• using R Under development (unstable) (2026-06-06 r90114)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-1) 16.1.0     GNU Fortran (Debian 16.1.0-1) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-06-07 13:26:42 UTC
• checking for file ‘msSPChelpR/DESCRIPTION’ ... OK
• this is package ‘msSPChelpR’ version ‘0.9.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘haven’
• 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 ‘msSPChelpR’ 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 ... [0s/0s] OK
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• checking whether the package can be unloaded cleanly ... [0s/0s] OK
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• checking whether the namespace can be unloaded cleanly ... [0s/0s] WARNING Fatal error: cannot create 'R_TempDir'
• checking loading without being on the library search path ... [0s/0s] 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 ... [11s/12s] OK
• checking Rd files ... [0s/1s] OK
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• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
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• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [2s/3s] 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 ... [4s/5s] ERROR Running examples in ‘msSPChelpR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: calc_futime > ### Title: Calculate follow-up time per case until end of follow-up > ### depending on pat_status - tidyverse version > ### Aliases: calc_futime > > ### ** Examples > > #load sample data > data("us_second_cancer") > > #prep step - make wide data as this is the required format > usdata_wide <- us_second_cancer %>% + msSPChelpR::reshape_wide_tidyr(case_id_var = "fake_id", + time_id_var = "SEQ_NUM", timevar_max = 10) > > #prep step - calculate p_spc variable > usdata_wide <- usdata_wide %>% + dplyr::mutate(p_spc = dplyr::case_when(is.na(t_site_icd.2) ~ "No SPC", + !is.na(t_site_icd.2) ~ "SPC developed", + TRUE ~ NA_character_)) %>% + dplyr::mutate(count_spc = dplyr::case_when(is.na(t_site_icd.2) ~ 1, + TRUE ~ 0)) > > #prep step - create patient status variable > usdata_wide <- usdata_wide %>% + msSPChelpR::pat_status(., fu_end = "2017-12-31", dattype = "seer", + status_var = "p_status", life_var = "p_alive.1", + birthdat_var = "datebirth.1", lifedat_var = "datedeath.1") Error in set_labels_helper(x = x[[vars[i]]], labels = labels[[i]], force.labels = force.labels, :   Package 'haven' required for this function. Please install it. Calls: %>% ... <Anonymous> -> %>% -> <Anonymous> -> set_labels_helper Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [4s/5s] ERROR   Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(msSPChelpR)   >   > test_check("msSPChelpR")   Saving _problems/test-pat_status-23.R   Long dataset had too many cases per patient. Wide dataset is limited to 2 cases per id as defined in timevar_max option.   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-pat_status.R:5:3'): custom variable name for status_var works ──   Error in `set_labels_helper(x = x[[vars[i]]], labels = labels[[i]], force.labels = force.labels, force.values = force.values, drop.na = drop.na, var.name = vars[i])`: Package 'haven' required for this function. Please install it.   Backtrace:       ▆    1. ├─... %>% ... at test-pat_status.R:5:3    2. ├─msSPChelpR::pat_status(...)    3. │ └─... %>% ...    4. └─sjlabelled::val_labels(...)    5. └─sjlabelled:::set_labels_helper(...)      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ...