• using R Under development (unstable) (2026-08-01 r90334)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-3) 16.1.0     GNU Fortran (Debian 16.1.0-3) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-08-02 14:03:14 UTC
• checking for file ‘compas/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘compas’ version ‘0.1.1’
• checking CRAN incoming feasibility ... [1s/1s] NOTE Maintainer: ‘Samuel W.K. Wong <samuel.wong@uwaterloo.ca>’ No Authors@R field in DESCRIPTION. Please add one, modifying   Authors@R: c(person(given = c("Samuel", "W.K."),                       family = "Wong",                       role = c("aut", "cre"),                       email = "samuel.wong@uwaterloo.ca"),                person(given = "Dylan",                       family = "Shi",                       role = "aut"),                person(given = "Megan",                       family = "Hazlett",                       role = "aut"),                person(given = "Jasmine",                       family = "Cheng",                       role = "aut")) as necessary.
• 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 ‘compas’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-16 (Debian 16.1.0-3) 16.1.0’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] 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 ... [4s/5s] OK
• checking Rd files ... [0s/0s] NOTE checkRd: (-1) atomdeps.Rd:9: Lost braces      9 | \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}        | ^ checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?     10 | \item{"names"}: {The component atoms of the amino acid side chain. Represents atom D in the dihedral.}        | ^ checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?     11 | \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}        | ^ checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?     12 | \item{"bangle"}: {Planar bond angle formed between B-C-D}        | ^ checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?     13 | \item{"blength"}: {Bond length between C-D}        | ^
• 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/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking examples ... [1s/1s] OK
• checking PDF version of manual ... [4s/5s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• checking for new files in some other directories ... NOTE Found the following files/directories:   ‘~/tmp/scratch/Rtmp1OUM5C’ ‘~/tmp/scratch/Rtmp2TO2mB’   ‘~/tmp/scratch/Rtmp2XDlON’ ‘~/tmp/scratch/Rtmp2pKSEZ’   ‘~/tmp/scratch/Rtmp3HMC9E’ ‘~/tmp/scratch/Rtmp3HUkG3’   ‘~/tmp/scratch/Rtmp3W6a6p’ ‘~/tmp/scratch/Rtmp3cggQU’   ‘~/tmp/scratch/Rtmp3pKwsD’ ‘~/tmp/scratch/Rtmp40qxlv’   ‘~/tmp/scratch/Rtmp5JhTRn’ ‘~/tmp/scratch/Rtmp5ztsc5’   ‘~/tmp/scratch/Rtmp62JXle’ ‘~/tmp/scratch/Rtmp82VDnZ’   ‘~/tmp/scratch/Rtmp8MtOAt’ ‘~/tmp/scratch/Rtmp8bb0jO’   ‘~/tmp/scratch/Rtmp8gKEcT’ ‘~/tmp/scratch/Rtmp9FidzH’   ‘~/tmp/scratch/RtmpA9Dh6U’ ‘~/tmp/scratch/RtmpAF8f89’   ‘~/tmp/scratch/RtmpAThCwV’ ‘~/tmp/scratch/RtmpAuSYfW’   ‘~/tmp/scratch/RtmpAvYZ85’ ‘~/tmp/scratch/RtmpBS2tRB’   ‘~/tmp/scratch/RtmpCEOcfE’ ‘~/tmp/scratch/RtmpCPM9bH’   ‘~/tmp/scratch/RtmpCc4pND’ ‘~/tmp/scratch/RtmpDKpJiH’   ‘~/tmp/scratch/RtmpDdX4km’ ‘~/tmp/scratch/RtmpEG9jGO’   ‘~/tmp/scratch/RtmpEMRaMK’ ‘~/tmp/scratch/RtmpFtkejZ’   ‘~/tmp/scratch/RtmpGAEIdq’ ‘~/tmp/scratch/RtmpGH9cLH’   ‘~/tmp/scratch/RtmpGUr6Ym’ ‘~/tmp/scratch/RtmpH8mJPC’   ‘~/tmp/scratch/RtmpI9ZZ8s’ ‘~/tmp/scratch/RtmpIEb8HQ’   ‘~/tmp/scratch/RtmpJSFwTW’ ‘~/tmp/scratch/RtmpKHWfHS’   ‘~/tmp/scratch/RtmpKf0T4n’ ‘~/tmp/scratch/RtmpKhbXag’   ‘~/tmp/scratch/RtmpLPNl7d’ ‘~/tmp/scratch/RtmpMew7nE’   ‘~/tmp/scratch/RtmpMmCBjs’ ‘~/tmp/scratch/RtmpN24yOe’   ‘~/tmp/scratch/RtmpNKA8GQ’ ‘~/tmp/scratch/RtmpNqfQDB’   ‘~/tmp/scratch/RtmpNu7keP’ ‘~/tmp/scratch/RtmpNyNff9’   ‘~/tmp/scratch/RtmpOJv45A’ ‘~/tmp/scratch/RtmpPPr7Mz’   ‘~/tmp/scratch/RtmpPymJw8’ ‘~/tmp/scratch/RtmpQnN6h4’   ‘~/tmp/scratch/RtmpRVITf8’ ‘~/tmp/scratch/RtmpSK0fxB’   ‘~/tmp/scratch/RtmpSnmiVl’ ‘~/tmp/scratch/RtmpTQooN6’   ‘~/tmp/scratch/RtmpU3tDOg’ ‘~/tmp/scratch/RtmpUp1oI6’   ‘~/tmp/scratch/RtmpVgDbZY’ ‘~/tmp/scratch/RtmpVgcltP’   ‘~/tmp/scratch/RtmpX0GPjw’ ‘~/tmp/scratch/RtmpXBxC3u’   ‘~/tmp/scratch/RtmpY7RVmw’ ‘~/tmp/scratch/RtmpYAcb4Z’   ‘~/tmp/scratch/RtmpYcZYQn’ ‘~/tmp/scratch/RtmpZJrkfm’   ‘~/tmp/scratch/RtmpZOs9qd’ ‘~/tmp/scratch/RtmpaPIDfQ’   ‘~/tmp/scratch/RtmpaRXE8j’ ‘~/tmp/scratch/Rtmpb8FLpy’   ‘~/tmp/scratch/RtmpbKXWWD’ ‘~/tmp/scratch/RtmpcH1BoM’   ‘~/tmp/scratch/RtmpdZT7mq’ ‘~/tmp/scratch/RtmpfFFTRY’   ‘~/tmp/scratch/Rtmpfd8Plk’ ‘~/tmp/scratch/RtmpfdSDu3’   ‘~/tmp/scratch/Rtmpfk7CXj’ ‘~/tmp/scratch/RtmpgOSs2P’   ‘~/tmp/scratch/RtmpgUmJyW’ ‘~/tmp/scratch/RtmphBH3bv’   ‘~/tmp/scratch/RtmpjQoCI5’ ‘~/tmp/scratch/Rtmpjub78i’   ‘~/tmp/scratch/RtmpjyLF2Y’ ‘~/tmp/scratch/RtmpkDRnxH’   ‘~/tmp/scratch/RtmpkcZpKW’ ‘~/tmp/scratch/Rtmpkuabqh’   ‘~/tmp/scratch/Rtmpm0Yjn1’ ‘~/tmp/scratch/RtmpmOua5N’   ‘~/tmp/scratch/RtmpmjpscX’ ‘~/tmp/scratch/RtmpptgZWA’   ‘~/tmp/scratch/RtmpptuiIO’ ‘~/tmp/scratch/Rtmpptwnaw’   ‘~/tmp/scratch/RtmpqcSfoD’ ‘~/tmp/scratch/Rtmpqf8DpG’   ‘~/tmp/scratch/RtmprnSLBM’ ‘~/tmp/scratch/Rtmps9Ei7I’   ‘~/tmp/scratch/RtmpsAly5m’ ‘~/tmp/scratch/RtmpsAmqtr’   ‘~/tmp/scratch/RtmptFB0Vc’ ‘~/tmp/scratch/RtmptQ7rtC’   ‘~/tmp/scratch/RtmpuJNsEZ’ ‘~/tmp/scratch/RtmpwKB6TU’   ‘~/tmp/scratch/RtmpxxizTy’ ‘~/tmp/scratch/Rtmpz48ZhC’   ‘~/tmp/scratch/RtmpzGlAQ7’ ‘~/tmp/scratch/RtmpzQGvrn’   ‘~/tmp/scratch/xvfb-run.1ohXqo’ ‘~/tmp/scratch/xvfb-run.2Ih4cQ’   ‘~/tmp/scratch/xvfb-run.2lurm2’ ‘~/tmp/scratch/xvfb-run.2sszOa’   ‘~/tmp/scratch/xvfb-run.633rum’ ‘~/tmp/scratch/xvfb-run.7G9mQj’   ‘~/tmp/scratch/xvfb-run.9b7fbI’ ‘~/tmp/scratch/xvfb-run.LLvRAx’   ‘~/tmp/scratch/xvfb-run.NDDvyq’ ‘~/tmp/scratch/xvfb-run.NIEpZj’   ‘~/tmp/scratch/xvfb-run.OnYk7r’ ‘~/tmp/scratch/xvfb-run.Ou07IK’   ‘~/tmp/scratch/xvfb-run.PVmznp’ ‘~/tmp/scratch/xvfb-run.RMvR9B’   ‘~/tmp/scratch/xvfb-run.Ra9xYF’ ‘~/tmp/scratch/xvfb-run.SEpVrW’   ‘~/tmp/scratch/xvfb-run.V09wuS’ ‘~/tmp/scratch/xvfb-run.WCrHdt’   ‘~/tmp/scratch/xvfb-run.Wgyw0U’ ‘~/tmp/scratch/xvfb-run.XQ4VSc’   ‘~/tmp/scratch/xvfb-run.Y2Q4c6’ ‘~/tmp/scratch/xvfb-run.YhpZh7’   ‘~/tmp/scratch/xvfb-run.aX8qmf’ ‘~/tmp/scratch/xvfb-run.bq3XKt’   ‘~/tmp/scratch/xvfb-run.c5nU2I’ ‘~/tmp/scratch/xvfb-run.fRbYOD’   ‘~/tmp/scratch/xvfb-run.gZO6rF’ ‘~/tmp/scratch/xvfb-run.i3fEMs’   ‘~/tmp/scratch/xvfb-run.jEEJfv’ ‘~/tmp/scratch/xvfb-run.jVCR0Y’   ‘~/tmp/scratch/xvfb-run.kw1Drl’ ‘~/tmp/scratch/xvfb-run.mVHQ4J’   ‘~/tmp/scratch/xvfb-run.oxSkk5’ ‘~/tmp/scratch/xvfb-run.quHn6t’   ‘~/tmp/scratch/xvfb-run.rnn7vP’ ‘~/tmp/scratch/xvfb-run.w6yNDL’   ‘~/tmp/scratch/xvfb-run.xEmb2A’ ‘~/tmp/scratch/xvfb-run.yxSufe’   ‘~/tmp/scratch/xvfb-run.zEWWUC’
• DONE

Status: 3 NOTEs