• using R Under development (unstable) (2026-07-01 r90203)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 22.1.8 (1)     Debian flang version 22.1.8 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-02 19:58:50 UTC
• checking for file ‘TCGAretriever/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘TCGAretriever’ version ‘1.10.3’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 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 ‘TCGAretriever’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [1s/1s] 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 use of S3 registration ... 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 ... [7s/9s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/2s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [4s/22s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘get_started_with_TCGAretriever.Rmd’ using rmarkdown Quitting from get_started_with_TCGAretriever.Rmd:120-135 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `auto_copy()`: ! `x` and `y` must share the same src. ℹ `x` is a <data.frame> object. ℹ `y` is `NULL`. ℹ Set `copy = TRUE` if `y` can be copied to the same source as `x` (may be   slow). --- Backtrace:     ▆  1. └─TCGAretriever::get_clinical_data(csid = q_csid, case_list_id = q_cases)  2. ├─dplyr::left_join(...)  3. └─dplyr:::left_join.data.frame(...)  4. └─dplyr::auto_copy(x, y, copy = copy) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'get_started_with_TCGAretriever.Rmd' failed with diagnostics: `x` and `y` must share the same src. ℹ `x` is a <data.frame> object. ℹ `y` is `NULL`. ℹ Set `copy = TRUE` if `y` can be copied to the same source as `x` (may be   slow). --- failed re-building ‘get_started_with_TCGAretriever.Rmd’ SUMMARY: processing the following file failed:   ‘get_started_with_TCGAretriever.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR