* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/LZeroSpikeInference.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 18.1.4 flang-new version 18.1.4 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘LZeroSpikeInference/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘LZeroSpikeInference’ version ‘1.0.3’ * 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 whether package ‘LZeroSpikeInference’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/LZeroSpikeInference-00install.html' for details. * checking installed package size ... OK * 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 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 ... OK * checking Rd files ... NOTE checkRd: (-1) LZeroSpikeInference.Rd:20: Lost braces; missing escapes or markup? 20 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:20: Lost braces; missing escapes or markup? 20 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:20: Lost braces; missing escapes or markup? 20 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:20: Lost braces 20 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:20: Lost braces; missing escapes or markup? 20 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:28: Lost braces; missing escapes or markup? 28 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:28: Lost braces; missing escapes or markup? 28 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:28: Lost braces; missing escapes or markup? 28 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:28: Lost braces 28 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:28: Lost braces; missing escapes or markup? 28 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:28: Lost braces; missing escapes or markup? 28 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) LZeroSpikeInference.Rd:29: Lost braces; missing escapes or markup? 29 | where the indicator variable 1_{(A,B)} equals 1 if the event A cup B holds, and equals zero otherwise. | ^ checkRd: (-1) cv.estimateSpikes.Rd:50: Lost braces; missing escapes or markup? 50 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:50: Lost braces; missing escapes or markup? 50 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:50: Lost braces; missing escapes or markup? 50 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:50: Lost braces 50 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:50: Lost braces; missing escapes or markup? 50 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:59: Lost braces; missing escapes or markup? 59 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:59: Lost braces; missing escapes or markup? 59 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:59: Lost braces; missing escapes or markup? 59 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:59: Lost braces 59 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:59: Lost braces; missing escapes or markup? 59 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:59: Lost braces; missing escapes or markup? 59 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) cv.estimateSpikes.Rd:60: Lost braces; missing escapes or markup? 60 | where the indicator variable 1_{(A,B)} equals 1 if the event A cup B holds, and equals zero otherwise. | ^ checkRd: (-1) estimateSpikes.Rd:41: Lost braces; missing escapes or markup? 41 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:41: Lost braces; missing escapes or markup? 41 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:41: Lost braces; missing escapes or markup? 41 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:41: Lost braces 41 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:41: Lost braces; missing escapes or markup? 41 | minimize_{c1,...,cT} 0.5 sum_{t=1}^T ( y_t - c_t )^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:49: Lost braces; missing escapes or markup? 49 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:49: Lost braces; missing escapes or markup? 49 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:49: Lost braces; missing escapes or markup? 49 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:49: Lost braces 49 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:49: Lost braces; missing escapes or markup? 49 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:49: Lost braces; missing escapes or markup? 49 | minimize_{c1,...,cT,b1,...,bT} 0.5 sum_{t=1}^T (y_t - c_t - b_t)^2 + lambda sum_{t=2}^T 1_{c_t neq gamma c_{t-1}, b_t neq b_{t-1} } | ^ checkRd: (-1) estimateSpikes.Rd:50: Lost braces; missing escapes or markup? 50 | where the indicator variable 1_{(A,B)} equals 1 if the event A cup B holds, and equals zero otherwise. | ^ checkRd: (-1) simulateAR1.Rd:31: Lost braces; missing escapes or markup? 31 | c_t = gam * c_{t-1} + s_t | ^ * 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 LazyData ... NOTE 'LazyData' is specified without a 'data' directory * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... OK Running ‘testthat.R’ * checking PDF version of manual ... [7s/10s] 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