[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. 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} [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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} __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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} __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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} __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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} __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel