Hello, I am hoping to post to the right mailing list, if not apologies! I have recently written my first couple packages, relying on devtools and roxygen. Everything is done in RStudio (details regarding the setup: see end of text). But the help is not working! Specifically: On Windows 7: * functions: I cannot click the links in the 'help'-panel. Or at least nothing happens when I click them. * DESCRIPTION: If I build the package locally, it has the same issues as the packages. If I install the packages from Github (devtools::install_github) or from a network drive, it works. * The "my_package::my_function" syntax throws an error. Once I enter 'my_package::' and click TAB, the following error appears in the console: "Error in gzfile(file, "rb") : cannot open the connection" * "?my_package::my_function" brings me to the function overview page for the package, but not to the help page for the my_function() * the link itself (on the function overview page) looks inocuous: http://127.0.0.1:44391/help/library/helpers/html/my_function.html I would love to do a Traceback on this, but I do not know how, since it only happens when hitting TAB. I have done a Traceback for "?my_package::my_function", it just returns the path to where the help should be, like "D:/Home/R/Rpackages/my_package/help/my_function". On MacOS Sierra: * DESCRIPTION can always be opened, no matter how the package is installed * when clicking on functions in the help panel, the known error appears (as text in the help panel): "Error in gzfile(file, "rb") : cannot open the connection" It gets much weirder: When installing the package for the very first time, it seems to work! But after that it quits working, even not when I delete the package, re-install R, re-install RStudio, and create the package from scratch. I really wish I was kidding with all of this. I have tried every debugging-idea that came to my mind, including (but not limited to): * the .Rd-files are generated, they definitely are not missing * taking an auto-generated DESCRIPTION file * removing every function file save for a test file * copying content from a function file into the auto-generated "hello.R" file * changing the encoding from UTF-8 to WINDOWS-1252 * as mentioned, trying everying both on Windows and MacOS, and trying different ways of installation * as mentioned, re-installing both R and RStudio I would enormously appreciate it if anyone has an idea how to get a handle on this, any suggestions are welcome! David ______________________ My setup: * Windows 7 / MacOS Sierra * R 3.4.1 * RStudio 1.0.153 * devtools 1.13.3 * roxygen2 6.0.1
[R-pkg-devel] The Help (e.g. links) is not working for my packages
9 messages · Duncan Murdoch, Dirk Eddelbuettel, Michael Dewey +2 more
2 days later
On 07/08/2017 3:41 AM, David.Kaethner at dlr.de wrote:
Hello, I am hoping to post to the right mailing list, if not apologies! I have recently written my first couple packages, relying on devtools and roxygen. Everything is done in RStudio (details regarding the setup: see end of text). But the help is not working! Specifically: On Windows 7: * functions: I cannot click the links in the 'help'-panel. Or at least nothing happens when I click them. * DESCRIPTION: If I build the package locally, it has the same issues as the packages. If I install the packages from Github (devtools::install_github) or from a network drive, it works. * The "my_package::my_function" syntax throws an error. Once I enter 'my_package::' and click TAB, the following error appears in the console: "Error in gzfile(file, "rb") : cannot open the connection" * "?my_package::my_function" brings me to the function overview page for the package, but not to the help page for the my_function() * the link itself (on the function overview page) looks inocuous: http://127.0.0.1:44391/help/library/helpers/html/my_function.html I would love to do a Traceback on this, but I do not know how, since it only happens when hitting TAB. I have done a Traceback for "?my_package::my_function", it just returns the path to where the help should be, like "D:/Home/R/Rpackages/my_package/help/my_function". On MacOS Sierra: * DESCRIPTION can always be opened, no matter how the package is installed * when clicking on functions in the help panel, the known error appears (as text in the help panel): "Error in gzfile(file, "rb") : cannot open the connection" It gets much weirder: When installing the package for the very first time, it seems to work! But after that it quits working, even not when I delete the package, re-install R, re-install RStudio, and create the package from scratch. I really wish I was kidding with all of this. I have tried every debugging-idea that came to my mind, including (but not limited to): * the .Rd-files are generated, they definitely are not missing * taking an auto-generated DESCRIPTION file * removing every function file save for a test file * copying content from a function file into the auto-generated "hello.R" file * changing the encoding from UTF-8 to WINDOWS-1252 * as mentioned, trying everying both on Windows and MacOS, and trying different ways of installation * as mentioned, re-installing both R and RStudio I would enormously appreciate it if anyone has an idea how to get a handle on this, any suggestions are welcome!
Nothing that you've written is reproducible by others. See if you can put together a short self-contained series of instructions that display the problems (or just one of them). It might involve installing from Github, or making a package tarball available somewhere. Duncan Murdoch
On 9 August 2017 at 08:38, Duncan Murdoch wrote:
| Nothing that you've written is reproducible by others. See if you can | put together a short self-contained series of instructions that display | the problems (or just one of them). It might involve installing from | Github, or making a package tarball available somewhere. I am fairly certain I have observed this myself, and I *think* it simply stems from running R CMD INSTALL (and alike) from a source directory, as opposed to a tarball. I filed it under minor nuisance and didn't care too much either as the official two-step of 'R CMD build ...; R CMD INSTALL ...' is just that: the official and recommended way. With which things work. Dirk
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Thank you for the replies!
First of all, here is the test package:
https://github.com/c06n/helpers2
Session info and the log of R CMD check at the end. There is an error: "LaTeX errors when creating PDF version." However, it says "checking Rd files ... OK".
I have tried the install now on 4 different computers (via devtools::install_github), they all did not work.
Further points:
- Unfortunately, installation from a tarball did not work either. I build the tarball from the command line (Cygwin), then used R CMD, but tried it also from within RStudio ("Build Source Package", then "install.packages")
- I have managed to create another package WHICH WORKS. I have not been able to do it again though, I just don't know what I did differently.
- I played around with the documentation lines in the test package, to no avail.
I am sure that it is something very minor where I went wrong, and in all likelihood the problem is on my side. I just cannot figure out what it might be.
David
-----
sessionInfo()
R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] _0.1.0 loaded via a namespace (and not attached): [1] compiler_3.4.1 tools_3.4.1 -------- * using log directory '/cygdrive/d/Home/projects/R_package_dev/helpers2.Rcheck' * using R version 3.4.0 (2017-04-21) * using platform: x86_64-unknown-cygwin (64-bit) * using session charset: ISO8859-1 * checking for file 'helpers2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'helpers2' version '0.1.0' * package encoding: UTF-8 * 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 whether package 'helpers2' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: testlicense Standardizable: FALSE * 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 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 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 examples ... NONE * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index ... ERROR * DONE Status: 1 ERROR, 2 WARNINGs -----Urspr?ngliche Nachricht----- Von: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] Im Auftrag von Dirk Eddelbuettel Gesendet: Donnerstag, 10. August 2017 14:32 An: Duncan Murdoch Cc: K?thner, David; r-package-devel at r-project.org Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages
On 9 August 2017 at 08:38, Duncan Murdoch wrote:
| Nothing that you've written is reproducible by others. See if you can | put together a short self-contained series of instructions that | display the problems (or just one of them). It might involve | installing from Github, or making a package tarball available somewhere. I am fairly certain I have observed this myself, and I *think* it simply stems from running R CMD INSTALL (and alike) from a source directory, as opposed to a tarball. I filed it under minor nuisance and didn't care too much either as the official two-step of 'R CMD build ...; R CMD INSTALL ...' is just that: the official and recommended way. With which things work. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Your log says you have no examples but you do in your Rd file. Your examples look the wrong way round x(function) rather than function(x) Not sure whether those are relevant issues but perhaps they help.
On 10/08/2017 15:47, David.Kaethner at dlr.de wrote:
Thank you for the replies!
First of all, here is the test package:
https://github.com/c06n/helpers2
Session info and the log of R CMD check at the end. There is an error: "LaTeX errors when creating PDF version." However, it says "checking Rd files ... OK".
I have tried the install now on 4 different computers (via devtools::install_github), they all did not work.
Further points:
- Unfortunately, installation from a tarball did not work either. I build the tarball from the command line (Cygwin), then used R CMD, but tried it also from within RStudio ("Build Source Package", then "install.packages")
- I have managed to create another package WHICH WORKS. I have not been able to do it again though, I just don't know what I did differently.
- I played around with the documentation lines in the test package, to no avail.
I am sure that it is something very minor where I went wrong, and in all likelihood the problem is on my side. I just cannot figure out what it might be.
