- using R Under development (unstable) (2024-03-26 r86210)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.2.0-13) 13.2.0
GNU Fortran (Debian 13.2.0-13) 13.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘cobalt/DESCRIPTION’ ... OK
- this is package ‘cobalt’ version ‘4.5.4’
- package encoding: UTF-8
- 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 serialization versions ... OK
- checking whether package ‘cobalt’ 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/2s] 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/2s] OK
- checking loading without being on the library search path ... [1s/2s] OK
- checking whether startup messages can be suppressed ... [1s/2s] 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 ... [56s/89s] OK
- checking Rd files ... [1s/2s] 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/1s] 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 ... [17s/29s] ERROR
Running examples in ‘cobalt-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bal.tab.weightit
> ### Title: Balance Statistics for 'WeightIt' Objects
> ### Aliases: bal.tab.weightit
>
> ### ** Examples
>
> ## Don't show:
> if (all(sapply(c("WeightIt", "twang"), requireNamespace, quietly = TRUE))) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ library(WeightIt)
+ data("lalonde", package = "cobalt")
+
+ ## Basic propensity score weighting
+ w.out1 <- weightit(treat ~ age + educ + race +
+ married + nodegree + re74 + re75,
+ data = lalonde, method = "ps")
+ bal.tab(w.out1, un = TRUE, m.threshold = .1,
+ v.threshold = 2)
+
+ ## Weighting with a multi-category treatment
+ w.out2 <- weightit(race ~ age + educ + married +
+ nodegree + re74 + re75,
+ data = lalonde, method = "ps",
+ estimand = "ATE", use.mlogit = FALSE)
+ bal.tab(w.out2, un = TRUE)
+ bal.tab(w.out2, un = TRUE, pairwise = FALSE)
+
+ ## IPW for longitudinal treatments
+ data("iptwExWide", package = "twang")
+ wmsm.out <- weightitMSM(list(tx1 ~ use0 + gender,
+ tx2 ~ use0 + gender + use1 + tx1,
+ tx3 ~ use0 + gender + use1 + tx1 + use2 + tx2),
+ data = iptwExWide,
+ stabilize = TRUE)
+ bal.tab(wmsm.out)
+ ## Don't show:
+ }) # examplesIf
> library(WeightIt)
> data("lalonde", package = "cobalt")
> w.out1 <- weightit(treat ~ age + educ + race + married + nodegree + re74 +
+ re75, data = lalonde, method = "ps")
> bal.tab(w.out1, un = TRUE, m.threshold = 0.1, v.threshold = 2)
Balance Measures
Type Diff.Un V.Ratio.Un Diff.Adj M.Threshold V.Ratio.Adj
prop.score Distance 1.7569 0.9211 0.1360 0.9758
age Contin. -0.2419 0.4400 -0.1676 Not Balanced, >0.1 0.3689
educ Contin. 0.0448 0.4959 0.1296 Not Balanced, >0.1 0.5657
race_black Binary 0.6404 . 0.0499 Balanced, <0.1 .
race_hispan Binary -0.0827 . 0.0047 Balanced, <0.1 .
race_white Binary -0.5577 . -0.0546 Balanced, <0.1 .
married Binary -0.3236 . -0.0944 Balanced, <0.1 .
nodegree Binary 0.1114 . -0.0547 Balanced, <0.1 .
re74 Contin. -0.5958 0.5181 -0.2740 Not Balanced, >0.1 0.8208
re75 Contin. -0.2870 0.9563 -0.1579 Not Balanced, >0.1 0.9562
V.Threshold
prop.score Balanced, <2
age Not Balanced, >2
educ Balanced, <2
race_black
race_hispan
race_white
married
nodegree
re74 Balanced, <2
re75 Balanced, <2
Balance tally for mean differences
count
Balanced, <0.1 5
Not Balanced, >0.1 4
Variable with the greatest mean difference
Variable Diff.Adj M.Threshold
re74 -0.274 Not Balanced, >0.1
Balance tally for variance ratios
count
Balanced, <2 4
Not Balanced, >2 1
Variable with the greatest variance ratio
Variable V.Ratio.Adj V.Threshold
age 0.3689 Not Balanced, >2
Effective sample sizes
Control Treated
Unadjusted 429. 185.
Adjusted 329.01 58.33
> w.out2 <- weightit(race ~ age + educ + married + nodegree + re74 + re75,
+ data = lalonde, method = "ps", estimand = "ATE", use.mlogit = FALSE)
Error in `weightit()`:
! `use.mlogit` is no longer accepted and will be ignored; use `multi.method` instead. See `help("method_glm")` for details.
Backtrace:
▆
1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
2. │ └─base::source(...)
3. │ ├─base::withVisible(eval(ei, envir))
4. │ └─base::eval(ei, envir)
5. │ └─base::eval(ei, envir)
6. └─WeightIt::weightit(...)
7. ├─base::do.call("weightit.fit", A)
8. └─WeightIt::weightit.fit(...)
9. ├─base::do.call(...)
10. └─WeightIt:::weightit2glm.multi(...)
11. └─WeightIt:::.err("`use.mlogit` is no longer accepted and will be ignored; use `multi.method` instead. See `help(\"method_glm\")` for details")
12. └─chk::err(..., call = pkg_caller_call(start = 2))
13. └─rlang::abort(msg, class = class, !!!args[named], call = call)
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [2s/4s] OK
Running ‘testthat.R’ [2s/3s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [117s/187s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cobalt.Rmd’ using rmarkdown
--- finished re-building ‘cobalt.Rmd’
--- re-building ‘faq.Rmd’ using rmarkdown
--- finished re-building ‘faq.Rmd’
--- re-building ‘longitudinal-treat.Rmd’ using rmarkdown
--- finished re-building ‘longitudinal-treat.Rmd’
--- re-building ‘love.plot.Rmd’ using rmarkdown
--- finished re-building ‘love.plot.Rmd’
--- re-building ‘optimizing-balance.Rmd’ using rmarkdown
--- finished re-building ‘optimizing-balance.Rmd’
--- re-building ‘other-packages.Rmd’ using rmarkdown
--- finished re-building ‘other-packages.Rmd’
--- re-building ‘segmented-data.Rmd’ using rmarkdown
Quitting from lines 202-208 [unnamed-chunk-15] (segmented-data.Rmd)
Error: processing vignette 'segmented-data.Rmd' failed with diagnostics:
`use.mlogit` is no longer accepted and will be ignored; use `multi.method` instead. See `help("method_glm")` for details.
--- failed re-building ‘segmented-data.Rmd’
SUMMARY: processing the following file failed:
‘segmented-data.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [11s/24s] OK
- checking HTML version of manual ... [4s/9s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs