Re: [R-pkg-devel] problems documenting data sets
Thanks a lot - I tried your script but it didn't turn up anything like Brom
but in one place I had Bromic acid - which I changed to bromic acid to no
avail.
So I continue trying to find out what goes on
BW
Troels
Fra: Berry Boessenkool
Sendt: 19. januar 2019 23:47
Til: Troels Ring ; R package devel
Emne: Re: [R-pkg-devel] problems documenting data sets
I was first thinking there could be an occurence of Brom with a capital B in
the package somewhere.
In which case you could run from the current package main directory:
cat("All files in R folder\n", file="AllFiles.R")
for(f in dir("R",full=T)) cat(readLines(f), file="AllFiles.R", sep="\n",
append=TRUE)
and search for Brom in that file...
But Rolf is likely right. I was thinking the wrong way around...
Berry
_
From: R-package-devel mailto:r-package-devel-boun...@r-project.org> > on behalf of Troels Ring
mailto:tr...@gvdnet.dk> >
Sent: Saturday, January 19, 2019 11:46
To: package-develop
Subject: [R-pkg-devel] problems documenting data sets
Dear friends - I still get some warning although the package runs just fine.
checking for missing documentation entries ... WARNING
Undocumented data sets:
'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'
'Brom' 'pHOBS'
All user-level objects in a package should have documentation entries.
[SNIP]
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] problems documenting data sets
Thank you so much - I used the search in files function in RStudio and also
looked everywhere as well as I could - but seemingly: no - everywhere only
"brom". So since the functions runs as expected and I can make a workable
binary package I guess I will just continue improving the functionalities and
see if I eventually get a hunch
All best wishes
Troels
-Oprindelig meddelelse-
Fra: Rolf Turner
Sendt: 19. januar 2019 23:12
Til: Troels Ring
Cc: package-develop
Emne: Re: [R-pkg-devel] problems documenting data sets
It's hard to be sure without seeing your package, but it *sounds* as though you
have a data set "Brom" (in /data ?) but you have
*documented* a data set named "brom". So you should either change the name of
the data set to "brom" or change your help file to document "Brom".
It is of course entirely possible that I am misunderstanding what is going on,
in which case I apologise for the noise.
cheers,
Rolf
--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
On 1/19/19 11:46 PM, Troels Ring wrote:
> Dear friends – I still get some warning although the package runs just fine.
>
> checking for missing documentation entries ... WARNING
>
>Undocumented data sets:
>
> 'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'
>
> 'Brom' 'pHOBS'
>
>All user-level objects in a package should have documentation entries.
>
>See chapter 'Writing R documentation files' in the 'Writing R
>
>Extensions' manual.
>
>
>
> 0 errors v | 1 warning x | 0 notes v
>
> Fejl: R CMD check found WARNINGs
>
> K rsel stoppet (run stopped)
>
>
>
> But the only place I have any mentions of brom is here below and in no place
> I have capital Brom. So what should I make of this?
>
>
>
> \name{brom}
>
> \alias{brom}
>
> \docType{data}
>
> \title{
>
> Bromic acid data from Glaser et al 2014
>
> }
>
> \description{
>
>Data to find optimal pK for bromic acid
>
> }
>
> \usage{data("brom")}
>
> \format{
>
> A workspace.
>
>\describe{
>
> \item{brom}{Dataframe of Table S4 in Glaser et al.}
>
> \item{WA}{List of buffers with list of dissociation constants.}
>
>}
>
> }
>
> \source{
>
> Glaser RE et al. Dynamical approach to multiequilibriia problems for
> mixtures of
>
> acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016
>
> }
>
> \examples{
>
> data(brom)
>
> ## maybe str(brom) ; plot(brom) ...
>
> }
>
> \keyword{datasets}
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Re: [R-pkg-devel] problems documenting data sets
Did you mention where your package source can be downloaded from, e.g., github?
Because obviously it is then much easier for people to help.
Martin Morgan
On 1/20/19, 12:55 PM, "R-package-devel on behalf of Troels Ring"
wrote:
Thank you so much - I used the search in files function in RStudio and also
looked everywhere as well as I could - but seemingly: no - everywhere only
"brom". So since the functions runs as expected and I can make a workable
binary package I guess I will just continue improving the functionalities and
see if I eventually get a hunch
All best wishes
Troels
-Oprindelig meddelelse-
Fra: Rolf Turner
Sendt: 19. januar 2019 23:12
Til: Troels Ring
Cc: package-develop
Emne: Re: [R-pkg-devel] problems documenting data sets
It's hard to be sure without seeing your package, but it *sounds* as though
you have a data set "Brom" (in /data ?) but you have
*documented* a data set named "brom". So you should either change the name
of the data set to "brom" or change your help file to document "Brom".
It is of course entirely possible that I am misunderstanding what is going
on, in which case I apologise for the noise.
cheers,
Rolf
--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
On 1/19/19 11:46 PM, Troels Ring wrote:
> Dear friends – I still get some warning although the package runs just
fine.
>
> checking for missing documentation entries ... WARNING
>
>Undocumented data sets:
>
> 'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'
>
> 'Brom' 'pHOBS'
>
>All user-level objects in a package should have documentation entries.
>
>See chapter 'Writing R documentation files' in the 'Writing R
>
>Extensions' manual.
>
>
>
> 0 errors v | 1 warning x | 0 notes v
>
> Fejl: R CMD check found WARNINGs
>
> K rsel stoppet (run stopped)
>
>
>
> But the only place I have any mentions of brom is here below and in no
place I have capital Brom. So what should I make of this?
>
>
>
> \name{brom}
>
> \alias{brom}
>
> \docType{data}
>
> \title{
>
> Bromic acid data from Glaser et al 2014
>
> }
>
> \description{
>
>Data to find optimal pK for bromic acid
>
> }
>
> \usage{data("brom")}
>
> \format{
>
> A workspace.
>
>\describe{
>
> \item{brom}{Dataframe of Table S4 in Glaser et al.}
>
> \item{WA}{List of buffers with list of dissociation constants.}
>
>}
>
> }
>
> \source{
>
> Glaser RE et al. Dynamical approach to multiequilibriia problems for
> mixtures of
>
> acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016
>
> }
>
> \examples{
>
> data(brom)
>
> ## maybe str(brom) ; plot(brom) ...
>
> }
>
> \keyword{datasets}
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Re: [R-pkg-devel] problems documenting data sets
Thank you so much - this is just the first package I've made so I didn't put
it out yet. Will follow your suggestion next time
BW
Troels
-Oprindelig meddelelse-
Fra: Martin Morgan
Sendt: 20. januar 2019 19:14
Til: Troels Ring ; 'Rolf Turner'
Cc: 'package-develop'
Emne: Re: [R-pkg-devel] problems documenting data sets
Did you mention where your package source can be downloaded from, e.g., github?
Because obviously it is then much easier for people to help.
Martin Morgan
On 1/20/19, 12:55 PM, "R-package-devel on behalf of Troels Ring"
wrote:
Thank you so much - I used the search in files function in RStudio and also
looked everywhere as well as I could - but seemingly: no - everywhere only
"brom". So since the functions runs as expected and I can make a workable
binary package I guess I will just continue improving the functionalities and
see if I eventually get a hunch
All best wishes
Troels
-Oprindelig meddelelse-
Fra: Rolf Turner
Sendt: 19. januar 2019 23:12
Til: Troels Ring
Cc: package-develop
Emne: Re: [R-pkg-devel] problems documenting data sets
It's hard to be sure without seeing your package, but it *sounds* as though
you have a data set "Brom" (in /data ?) but you have
*documented* a data set named "brom". So you should either change the name
of the data set to "brom" or change your help file to document "Brom".
It is of course entirely possible that I am misunderstanding what is going
on, in which case I apologise for the noise.
cheers,
Rolf
--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
On 1/19/19 11:46 PM, Troels Ring wrote:
> Dear friends – I still get some warning although the package runs just
fine.
>
> checking for missing documentation entries ... WARNING
>
>Undocumented data sets:
>
> 'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'
>
> 'Brom' 'pHOBS'
>
>All user-level objects in a package should have documentation entries.
>
>See chapter 'Writing R documentation files' in the 'Writing R
>
>Extensions' manual.
>
>
>
> 0 errors v | 1 warning x | 0 notes v
>
> Fejl: R CMD check found WARNINGs
>
> K rsel stoppet (run stopped)
>
>
>
> But the only place I have any mentions of brom is here below and in no
place I have capital Brom. So what should I make of this?
>
>
>
> \name{brom}
>
> \alias{brom}
>
> \docType{data}
>
> \title{
>
> Bromic acid data from Glaser et al 2014
>
> }
>
> \description{
>
>Data to find optimal pK for bromic acid
>
> }
>
> \usage{data("brom")}
>
> \format{
>
> A workspace.
>
>\describe{
>
> \item{brom}{Dataframe of Table S4 in Glaser et al.}
>
> \item{WA}{List of buffers with list of dissociation constants.}
>
>}
>
> }
>
> \source{
>
> Glaser RE et al. Dynamical approach to multiequilibriia problems for
> mixtures of
>
> acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016
>
> }
>
> \examples{
>
> data(brom)
>
> ## maybe str(brom) ; plot(brom) ...
>
> }
>
> \keyword{datasets}
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[R-pkg-devel] Failure at pretest stage on Debian CRAN server due to system requirements (nlopt)
Hi,
I am trying to submit a package to CRAN that fails during the pretest
process on Debian.
I use the some C++ code that interfaces to the nlopt optimization
library with Rcpp/RcppArmadillo. Thus, my package requires a system
version of nlopt that can be installed via the deb package
libnlopt-dev (I added this to the SystemRequirements field).
I use a configure script and pkg-config to retrieve the (hopefully)
appropriate compiler flags which I then send to src/Makevars
NLOPT_LIBS=`pkg-config --libs ${PKG_CONFIG_NAME}`
NLOPT_FLAG=`pkg-config --cflags ${PKG_CONFIG_NAME}`
This approach works on my system (Ubuntu 18.04, R 3.5.2) and on Travis
(linux and mac OS), but fails on the Debian CRAN server :
https://win-builder.r-project.org/incoming_pretest/PLNmodels_0.7_20190119_161032/Debian/00install.out
I added some verbosity to check that the flags were correctly exported
on CRAN servers, and they seems alright to me: at least, a version of
nlopt is found on the system (see below, NLOPT_LIBS=-lnlopt -lm).
However, the is not found latter on...
Any help would be greatly appreciated. Thank for taking the time to read this.
* installing *source* package ‘PLNmodels’ ...
Using NLOPT_LIBS=-lnlopt -lm
Using NLOPT_FLAG=
** libs
g++-8 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -fopenmp
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/Rcpp/include"
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/RcppArmadillo/include"
-I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic
-mtune=native -c RcppExports.cpp -o RcppExports.o
g++-8 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -fopenmp
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/Rcpp/include"
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/RcppArmadillo/include"
-I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic
-mtune=native -c call_nlopt_PLN_VE.cpp -o call_nlopt_PLN_VE.o
In file included from call_nlopt_PLN_VE.cpp:6:
utils.h:5:10: fatal error: nlopt.hpp: No such file or directory
#include
^~~
compilation terminated.
make: *** [/home/hornik/tmp/R/etc/Makeconf:173: call_nlopt_PLN_VE.o] Error 1
ERROR: compilation failed for package ‘PLNmodels’
* removing ‘/srv/hornik/tmp/CRAN/PLNmodels.Rcheck/PLNmodels’
Regards,
Julien Chiquet
http://julien.cremeriefamily.info
mel: julien.chiq...@inra.fr
tel: +33(0)1 44 08 16 73
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