David
-----
sessionInfo()
R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] _0.1.0 loaded via a namespace (and not attached): [1] compiler_3.4.1 tools_3.4.1 -------- * using log directory '/cygdrive/d/Home/projects/R_package_dev/helpers2.Rcheck' * using R version 3.4.0 (2017-04-21) * using platform: x86_64-unknown-cygwin (64-bit) * using session charset: ISO8859-1 * checking for file 'helpers2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'helpers2' version '0.1.0' * package encoding: UTF-8 * 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 whether package 'helpers2' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: testlicense Standardizable: FALSE * 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 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 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 examples ... NONE * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index ... ERROR * DONE Status: 1 ERROR, 2 WARNINGs -----Urspr?ngliche Nachricht----- Von: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] Im Auftrag von Dirk Eddelbuettel Gesendet: Donnerstag, 10. August 2017 14:32 An: Duncan Murdoch Cc: K?thner, David; r-package-devel at r-project.org Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages On 9 August 2017 at 08:38, Duncan Murdoch wrote: | Nothing that you've written is reproducible by others. See if you can | put together a short self-contained series of instructions that | display the problems (or just one of them). It might involve | installing from Github, or making a package tarball available somewhere. I am fairly certain I have observed this myself, and I *think* it simply stems from running R CMD INSTALL (and alike) from a source directory, as opposed to a tarball. I filed it under minor nuisance and didn't care too much either as the official two-step of 'R CMD build ...; R CMD INSTALL ...' is just that: the official and recommended way. With which things work. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel --- This email has been checked for viruses by AVG. http://www.avg.com
Thank you for pointing that out, this solved the ERROR in the R CMD check. I've updated the repo. Unfortunately, it did not solve the problem. So when you clone/pull the repo now, the error should persist. * using log directory ?/Users/spaceicons/code/R_package_dev/helpers2/helpers2.Rcheck? * using R version 3.4.1 (2017-06-30) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * checking for file ?helpers2/DESCRIPTION? ... OK * checking extension type ... Package * this is package ?helpers2? version ?0.1.0? * package encoding: UTF-8 * 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 whether package ?helpers2? can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: What license is it under? Standardizable: FALSE * 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 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 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 examples ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING
Von: Michael Dewey [lists at dewey.myzen.co.uk]
Gesendet: Donnerstag, 10. August 2017 17:38 An: K?thner, David; edd at debian.org; murdoch.duncan at gmail.com Cc: r-package-devel at r-project.org Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages Your log says you have no examples but you do in your Rd file. Your examples look the wrong way round x(function) rather than function(x) Not sure whether those are relevant issues but perhaps they help. On 10/08/2017 15:47, David.Kaethner at dlr.de wrote: > Thank you for the replies! > > First of all, here is the test package: > https://github.com/c06n/helpers2 > > Session info and the log of R CMD check at the end. There is an error: "LaTeX errors when creating PDF version." However, it says "checking Rd files ... OK". > > I have tried the install now on 4 different computers (via devtools::install_github), they all did not work. > > Further points: > - Unfortunately, installation from a tarball did not work either. I build the tarball from the command line (Cygwin), then used R CMD, but tried it also from within RStudio ("Build Source Package", then "install.packages") > - I have managed to create another package WHICH WORKS. I have not been able to do it again though, I just don't know what I did differently. > - I played around with the documentation lines in the test package, to no avail. > > I am sure that it is something very minor where I went wrong, and in all likelihood the problem is on my side. I just cannot figure out what it might be. > > David > > ----- >> sessionInfo() > R version 3.4.1 (2017-06-30) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 7 x64 (build 7601) Service Pack 1 > > Matrix products: default > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] _0.1.0 > > loaded via a namespace (and not attached): > [1] compiler_3.4.1 tools_3.4.1 > > -------- > * using log directory '/cygdrive/d/Home/projects/R_package_dev/helpers2.Rcheck' > * using R version 3.4.0 (2017-04-21) > * using platform: x86_64-unknown-cygwin (64-bit) > * using session charset: ISO8859-1 > * checking for file 'helpers2/DESCRIPTION' ... OK > * checking extension type ... Package > * this is package 'helpers2' version '0.1.0' > * package encoding: UTF-8 > * 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 whether package 'helpers2' can be installed ... OK > * checking installed package size ... OK > * checking package directory ... OK > * checking DESCRIPTION meta-information ... WARNING > Non-standard license specification: > testlicense > Standardizable: FALSE > * 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 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 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 examples ... NONE > * checking PDF version of manual ... WARNING > LaTeX errors when creating PDF version. > This typically indicates Rd problems. > * checking PDF version of manual without hyperrefs or index ... ERROR > * DONE > Status: 1 ERROR, 2 WARNINGs > > > > > > > > > > > > > -----Urspr?ngliche Nachricht----- > Von: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] Im Auftrag von Dirk Eddelbuettel > Gesendet: Donnerstag, 10. August 2017 14:32 > An: Duncan Murdoch > Cc: K?thner, David; r-package-devel at r-project.org > Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages > > > On 9 August 2017 at 08:38, Duncan Murdoch wrote: > | Nothing that you've written is reproducible by others. See if you can > | put together a short self-contained series of instructions that > | display the problems (or just one of them). It might involve > | installing from Github, or making a package tarball available somewhere. > > I am fairly certain I have observed this myself, and I *think* it simply stems from running R CMD INSTALL (and alike) from a source directory, as opposed to a tarball. I filed it under minor nuisance and didn't care too much either as the official two-step of 'R CMD build ...; R CMD INSTALL ...' > is just that: the official and recommended way. With which things work. > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > > ______________________________________________ > R-package-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > --- > This email has been checked for viruses by AVG. > http://www.avg.com > > -- Michael http://www.dewey.myzen.co.uk/home.html
It tells you what the warning is. You need to specify a license in your DESCRIPTION file. You should really fill the entire thing out properly anyways.
On Aug 10, 2017 12:39 PM, <David.Kaethner at dlr.de> wrote:
Thank you for pointing that out, this solved the ERROR in the R CMD check. I've updated the repo. Unfortunately, it did not solve the problem. So when you clone/pull the repo now, the error should persist. * using log directory ?/Users/spaceicons/code/R_ package_dev/helpers2/helpers2.Rcheck? * using R version 3.4.1 (2017-06-30) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * checking for file ?helpers2/DESCRIPTION? ... OK * checking extension type ... Package * this is package ?helpers2? version ?0.1.0? * package encoding: UTF-8 * 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 whether package ?helpers2? can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: What license is it under? Standardizable: FALSE * 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 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 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 examples ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING
________________________________________
Von: Michael Dewey [lists at dewey.myzen.co.uk]
Gesendet: Donnerstag, 10. August 2017 17:38
An: K?thner, David; edd at debian.org; murdoch.duncan at gmail.com
Cc: r-package-devel at r-project.org
Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my
packages
Your log says you have no examples but you do in your Rd file.
Your examples look the wrong way round x(function) rather than function(x)
Not sure whether those are relevant issues but perhaps they help.
On 10/08/2017 15:47, David.Kaethner at dlr.de wrote:
Thank you for the replies!
First of all, here is the test package:
https://github.com/c06n/helpers2
Session info and the log of R CMD check at the end. There is an error:
"LaTeX errors when creating PDF version." However, it says "checking Rd
files ... OK".
I have tried the install now on 4 different computers (via
devtools::install_github), they all did not work.
Further points:
- Unfortunately, installation from a tarball did not work either. I
build the tarball from the command line (Cygwin), then used R CMD, but
tried it also from within RStudio ("Build Source Package", then
"install.packages")
- I have managed to create another package WHICH WORKS. I have not been
able to do it again though, I just don't know what I did differently.
- I played around with the documentation lines in the test package, to
no avail.
I am sure that it is something very minor where I went wrong, and in all
likelihood the problem is on my side. I just cannot figure out what it
might be.
David
-----
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] _0.1.0
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
--------
* using log directory '/cygdrive/d/Home/projects/R_
package_dev/helpers2.Rcheck'
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-unknown-cygwin (64-bit)
* using session charset: ISO8859-1
* checking for file 'helpers2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'helpers2' version '0.1.0'
* package encoding: UTF-8
* 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 whether package 'helpers2' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
testlicense
Standardizable: FALSE
* 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 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 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 examples ... NONE
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
Status: 1 ERROR, 2 WARNINGs
-----Urspr?ngliche Nachricht-----
Von: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] Im Auftrag
von Dirk Eddelbuettel
Gesendet: Donnerstag, 10. August 2017 14:32
An: Duncan Murdoch
Cc: K?thner, David; r-package-devel at r-project.org
Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my
packages
On 9 August 2017 at 08:38, Duncan Murdoch wrote:
| Nothing that you've written is reproducible by others. See if you can
| put together a short self-contained series of instructions that
| display the problems (or just one of them). It might involve
| installing from Github, or making a package tarball available
somewhere.
I am fairly certain I have observed this myself, and I *think* it simply
stems from running R CMD INSTALL (and alike) from a source directory, as
opposed to a tarball. I filed it under minor nuisance and didn't care too
much either as the official two-step of 'R CMD build ...; R CMD INSTALL ...'
is just that: the official and recommended way. With which things work.
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
______________________________________________
R-package-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
---
This email has been checked for viruses by AVG.
http://www.avg.com
--
Michael
http://www.dewey.myzen.co.uk/home.html
______________________________________________
R-package-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
sorry, I got sloppy - I had played around before with the DESCRIPTION file, that does not seem to be the culprit. But you are right of course, it should run without warnings in any case. * using log directory ?/Users/spaceicons/code/R_package_dev/helpers2/helpers2.Rcheck? * using R version 3.4.1 (2017-06-30) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * checking for file ?helpers2/DESCRIPTION? ... OK * this is package ?helpers2? version ?0.1? * package encoding: UTF-8 * 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 whether package ?helpers2? can be installed ... OK * checking installed package size ... OK * checking package 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 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 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 examples ... OK * checking PDF version of manual ... OK * DONE Status: OK
Von: Dason Kurkiewicz [dasonk at gmail.com]
Gesendet: Donnerstag, 10. August 2017 18:42 An: K?thner, David Cc: Duncan Murdoch; R package devel; edd at debian.org; lists at dewey.myzen.co.uk Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages It tells you what the warning is. You need to specify a license in your DESCRIPTION file. You should really fill the entire thing out properly anyways. On Aug 10, 2017 12:39 PM, <David.Kaethner at dlr.de<mailto:David.Kaethner at dlr.de>> wrote: Thank you for pointing that out, this solved the ERROR in the R CMD check. I've updated the repo. Unfortunately, it did not solve the problem. So when you clone/pull the repo now, the error should persist. * using log directory ?/Users/spaceicons/code/R_package_dev/helpers2/helpers2.Rcheck? * using R version 3.4.1 (2017-06-30) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * checking for file ?helpers2/DESCRIPTION? ... OK * checking extension type ... Package * this is package ?helpers2? version ?0.1.0? * package encoding: UTF-8 * 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 whether package ?helpers2? can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: What license is it under? Standardizable: FALSE * 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 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 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 examples ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING ________________________________________ Von: Michael Dewey [lists at dewey.myzen.co.uk<mailto:lists at dewey.myzen.co.uk>] Gesendet: Donnerstag, 10. August 2017 17:38 An: K?thner, David; edd at debian.org<mailto:edd at debian.org>; murdoch.duncan at gmail.com<mailto:murdoch.duncan at gmail.com> Cc: r-package-devel at r-project.org<mailto:r-package-devel at r-project.org> Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages Your log says you have no examples but you do in your Rd file. Your examples look the wrong way round x(function) rather than function(x) Not sure whether those are relevant issues but perhaps they help. On 10/08/2017 15:47, David.Kaethner at dlr.de<mailto:David.Kaethner at dlr.de> wrote: > Thank you for the replies! > > First of all, here is the test package: > https://github.com/c06n/helpers2 > > Session info and the log of R CMD check at the end. There is an error: "LaTeX errors when creating PDF version." However, it says "checking Rd files ... OK". > > I have tried the install now on 4 different computers (via devtools::install_github), they all did not work. > > Further points: > - Unfortunately, installation from a tarball did not work either. I build the tarball from the command line (Cygwin), then used R CMD, but tried it also from within RStudio ("Build Source Package", then "install.packages") > - I have managed to create another package WHICH WORKS. I have not been able to do it again though, I just don't know what I did differently. > - I played around with the documentation lines in the test package, to no avail. > > I am sure that it is something very minor where I went wrong, and in all likelihood the problem is on my side. I just cannot figure out what it might be. > > David > > ----- >> sessionInfo() > R version 3.4.1 (2017-06-30) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 7 x64 (build 7601) Service Pack 1 > > Matrix products: default > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] _0.1.0 > > loaded via a namespace (and not attached): > [1] compiler_3.4.1 tools_3.4.1 > > -------- > * using log directory '/cygdrive/d/Home/projects/R_package_dev/helpers2.Rcheck' > * using R version 3.4.0 (2017-04-21) > * using platform: x86_64-unknown-cygwin (64-bit) > * using session charset: ISO8859-1 > * checking for file 'helpers2/DESCRIPTION' ... OK > * checking extension type ... Package > * this is package 'helpers2' version '0.1.0' > * package encoding: UTF-8 > * 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 whether package 'helpers2' can be installed ... OK > * checking installed package size ... OK > * checking package directory ... OK > * checking DESCRIPTION meta-information ... WARNING > Non-standard license specification: > testlicense > Standardizable: FALSE > * 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 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 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 examples ... NONE > * checking PDF version of manual ... WARNING > LaTeX errors when creating PDF version. > This typically indicates Rd problems. > * checking PDF version of manual without hyperrefs or index ... ERROR > * DONE > Status: 1 ERROR, 2 WARNINGs > > > > > > > > > > > > > -----Urspr?ngliche Nachricht----- > Von: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com<mailto:dirk.eddelbuettel at gmail.com>] Im Auftrag von Dirk Eddelbuettel > Gesendet: Donnerstag, 10. August 2017 14:32 > An: Duncan Murdoch > Cc: K?thner, David; r-package-devel at r-project.org<mailto:r-package-devel at r-project.org> > Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages > > > On 9 August 2017 at 08:38, Duncan Murdoch wrote: > | Nothing that you've written is reproducible by others. See if you can > | put together a short self-contained series of instructions that > | display the problems (or just one of them). It might involve > | installing from Github, or making a package tarball available somewhere. > > I am fairly certain I have observed this myself, and I *think* it simply stems from running R CMD INSTALL (and alike) from a source directory, as opposed to a tarball. I filed it under minor nuisance and didn't care too much either as the official two-step of 'R CMD build ...; R CMD INSTALL ...' > is just that: the official and recommended way. With which things work. > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org<mailto:edd at debian.org> > > ______________________________________________ > R-package-devel at r-project.org<mailto:R-package-devel at r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > --- > This email has been checked for viruses by AVG. > http://www.avg.com > > -- Michael http://www.dewey.myzen.co.uk/home.html ______________________________________________ R-package-devel at r-project.org<mailto:R-package-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
4 days later
Hello, for the archive: I believe I found the solution, validated on Win7 and MacOS. This error occurs for any package that starts with "help". So "hell" is ok, "help12345" is not ok as a package name. Is this documented behavior? Apologies if I missed that. -----Urspr?ngliche Nachricht----- Von: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] Gesendet: Mittwoch, 9. August 2017 14:39 An: K?thner, David; r-package-devel at r-project.org Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages
On 07/08/2017 3:41 AM, David.Kaethner at dlr.de wrote:
Hello, I am hoping to post to the right mailing list, if not apologies! I have recently written my first couple packages, relying on devtools and roxygen. Everything is done in RStudio (details regarding the setup: see end of text). But the help is not working! Specifically: On Windows 7: * functions: I cannot click the links in the 'help'-panel. Or at least nothing happens when I click them. * DESCRIPTION: If I build the package locally, it has the same issues as the packages. If I install the packages from Github (devtools::install_github) or from a network drive, it works. * The "my_package::my_function" syntax throws an error. Once I enter 'my_package::' and click TAB, the following error appears in the console: "Error in gzfile(file, "rb") : cannot open the connection" * "?my_package::my_function" brings me to the function overview page for the package, but not to the help page for the my_function() * the link itself (on the function overview page) looks inocuous: http://127.0.0.1:44391/help/library/helpers/html/my_function.html I would love to do a Traceback on this, but I do not know how, since it only happens when hitting TAB. I have done a Traceback for "?my_package::my_function", it just returns the path to where the help should be, like "D:/Home/R/Rpackages/my_package/help/my_function". On MacOS Sierra: * DESCRIPTION can always be opened, no matter how the package is installed * when clicking on functions in the help panel, the known error appears (as text in the help panel): "Error in gzfile(file, "rb") : cannot open the connection" It gets much weirder: When installing the package for the very first time, it seems to work! But after that it quits working, even not when I delete the package, re-install R, re-install RStudio, and create the package from scratch. I really wish I was kidding with all of this. I have tried every debugging-idea that came to my mind, including (but not limited to): * the .Rd-files are generated, they definitely are not missing * taking an auto-generated DESCRIPTION file * removing every function file save for a test file * copying content from a function file into the auto-generated "hello.R" file * changing the encoding from UTF-8 to WINDOWS-1252 * as mentioned, trying everying both on Windows and MacOS, and trying different ways of installation * as mentioned, re-installing both R and RStudio I would enormously appreciate it if anyone has an idea how to get a handle on this, any suggestions are welcome!
Nothing that you've written is reproducible by others. See if you can put together a short self-contained series of instructions that display the problems (or just one of them). It might involve installing from Github, or making a package tarball available somewhere. Duncan Murdoch