[R-pkg-devel] R-package-devel Digest, Vol 105, Issue 19

[Simon Urbanek]

This is a reminder why one should never build packages directly in their source directory since it can only be done once (for packages with native source code) - always use

R CMD build --no-build-vignettes foo && R CMD INSTALL foo_*.tar.gz

if you plan to edit files in the source directory and re-use it.

Cheers,
Simon


> On 25/01/2024, at 8:34 AM, Carl Schwarz <cschwarzstatsfuca using gmail.com> wrote:
> 
> 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 of the package that must be "out of date" because once I removed those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A newer version of the .o and .so objects are now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
>>> ************************************************
>> 
>> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>