[R-pkg-devel] R-package-devel Digest, Vol 105, Issue 19
Carl Schwarz
c@chw@rz@t@t@|uc@ @end|ng |rom gm@||@com
Wed Jan 24 20:34:51 CET 2024
Solved...
The src/ directory also included a .o and .so objects from the last build
of the package that must be "out of date" because once I removed those
older objects, the Build -> Document and build -> Check package now work
fine without crashing...A newer version of the .o and .so objects are now
built and it now works fine.
Thanks
Carl Schwarz
On Wed, Jan 24, 2024 at 10:57 AM Carl Schwarz <cschwarzstatsfuca using gmail.com>
wrote:
> Thanks for your suggestions. I followed the suggestion in today's message
> (see results below) which all run without issue.
> I tried to isolate the problem more....
>
> The issue appears to be with load_dll()
>
> When I try
> > getwd()
> [1] "/Users/cschwarz/Library/CloudStorage/Dropbox/SPAS-R/SPAS"
> > load_dll()
>
> It crashes.
>
>
> I moved the package outside of CloudStorage to see if that is the issue.
> > getwd()
> [1] "/Users/cschwarz/Desktop/SPAS"
> > load_dll()
>
> It crashes.
>
>
> I tried doing a dll_load() where there is NO c++ object, i.e. a random
> directory and it terminates with a sensible error message....
> > setwd("/Users/cschwarz/Desktop/BikePics")
> > library(pkgload)
> > load_dll()
> Error in `value[[3L]]()`:
> ! Could not find a root 'DESCRIPTION' file that starts with '^Package' in
> /Users/cschwarz/Desktop/BikePics.
> ℹ Are you in your project directory and does your project have a
> 'DESCRIPTION' file?
> Run `rlang::last_trace()` to see where the error occurred.
>
> I'm following the suggestions on including TMB code in a package at
>
> https://stackoverflow.com/questions/48627069/guidelines-for-including-tmb-c-code-in-an-r-package
> and appear to have all the necessary files
>
> I created my own load_dll() function by copying over the code and adding a
> browser().
> It appears to run fine until the statement library.dynam2(path.lib) where
> it cannot find the function library.dynam2
>
>
> > my_load_dll()
> Called from: my_load_dll()
> Browse[1]> n
> debug at #4: package <- pkg_name(path)
> Browse[2]> n
> debug at #5: env <- ns_env(package)
> Browse[2]> n
> debug at #6: nsInfo <- parse_ns_file(path)
> Browse[2]> n
> debug at #7: dlls <- list()
> Browse[2]> n
> debug at #8: dynLibs <- nsInfo$dynlibs
> Browse[2]> n
> debug at #9: nativeRoutines <- list()
> Browse[2]> n
> debug at #10: for (i in seq_along(dynLibs)) {
> lib <- dynLibs[i]
> dlls[[lib]] <- library.dynam2(path, lib)
> routines <- assignNativeRoutines(dlls[[lib]], lib, env,
> nsInfo$nativeRoutines[[lib]])
> nativeRoutines[[lib]] <- routines
> if (!is.null(names(nsInfo$dynlibs)) &&
> nzchar(names(nsInfo$dynlibs)[i]))
> env[[names(nsInfo$dynlibs)[i]]] <- dlls[[lib]]
> setNamespaceInfo(env, "DLLs", dlls)
> }
> Browse[2]> n
> debug at #11: lib <- dynLibs[i]
> Browse[2]> n
> debug at #12: dlls[[lib]] <- library.dynam2(path, lib)
> Browse[2]> n
> Error in library.dynam2(path, lib) :
> could not find function "library.dynam2"
>
> I'm unable to find where the library.dynam2() function lies... A google
> search for library.dynam2 doesn't show anything except for a cryptic
> comment in
> https://rdrr.io/cran/pkgload/src/R/load-dll.R
> which says
>
> ## The code below taken directly from base::loadNamespace
> ## https://github.com/wch/r-source/blob/tags/R-3-3-0/src/library/base/R/namespace.R#L466-L485
> ## except for the call to library.dynam2, which is a special version of
> ## library.dynam
>
> This is now beyond my pay grade..
>
> Suggestions?
>
>
> ------------------------------
>
> From James Lamb <jaylamb20 using gmail.com>
>
> Using the shell:
>
> R CMD build .
> - success with
>
> * checking for file ‘./DESCRIPTION’ ... OK
>
> * preparing ‘SPAS’:
>
> * checking DESCRIPTION meta-information ... OK
>
> * cleaning src
>
> * installing the package to build vignettes
>
> * creating vignettes ... OK
>
> * cleaning src
>
> * checking for LF line-endings in source and make files and shell scripts
>
> * checking for empty or unneeded directories
>
> * building ‘SPAS_2024.1.31.tar.gz’
>
>
> R CMD INSTALL --with-keep.source ./SPAS_*.tar.gz
> - success. Lots of warning from the C compiler but appears to terminate
> successfully with
> ....
>
> installing to /Users/cschwarz/Rlibs/00LOCK-SPAS/00new/SPAS/libs
>
> ** R
>
> ** inst
>
> ** byte-compile and prepare package for lazy loading
>
> ** help
>
> *** installing help indices
>
> ** building package indices
>
> ** installing vignettes
>
> ** testing if installed package can be loaded from temporary location
>
> ** checking absolute paths in shared objects and dynamic libraries
>
> ** testing if installed package can be loaded from final location
>
> ** testing if installed package keeps a record of temporary installation
> path
>
> * DONE (SPAS)
>
>
> # (assuming you use roxygen2)
> Rscript -e "roxygen2::roxygenize(load = 'installed')"
>
>
> - success?, it just returns with no messages
>
> cschwarz using schwarz-iMac-2020 SPAS % Rscript -e "roxygen2::roxygenize(load =
> 'installed')"
>
> cschwarz using schwarz-iMac-2020 SPAS %
>
>
> R CMD check --as-cran ./SPAS_*.tar.gz
>
> - successful...runs the checks, but does NOT find the note from the
> development versions of R that triggered CRAN to ask for a resubmission..
>
> It does find some problems in the html which I will also need to check
> out, but this appears to be ok as well.
>
>
> cschwarz using schwarz-iMac-2020 SPAS % R CMD check --as-cran ./SPAS_*.tar.gz
>
> * using log directory
> ‘/Users/cschwarz/Library/CloudStorage/Dropbox/SPAS-R/SPAS/SPAS.Rcheck’
>
> * using R version 4.3.2 (2023-10-31)
>
> * using platform: x86_64-apple-darwin20 (64-bit)
>
> * R was compiled by
>
> Apple clang version 14.0.0 (clang-1400.0.29.202)
>
> GNU Fortran (GCC) 12.2.0
>
> * running under: macOS Sonoma 14.2.1
>
> * using session charset: UTF-8
>
> * using option ‘--as-cran’
>
> * checking for file ‘SPAS/DESCRIPTION’ ... OK
>
> * checking extension type ... Package
>
> * this is package ‘SPAS’ version ‘2024.1.31’
>
> * package encoding: UTF-8
>
> * checking CRAN incoming feasibility ... [3s/16s] NOTE
>
> Maintainer: ‘Carl James Schwarz <cschwarz.stat.sfu.ca using gmail.com>’
>
>
> Found the following (possibly) invalid URLs:
>
> URL: https://cdnsciencepub.com/doi/10.1139/f97-238
>
> From: DESCRIPTION
>
> Status: 403
>
> Message: Forbidden
>
> URL: https://www.jstor.org/stable/2332748
>
> From: DESCRIPTION
>
> Status: 403
>
> Message: Forbidden
>
> * 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 ‘SPAS’ can be installed ... [28s/30s] OK
>
> * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
>
> * used SDK: ‘’
>
> * checking installed package size ... NOTE
>
> installed size is 12.8Mb
>
> sub-directories of 1Mb or more:
>
> libs 12.1Mb
>
> * checking package directory ... OK
>
> * checking for future file timestamps ... 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 R 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 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 ... OK
>
> * checking Rd files ... OK
>
> * 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 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 ... OK
>
> * checking installed files from ‘inst/doc’ ... OK
>
> * checking files in ‘vignettes’ ... OK
>
> * checking examples ... OK
>
> * checking for unstated dependencies in vignettes ... OK
>
> * checking package vignettes in ‘inst/doc’ ... OK
>
> * checking re-building of vignette outputs ... [11s/13s] OK
>
> * checking PDF version of manual ... OK
>
> * checking HTML version of manual ... NOTE
>
> Found the following HTML validation problems:
>
> SPAS.autopool.html:4:1 (SPAS.autopool.Rd:5): Warning: <link> inserting
> "type" attribute
>
> SPAS.autopool.html:12:1 (SPAS.autopool.Rd:5): Warning: <script>
> proprietary attribute "onload"
>
> SPAS.autopool.html:12:1 (SPAS.autopool.Rd:5): Warning: <script> inserting
> "type" attribute
>
> SPAS.autopool.html:17:1 (SPAS.autopool.Rd:5): Warning: <table> lacks
> "summary" attribute
>
> SPAS.autopool.html:46:1 (SPAS.autopool.Rd:19): Warning: <table> lacks
> "summary" attribute
>
> SPAS.extract.par.est.html:4:1 (SPAS.extract.par.est.Rd:5): Warning: <link>
> inserting "type" attribute
>
> SPAS.extract.par.est.html:12:1 (SPAS.extract.par.est.Rd:5): Warning:
> <script> proprietary attribute "onload"
>
> SPAS.extract.par.est.html:12:1 (SPAS.extract.par.est.Rd:5): Warning:
> <script> inserting "type" attribute
>
> SPAS.extract.par.est.html:17:1 (SPAS.extract.par.est.Rd:5): Warning:
> <table> lacks "summary" attribute
>
> SPAS.extract.par.est.html:35:1 (SPAS.extract.par.est.Rd:10): Warning:
> <table> lacks "summary" attribute
>
> SPAS.fit.model.html:4:1 (SPAS.fit.model.Rd:5): Warning: <link> inserting
> "type" attribute
>
> SPAS.fit.model.html:12:1 (SPAS.fit.model.Rd:5): Warning: <script>
> proprietary attribute "onload"
>
> SPAS.fit.model.html:12:1 (SPAS.fit.model.Rd:5): Warning: <script>
> inserting "type" attribute
>
> SPAS.fit.model.html:17:1 (SPAS.fit.model.Rd:5): Warning: <table> lacks
> "summary" attribute
>
> SPAS.fit.model.html:56:1 (SPAS.fit.model.Rd:28): Warning: <table> lacks
> "summary" attribute
>
> SPAS.likelihood.star.DM.html:4:1 (SPAS.likelihood.star.DM.Rd:5): Warning:
> <link> inserting "type" attribute
>
> SPAS.likelihood.star.DM.html:12:1 (SPAS.likelihood.star.DM.Rd:5): Warning:
> <script> proprietary attribute "onload"
>
> SPAS.likelihood.star.DM.html:12:1 (SPAS.likelihood.star.DM.Rd:5): Warning:
> <script> inserting "type" attribute
>
> SPAS.likelihood.star.DM.html:17:1 (SPAS.likelihood.star.DM.Rd:5): Warning:
> <table> lacks "summary" attribute
>
> SPAS.print.model.html:4:1 (SPAS.print.model.Rd:5): Warning: <link>
> inserting "type" attribute
>
> SPAS.print.model.html:12:1 (SPAS.print.model.Rd:5): Warning: <script>
> proprietary attribute "onload"
>
> SPAS.print.model.html:12:1 (SPAS.print.model.Rd:5): Warning: <script>
> inserting "type" attribute
>
> SPAS.print.model.html:17:1 (SPAS.print.model.Rd:5): Warning: <table> lacks
> "summary" attribute
>
> SPAS.print.model.html:36:1 (SPAS.print.model.Rd:10): Warning: <table>
> lacks "summary" attribute
>
> dot-onAttach.html:4:1 (dot-onAttach.Rd:5): Warning: <link> inserting
> "type" attribute
>
> dot-onAttach.html:12:1 (dot-onAttach.Rd:5): Warning: <script> proprietary
> attribute "onload"
>
> dot-onAttach.html:12:1 (dot-onAttach.Rd:5): Warning: <script> inserting
> "type" attribute
>
> dot-onAttach.html:17:1 (dot-onAttach.Rd:5): Warning: <table> lacks
> "summary" attribute
>
> dot-onAttach.html:19:1 (dot-onAttach.Rd:5): Warning: <h2> attribute "id"
> has invalid value ".onAttach"
>
> dummy.html:4:1 (dummy.Rd:5): Warning: <link> inserting "type" attribute
>
> dummy.html:12:1 (dummy.Rd:5): Warning: <script> proprietary attribute
> "onload"
>
> dummy.html:12:1 (dummy.Rd:5): Warning: <script> inserting "type" attribute
>
> dummy.html:17:1 (dummy.Rd:5): Warning: <table> lacks "summary" attribute
>
> logit.html:4:1 (logit.Rd:5): Warning: <link> inserting "type" attribute
>
> logit.html:12:1 (logit.Rd:5): Warning: <script> proprietary attribute
> "onload"
>
> logit.html:12:1 (logit.Rd:5): Warning: <script> inserting "type" attribute
>
> logit.html:17:1 (logit.Rd:5): Warning: <table> lacks "summary" attribute
>
> logit.html:35:1 (logit.Rd:10): Warning: <table> lacks "summary" attribute
>
> * checking for non-standard things in the check directory ... OK
>
> * checking for detritus in the temp directory ... OK
>
> * DONE
>
>
> Status: 3 NOTEs
>
> See
>
>
> ‘/Users/cschwarz/Library/CloudStorage/Dropbox/SPAS-R/SPAS/SPAS.Rcheck/00check.log’
>
> for details.
>
>
>
> cschwarz using schwarz-iMac-2020 SPAS %
>
>
>
> From: Serguei Sokol <serguei.sokol using gmail.com>
>
> Why not simply run devtools::document() from 'R -d gdb' ?
>
>
> This didn't work on my Mac
>
>
> cschwarz using schwarz-iMac-2020 SPAS % R -d gdb
>
> /usr/local/bin/R: line 299: exec: gdb: not found
>
>
> But then I tried launching R by it self, i.e. not from RStudios and
> devtools::document()
>
> and it too crashes so it appears to be something in devtools::document()??
>
>
>
> [1] "/Users/cschwarz/Library/CloudStorage/Dropbox/SPAS-R/SPAS"
>
> > devtools::document()
>
> ℹ Updating SPAS documentation
>
> ℹ Loading SPAS
>
>
> *** caught segfault ***
>
> address 0x54e40, cause 'memory not mapped'
>
>
> Traceback:
>
> 1: dyn.load(dll_copy_file)
>
> 2: library.dynam2(path, lib)
>
> 3: load_dll(path)
>
> 4: pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
>
> 5: load_code(base_path)
>
> 6: roxygen2::roxygenise(pkg$path, roclets)
>
> 7: devtools::document()
>
>
> Possible actions:
>
> 1: abort (with core dump, if enabled)
>
> 2: normal R exit
>
> 3: exit R without saving workspace
>
> 4: exit R saving workspace
>
> Selection:
>
>
>
>
>
> On Wed, Jan 24, 2024 at 3:01 AM <r-package-devel-request using r-project.org>
> wrote:
>
>> Send R-package-devel mailing list submissions to
>> r-package-devel using r-project.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> or, via email, send a message with subject or body 'help' to
>> r-package-devel-request using r-project.org
>>
>> You can reach the person managing the list at
>> r-package-devel-owner using r-project.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of R-package-devel digest..."
>>
>>
>> Today's Topics:
>>
>> 1. lost braces note on CRAN pretest related to \itemize
>> (Patrick Giraudoux)
>> 2. Re: lost braces note on CRAN pretest related to \itemize
>> (Dirk Eddelbuettel)
>> 3. Re: lost braces note on CRAN pretest related to \itemize
>> (Ivan Krylov)
>> 4. Re: lost braces note on CRAN pretest related to \itemize
>> (Patrick Giraudoux)
>> 5. Re: lost braces note on CRAN pretest related to \itemize
>> (Georgi Boshnakov)
>> 6. How to debug segfault when running build -> document in
>> Rstudio that includes TMB module (Carl Schwarz)
>> 7. Re: How to debug segfault when running build -> document in
>> Rstudio that includes TMB module (James Lamb)
>> 8. Re: How to debug segfault when running build -> document in
>> Rstudio that includes TMB module (Serguei Sokol)
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 23 Jan 2024 19:39:54 +0100
>> From: Patrick Giraudoux <patrick.giraudoux using univ-fcomte.fr>
>> To: R Package Development <r-package-devel using r-project.org>
>> Subject: [R-pkg-devel] lost braces note on CRAN pretest related to
>> \itemize
>> Message-ID: <94a7abb7-fbcd-4852-8170-2532b9af58aa using univ-fcomte.fr>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear listers,
>>
>> I meet a problem with the submission of the package pgirmess. In fact
>> the package goes through R CMD check --as-cran and R-wind-builder
>> smoothly with no problem, but submitted to CRAN, I get this:
>>
>> Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
>> Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
>> Maintainer: 'Patrick Giraudoux<patrick.giraudoux using univ-fcomte.fr>'
>>
>> Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
>> Check: Rd files, Result: NOTE
>> checkRd: (-1) mergeTrackObs.rd:24: Lost braces in \itemize; \value
>> handles \item{}{} directly
>> checkRd: (-1) mergeTrackObs.rd:25: Lost braces in \itemize; \value
>> handles \item{}{} directly
>> checkRd: (-1) mergeTrackObs.rd:26: Lost braces in \itemize; \value
>> handles \item{}{} directly
>> checkRd: (-1) selMod.rd:29-31: Lost braces in \itemize; meant
>> \describe ?
