[R] R CMD check

Frank E Harrell Jr fharrell at virginia.edu
Wed May 15 20:22:13 CEST 2002

Thanks to those who helped with R CMD check yesterday.  Part of my problem was a faulty Linux directory (list directory bit turned off).

I have three further question.  First, I get an error related to the following piece of a .Rd file:

bystats(y, \dots, fun, nmiss, subset)
b <- bystats(y, \dots)
print(b, \dots)
latex(b, caption, title, rowlabel, \dots)
b <- bystats2(y, v. h. fun, nmiss, subset)
latex(b, caption, title, rowlabel, \dots)

* checking for undocumented arguments in \usage ... WARNING
Error in parse(file, n, text, prompt) : parse error
Error in checkDocArgs(package = "Hmisc") : 
        cannot source usages in documentation object 'bystats'
Execution halted

Other .Rd files have \dots and do not result in an error.

Second, I get this message:

Objects with usage in documentation object 'aregImpute' but missing from code:
[1] "plot"   "print"

The aregImpute function, like many others, has under the Usage section code such as plot(object) and print(object) but the aliases at the top of the .Rd file point to plot.aregImpute and print.aregImpute.  To me there should not be a warning about this.

Third, I use several non-standard keywords (e.g., bootstrap, imputation).  Is there a way to add user-provided keywords to the system (I'm using R 1.5 on Linux)?

Thanks,  Frank

Frank E Harrell Jr              Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine  http://hesweb1.med.virginia.edu/biostat
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