- using R version 4.4.0 alpha (2024-03-31 r86238)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘bulkAnalyseR/DESCRIPTION’ ... OK
- this is package ‘bulkAnalyseR’ version ‘1.1.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
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 ‘bulkAnalyseR’ can be installed ... [4s/4s] OK
See the install log for details.
- checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
doc 2.3Mb
extdata 3.4Mb
- 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 ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] 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 ... [2s/2s] ERROR
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:
> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ### matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
>
> ### ** Examples
>
> expression.matrix.preproc <- as.matrix(read.csv(
+ system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"),
+ row.names = 1
+ ))[1:100, 1:4]
>
> anno <- AnnotationDbi::select(
+ getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+ keys = rownames(expression.matrix.preproc),
+ keytype = 'ENSEMBL',
+ columns = 'SYMBOL'
+ ) %>%
+ dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+ dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [1s/1s] OK
Running ‘testthat.R’ [1s/1s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [18s/27s] OK
- checking PDF version of manual ... [4s/5s] OK
- DONE
Status: 1 ERROR, 2 NOTEs
- using check arguments '--no-clean-on-error '