>> checkRd: (-1) selMod.rd:32-33: Lost braces in \itemize; meant
>> \describe ?
>> checkRd: (-1) selMod.rd:54: Lost braces in \itemize; meant \describe ?
>> checkRd: (-1) selMod.rd:55: Lost braces in \itemize; meant \describe ?
>>
>> The code that seems to make problem (although braces are balanced; I
>> wonder why a claim 'lost braces') is
>>
>> - for mergeTrackObs.rd
>>
>> \value{
>> A \code{\link[sf]{sfc}} object, of POINT geometry, with the following
>> columns:
>> \itemize{
>> \item{ID}{ ID number}
>> \item{nObs}{ The number of observations in the interval}
>> \item{geometry} {POINT geometry}
>> }
>> }
>>
>> - for selMod.rd
>>
>> \details{
>> This function provides parameters used in the information theoretic
>> methods for model comparisons.
>> \itemize{
>> \item{.}{lm and glm objects can be passed directly as the upper scope
>> of term addition (all terms added).
>> Every model from y\eqn{\sim}{~}1 is computed adding one term at a
>> time until the upper scope model is derived. This is a stepwise analysis
>> where the terms are added sequentially and this does NOT provide all
>> combinations of terms and interactions. Offset terms cannot be proceeded
>> here.
>> }
>> \item{.}{A list of user specified lm, glm, nls, lme or nlme objects
>> (actually any object for which AIC and logLik functions are applicable)
>> to compare can alternately be passed.
>> }
>> }
>> }
>>
>> Has anyone an idea about what is going wrong ?
>>
>> Patrick
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 23 Jan 2024 12:58:46 -0600
>> From: Dirk Eddelbuettel <edd using debian.org>
>> To: Patrick Giraudoux <patrick.giraudoux using univ-fcomte.fr>
>> Cc: R Package Development <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] lost braces note on CRAN pretest related
>> to \itemize
>> Message-ID: <26032.3174.970615.617686 using rob.eddelbuettel.com>
>> Content-Type: text/plain; charset="us-ascii"
>>
>>
>> On 23 January 2024 at 19:39, Patrick Giraudoux wrote:
>> | Has anyone an idea about what is going wrong ?
>>
>> \item has no braces following it. From a package I submitted today and
>> for
>> which I still have NEWS.Rd in the editor (indented here):
>>
>> \section{Changes in version 0.0.22 (2024-01-23)}{
>> \itemize{
>> \item Replace empty examples macros to satisfy CRAN request.
>> }
>> }
>>
>> Hth, Dirk
>>
>> --
>> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 23 Jan 2024 21:59:54 +0300
>> From: Ivan Krylov <ikrylov using disroot.org>
>> To: R Package Development <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] lost braces note on CRAN pretest related
>> to \itemize
>> Message-ID: <20240123215954.0afb8e9d using Tarkus>
>> Content-Type: text/plain; charset="utf-8"
>>
>> В Tue, 23 Jan 2024 19:39:54 +0100
>> Patrick Giraudoux <patrick.giraudoux using univ-fcomte.fr> пишет:
>>
>> > \itemize{
>> > \item{.}{lm and glm objects can be passed directly as the upper
>> > scope of term addition (all terms added).
>>
>> Inside the \itemize and \enumerate commands, the \item command doesn't
>> take any arguments:
>> https://cran.r-project.org/doc/manuals/R-exts.html#Lists-and-tables
>>
>> Instead, it starts a new paragraph with a number (\enumerate) or a
>> bullet point (\itemize). R CMD check is reminding you that \itemize{
>> \item{foo}{bar} } is equivalent to \itemize{ \item foo bar } without
>> any braces.
>>
>> If you meant to highlight a word by making it an argument of the \item
>> command, use the \describe command. Here, you're highlighting a dot,
>> which would be rendered with a bullet point before it, so it's probably
>> neither semantically nor visually appropriate.
>>
>> > \value{
>> > A \code{\link[sf]{sfc}} object, of POINT geometry, with the
>> > following columns:
>> > \itemize{
>> > \item{ID}{ ID number}
>>
>> The same problem applies here.
>>
>> Additionally, R CMD check is reminding you that \value{} is implicitly
>> a special case of a \describe{} environment:
>> https://cran.r-project.org/doc/manuals/R-exts.html#index-_005cvalue
>>
>> Since you're already using \item{}{} labels to name the components of
>> the value, just drop the \itemize{} (but keep its contents). \value{} is
>> enough.
>>
>> --
>> Best regards,
>> Ivan
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Tue, 23 Jan 2024 20:08:20 +0100
>> From: Patrick Giraudoux <patrick.giraudoux using univ-fcomte.fr>
>> To: Dirk Eddelbuettel <edd using debian.org>
>> Cc: R Package Development <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] lost braces note on CRAN pretest related
>> to \itemize
>> Message-ID: <68b9da72-26ad-4f27-8839-aa5b2a65cc6a using univ-fcomte.fr>
>> Content-Type: text/plain; charset="utf-8"
>>
>> OK. Clear enough. CRAN applies a new "filter" as it was going through
>> without crying a note since decades ;-). However, indeed, re-checking
>> the manual "Writing R extensions" my syntax was wrong...
>> Thanks for the guidance,
>> Patrick
>>
>> Le 23/01/2024 à 19:58, Dirk Eddelbuettel a écrit :
>> > On 23 January 2024 at 19:39, Patrick Giraudoux wrote:
>> > | Has anyone an idea about what is going wrong ?
>> >
>> > \item has no braces following it. From a package I submitted today and
>> for
>> > which I still have NEWS.Rd in the editor (indented here):
>> >
>> > \section{Changes in version 0.0.22 (2024-01-23)}{
>> > \itemize{
>> > \item Replace empty examples macros to satisfy CRAN request.
>> > }
>> > }
>> >
>> > Hth, Dirk
>> >
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 23 Jan 2024 20:14:13 +0000
>> From: Georgi Boshnakov <georgi.boshnakov using manchester.ac.uk>
>> To: Patrick Giraudoux <patrick.giraudoux using univ-fcomte.fr>, Dirk
>> Eddelbuettel <edd using debian.org>
>> Cc: R Package Development <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] lost braces note on CRAN pretest related
>> to \itemize
>> Message-ID:
>> <
>> LO0P265MB63252FC9F918C154634DD11BAE742 using LO0P265MB6325.GBRP265.PROD.OUTLOOK.COM
>> >
>>
>> Content-Type: text/plain; charset="utf-8"
>>
>> The notes you get illustrate why they are useful, if you look at your
>> rendered documentation you probably will see something wrong. Thousands of
>> packages on CRAN, including some of mines have had this kind of
>> infelicities for years.
>>
>> Firstly, the two sets of braces suggest that you meant a description
>> environment, not itemize (in which its only argument doesn't need braces).
>>
>> Secondly, in the value section, \item is implicitly enclosed in \describe
>> and you don't need to include the latter.
>>
>> Georgi Boshnakov
>>
>>
>> Sent from Outlook for Android<https://aka.ms/AAb9ysg>
>>
>> ________________________________
>> From: R-package-devel <r-package-devel-bounces using r-project.org> on behalf
>> of Patrick Giraudoux <patrick.giraudoux using univ-fcomte.fr>
>> Sent: Tuesday, January 23, 2024 7:09:22 pm
>> To: Dirk Eddelbuettel <edd using debian.org>
>> Cc: R Package Development <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] lost braces note on CRAN pretest related to
>> \itemize
>>
>> OK. Clear enough. CRAN applies a new "filter" as it was going through
>> without crying a note since decades ;-). However, indeed, re-checking
>> the manual "Writing R extensions" my syntax was wrong...
>> Thanks for the guidance,
>> Patrick
>>
>> Le 23/01/2024 � 19:58, Dirk Eddelbuettel a �crit :
>> > On 23 January 2024 at 19:39, Patrick Giraudoux wrote:
>> > | Has anyone an idea about what is going wrong ?
>> >
>> > \item has no braces following it. From a package I submitted today and
>> for
>> > which I still have NEWS.Rd in the editor (indented here):
>> >
>> > \section{Changes in version 0.0.22 (2024-01-23)}{
>> > \itemize{
>> > \item Replace empty examples macros to satisfy CRAN request.
>> > }
>> > }
>> >
>> > Hth, Dirk
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-package-devel using r-project.org mailing list
>>
>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-package-devel__;!!PDiH4ENfjr2_Jw!Gu9AhS4Yi4k5IC8TXv4B8xpznl-8-Jhl-cdxRZ6zVrRCdmDaSTVYpaG5XDoitdms9FuHQGV7adP-Q6WD6w2bMws_b5UnszsH5VsXFBMUIvFX4Nc$
>> [stat[.]ethz[.]ch]
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Tue, 23 Jan 2024 19:22:43 -0800
>> From: Carl Schwarz <cschwarzstatsfuca using gmail.com>
>> To: r-package-devel using r-project.org
>> Subject: [R-pkg-devel] How to debug segfault when running build ->
>> document in Rstudio that includes TMB module
>> Message-ID:
>> <
>> CADtpigYViZ+2GJq+XQyJ6GeyEZ_CWMnUPg20-LcdLKC3GWvVxA using mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> I'm trying to update my SPAS package to respond to a CRAN check. Before
>> starting the changes, I tried to rebuild my package, but now get a
>> segfault
>> when I try to do a devtools::document() or devtools::check(args =
>> c('--as-cran')). See below for output from the Rstudio "Build" window.
>>
>> I've
>> - reinstalled ALL packages
>> - reinstalled R (4.3.2 on MacOS Intel Chip)
>> - reinstalled Rstudio
>>
>> When I try a rebuild/document on a sister package it runs fine, so I
>> suspect that the problem is related to using a TMB module that is part of
>> the SPAS package written in Cpp.
>>
>> How do I start to "debug" this to identify the problem?
>>
>> Thanks
>> Carl Schwarz
>>
>>
>>
>>
>> ==> devtools::document(roclets = c('rd', 'collate', 'namespace',
>> 'vignette'))
>> ℹ Updating SPAS documentationℹ Loading SPAS
>>
>> *** caught segfault ***
>> address 0x54e40, cause 'memory not mapped'
>>
>> Traceback:
>> 1: dyn.load(dll_copy_file)
>> 2: library.dynam2(path, lib)
>> 3: load_dll(path)
>> 4: pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
>> 5: load_code(base_path)
>> 6: roxygen2::roxygenise(pkg$path, roclets)
>> 7: devtools::document(roclets = c("rd", "collate", "namespace",
>> "vignette"))
>> 8: withCallingHandlers(expr, packageStartupMessage = function(c)
>> tryInvokeRestart("muffleMessage"))
>> 9: suppressPackageStartupMessages({ oldLC <-
>> Sys.getlocale(category = "LC_COLLATE") Sys.setlocale(category =
>> "LC_COLLATE", locale = "C") on.exit(Sys.setlocale(category =
>> "LC_COLLATE", locale = oldLC)) devtools::document(roclets = c("rd",
>> "collate", "namespace", "vignette"))})
>> An irrecoverable exception occurred. R is aborting now ...
>>
>> Exited with status 139.
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Tue, 23 Jan 2024 21:35:31 -0600
>> From: James Lamb <jaylamb20 using gmail.com>
>> To: cschwarzstatsfuca using gmail.com, R Package Development
>> <r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] How to debug segfault when running build
>> -> document in Rstudio that includes TMB module
>> Message-ID:
>> <CADPubGQcowMyyZUCHYu=
>> 4ndjyB9xAu4gLLOjgKjtS1L_kqdNVQ using mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Carl,
>>
>> Consider performing these tasks without the use of the 'devtools' package,
>> running the following from a shell.
>>
>> ```shell
>> R CMD build .
>> R CMD INSTALL --with-keep.source ./SPAS_*.tar.gz
>>
>> # (assuming you use roxygen2)
>> Rscript -e "roxygen2::roxygenize(load = 'installed')"
>>
>> R CMD check --as-cran ./SPAS_*.tar.gz
>> ```
>>
>> If those commands are successful, then you know the problem lies somewhere
>> in the difference between that approach and what 'devtools' does, which
>> might help to narrow it down.
>>
>> Cheers,
>>
>> -James
>>
>>
>> On Tue, Jan 23, 2024 at 9:23 PM Carl Schwarz <cschwarzstatsfuca using gmail.com
>> >
>> wrote:
>>
>> > I'm trying to update my SPAS package to respond to a CRAN check. Before
>> > starting the changes, I tried to rebuild my package, but now get a
>> segfault
>> > when I try to do a devtools::document() or devtools::check(args =
>> > c('--as-cran')). See below for output from the Rstudio "Build" window.
>> >
>> > I've
>> > - reinstalled ALL packages
>> > - reinstalled R (4.3.2 on MacOS Intel Chip)
>> > - reinstalled Rstudio
>> >
>> > When I try a rebuild/document on a sister package it runs fine, so I
>> > suspect that the problem is related to using a TMB module that is part
>> of
>> > the SPAS package written in Cpp.
>> >
>> > How do I start to "debug" this to identify the problem?
>> >
>> > Thanks
>> > Carl Schwarz
>> >
>> >
>> >
>> >
>> > ==> devtools::document(roclets = c('rd', 'collate', 'namespace',
>> > 'vignette'))
>> > ℹ Updating SPAS documentationℹ Loading SPAS
>> >
>> > *** caught segfault ***
>> > address 0x54e40, cause 'memory not mapped'
>> >
>> > Traceback:
>> > 1: dyn.load(dll_copy_file)
>> > 2: library.dynam2(path, lib)
>> > 3: load_dll(path)
>> > 4: pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
>> > 5: load_code(base_path)
>> > 6: roxygen2::roxygenise(pkg$path, roclets)
>> > 7: devtools::document(roclets = c("rd", "collate", "namespace",
>> > "vignette"))
>> > 8: withCallingHandlers(expr, packageStartupMessage = function(c)
>> > tryInvokeRestart("muffleMessage"))
>> > 9: suppressPackageStartupMessages({ oldLC <-
>> > Sys.getlocale(category = "LC_COLLATE") Sys.setlocale(category =
>> > "LC_COLLATE", locale = "C") on.exit(Sys.setlocale(category =
>> > "LC_COLLATE", locale = oldLC)) devtools::document(roclets = c("rd",
>> > "collate", "namespace", "vignette"))})
>> > An irrecoverable exception occurred. R is aborting now ...
>> >
>> > Exited with status 139.
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-package-devel using r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> >
>>
>>
>> --
>> James Lamb (he/him)
>> GitHub <https://github.com/jameslamb> | LinkedIn
>> <https://www.linkedin.com/in/jameslamb1/>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Wed, 24 Jan 2024 09:03:11 +0100
>> From: Serguei Sokol <serguei.sokol using gmail.com>
>> To: r-package-devel using r-project.org
>> Subject: Re: [R-pkg-devel] How to debug segfault when running build
>> -> document in Rstudio that includes TMB module
>> Message-ID: <8a8e07b0-2fe9-410b-a9f4-15ab6ebe9f91 using gmail.com>
>> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>>
>> Le 24/01/2024 à 04:22, Carl Schwarz a écrit :
>> > I'm trying to update my SPAS package to respond to a CRAN check. Before
>> > starting the changes, I tried to rebuild my package, but now get a
>> segfault
>> > when I try to do a devtools::document() or devtools::check(args =
>> > c('--as-cran')). See below for output from the Rstudio "Build" window.
>> >
>> > I've
>> > - reinstalled ALL packages
>> > - reinstalled R (4.3.2 on MacOS Intel Chip)
>> > - reinstalled Rstudio
>> >
>> > When I try a rebuild/document on a sister package it runs fine, so I
>> > suspect that the problem is related to using a TMB module that is part
>> of
>> > the SPAS package written in Cpp.
>> >
>> > How do I start to "debug" this to identify the problem?
>> Why not simply run devtools::document() from 'R -d gdb' ?
>>
>> Best,
>> Serguei.
>>
>> >
>> > Thanks
>> > Carl Schwarz
>> >
>> >
>> >
>> >
>> > ==> devtools::document(roclets = c('rd', 'collate', 'namespace',
>> 'vignette'))
>> > ℹ Updating SPAS documentationℹ Loading SPAS
>> >
>> > *** caught segfault ***
>> > address 0x54e40, cause 'memory not mapped'
>> >
>> > Traceback:
>> > 1: dyn.load(dll_copy_file)
>> > 2: library.dynam2(path, lib)
>> > 3: load_dll(path)
>> > 4: pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
>> > 5: load_code(base_path)
>> > 6: roxygen2::roxygenise(pkg$path, roclets)
>> > 7: devtools::document(roclets = c("rd", "collate", "namespace",
>> > "vignette"))
>> > 8: withCallingHandlers(expr, packageStartupMessage = function(c)
>> > tryInvokeRestart("muffleMessage"))
>> > 9: suppressPackageStartupMessages({ oldLC <-
>> > Sys.getlocale(category = "LC_COLLATE") Sys.setlocale(category =
>> > "LC_COLLATE", locale = "C") on.exit(Sys.setlocale(category =
>> > "LC_COLLATE", locale = oldLC)) devtools::document(roclets = c("rd",
>> > "collate", "namespace", "vignette"))})
>> > An irrecoverable exception occurred. R is aborting now ...
>> >
>> > Exited with status 139.
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-package-devel using r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>
>>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> R-package-devel mailing list
>> R-package-devel using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>
>> ------------------------------
>>
>> End of R-package-devel Digest, Vol 105, Issue 19
>> ************************************************
>
>
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