* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/equivalence.Rcheck’
* using R Under development (unstable) (2025-02-14 r87716)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘equivalence/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘equivalence’ version ‘0.7.2’
* 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 ‘equivalence’ can be installed ... [11s/13s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/equivalence-00install.html' for details.
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking package 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [14s/19s] OK
* checking Rd files ... NOTE
checkRd: (-1) equivalence.xyplot.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) equivalence.xyplot.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rtost.Rd:7: Lost braces; missing escapes or markup?
7 | This function computes the TOST and key TOST quantities for the two one-sided test for equivalence [Schuirmann (1981) and Westlake (1981)], using the robust t-test of Yuen [Yuen and Dixon (1973), Yuen (1974)] in place of the standard Welch t test (t.test {stats}). The yuen t test makes no assumption of normality. The function computes the robust TOST for a sample of paired differences or for two samples. The function performs almost as well as the Welch t test when the population distribution is normal and is more robust than the Welch t test in the face of non-normality (e.g., distributions that are long-tailed, heteroscedastic, or contaminated by outliers)[Yuen and Dixon (1973), Yuen (1974)].
| ^
checkRd: (-1) rtost.Rd:23: Lost braces; missing escapes or markup?
23 | \details{The rtost function is wrapped around the yuen {PairedData} t test, a robust variant of the t test using trimmed means and winsorized variances. It provides tosts for the same range of designs, accepts the same arguments, and handles missing values the same way as tost {equivalence}. For the tost, the user must set epsilon, which is the magnitude of region similarity. Warning: with tr > 0.25 type I error control might be poor.
| ^
checkRd: (-1) rtost.Rd:23: Lost braces; missing escapes or markup?
23 | \details{The rtost function is wrapped around the yuen {PairedData} t test, a robust variant of the t test using trimmed means and winsorized variances. It provides tosts for the same range of designs, accepts the same arguments, and handles missing values the same way as tost {equivalence}. For the tost, the user must set epsilon, which is the magnitude of region similarity. Warning: with tr > 0.25 type I error control might be poor.
| ^
checkRd: (-1) rtost.Rd:60: Lost braces; missing escapes or markup?
60 | \note{This test is the tost for equivalence (tost {equivalence}) wrapped around the robust, trimmed mean, winsorized variance yuen.t.test (yuen {PairedData}).}
| ^
checkRd: (-1) rtost.Rd:60: Lost braces; missing escapes or markup?
60 | \note{This test is the tost for equivalence (tost {equivalence}) wrapped around the robust, trimmed mean, winsorized variance yuen.t.test (yuen {PairedData}).}
| ^
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘equivalence/libs/equivalence.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs