• 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 ‘pulseTD/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘pulseTD’ version ‘0.1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... NOTE Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
• 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 ‘pulseTD’ can be installed ... [22s/24s] OK See the install log for details.
• 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 ... [6s/7s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
• checking whether the package can be unloaded cleanly ... [7s/8s] OK
• checking whether the namespace can be loaded with stated dependencies ... [7s/9s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
• checking loading without being on the library search path ... [6s/7s] 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/14s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [7s/8s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [7s/7s] ERROR Running examples in ‘pulseTD-Ex.R’ failed The error most likely occurred in: > ### Name: estimateExpression > ### Title: Estimated Expression > ### Aliases: estimateExpression > > ### ** Examples > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) Error in library(TxDb.Hsapiens.UCSC.hg19.knownGene) :   there is no package called ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [12s/12s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘tutorial.Rmd’ using rmarkdown Quitting from lines 63-65 [import packages] (tutorial.Rmd) Error: processing vignette 'tutorial.Rmd' failed with diagnostics: there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene' --- failed re-building ‘tutorial.Rmd’ SUMMARY: processing the following file failed:   ‘tutorial.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/4s] OK
• DONE Status: 2 ERRORs, 1 NOTE
• using check arguments '--no-clean-on-error '