* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/EHR.Rcheck’ * using R Under development (unstable) (2024-04-05 r86344) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘EHR/DESCRIPTION’ ... OK * this is package ‘EHR’ version ‘0.4-11’ * 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 ‘EHR’ can be installed ... [17s/24s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/EHR-00install.html' for details. * checking package directory ... 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 ... 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 ... [36s/43s] OK * checking Rd files ... NOTE checkRd: (-1) build_lastdose.Rd:10: Lost braces 10 | code{build_lastdose}: build PK oral with lastdose information | ^ checkRd: (-1) mod-internal.Rd:18: Lost braces 18 | code{colflow_mod}: build a comparison of potentially duplicate flow data | ^ checkRd: (-1) mod-internal.Rd:21: Lost braces 21 | code{findMedFlowRow_mod}: find row numbers for matching ID and time | ^ checkRd: (-1) mod-internal.Rd:23: Lost braces 23 | code{flowData_mod}: correct flow data | ^ checkRd: (-1) mod-internal.Rd:25: Lost braces 25 | code{concData_mod}: correct concentration data | ^ checkRd: (-1) mod-internal.Rd:27: Lost braces 27 | code{infusionData_mod}: combine flow and MAR data; standardize hourly rate, | ^ checkRd: (-1) mod-internal.Rd:30: Lost braces 30 | code{resolveDoseDups_mod}: correct duplicated infusion and bolus doses | ^ checkRd: (-1) mod-internal.Rd:32: Lost braces 32 | code{writeCheckData} | ^ checkRd: (-1) mod-internal.Rd:34: Lost braces 34 | code{processErx}: prepare e-prescription data | ^ checkRd: (-1) mod-internal.Rd:36: Lost braces 36 | code{processErxAddl}: additional processing, checking for connected observations | ^ checkRd: (-1) mod-internal.Rd:38: Lost braces 38 | code{validateColumns}: check columns are in place | ^ checkRd: (-1) mod-internal.Rd:40: Lost braces 40 | code{read}: generic read function | ^ checkRd: (-1) mod-internal.Rd:42: Lost braces 42 | code{setDoseMar}: set unit/rate/date columns | ^ checkRd: (-1) pk-internal.Rd:19: Lost braces 19 | code{takeClosest}: take value at nearest time | ^ checkRd: (-1) pk-internal.Rd:22: Lost braces 22 | code{takeClosestTime}: find nearest time | ^ checkRd: (-1) pk-internal.Rd:24: Lost braces 24 | code{daysDiff}: number of days between two dates | ^ checkRd: (-1) pk-internal.Rd:26: Lost braces 26 | code{minDiff}: difference (in minutes) of time vector | ^ checkRd: (-1) pk-internal.Rd:28: Lost braces 28 | code{fixDates}: add leading zeroes to date | ^ checkRd: (-1) pk-internal.Rd:30: Lost braces 30 | code{joinFlowMar}: rbind two data sets | ^ checkRd: (-1) pk-internal.Rd:32: Lost braces 32 | code{updateInterval_mod}: replace maxint with difference between surgery time | ^ checkRd: (-1) pk-internal.Rd:35: Lost braces 35 | code{fix_serum_time}: create time variable | ^ checkRd: (-1) pk-internal.Rd:37: Lost braces 37 | code{merge_by_time}: impute in x by closest time in y | ^ checkRd: (-1) pk-internal.Rd:39: Lost braces 39 | code{merge_inf_bolus}: combine infusion and bolus into one hourly dose file | ^ checkRd: (-1) pk-internal.Rd:41: Lost braces 41 | code{addZeroDose}: add rows of zero dose, after a gap | ^ checkRd: (-1) pk-internal.Rd:43: Lost braces 43 | code{pkdata} | ^ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [21s/27s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [227s/283s] OK * checking PDF version of manual ... [12s/19s] 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: 1 NOTE