package: ‘DT’
The following objects are masked from ‘package:shiny’:
dataTableOutput, renderDataTable
clusterProfiler v4.15.1 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
Please cite:
S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
multiomics data. Nature Protocols. 2024, 19(11):3292-3320
Attaching package: ‘clusterProfiler’
The following object is masked from ‘package:stats’:
filter
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 object is masked from ‘package:clusterProfiler’:
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 object is masked from ‘package:clusterProfiler’:
slice
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:clusterProfiler’:
select
Error: Package 'org.Mm.eg.db' is required for this Shiny app. Install via BiocManager::install('org.Mm.eg.db')
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [35s/44s] OK
- checking PDF version of manual ... [6s/7s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '