Re: [Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder
Hi, Thanks for the ideas! It does work when using BiocStyle::doc_date(). I also have to load BiocStyle immediately after the YAML header. Otherwise I get an error that functions like Biocpkg() are not found. Best, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder
Hi Leonardo, thank you for reporting your issue with BiocStyle. I haven't experienced it before. The error you're getting indicates that BiocStyle might not be loaded before processing the code from the YAML header. This is normally handled by the BiocStyle::html_document() function which loads BiocStyle to expose the functions. You could try using date: "`r BiocStyle::doc_date()`" to see whether this helps.. Cheers, Andrzej On Tue, Nov 3, 2015 at 5:25 AM, Leonardo Collado Torres wrote: > I should add that in my local machine I have pandoc 1.13.1 installed. > Also, I just noted that metacran/r-builder uses pandoc 1.12.4.2 at > https://github.com/metacran/r-builder/blob/master/pkg-build.sh#L17 > > So this could be a pandoc issue. > > On Mon, Nov 2, 2015 at 11:07 PM, Leonardo Collado Torres > wrote: > > Hi, > > I was going to ask this as an issue at the Bioconductor/BiocStyle > > repo, but the issue tracker is disabled. > > I ran into a bug which I'm not sure where it comes from. It happens > > during R CMD build using BiocStyle to generate an html vignette. > > For example, here is one such error: > > Quitting from lines 2-17 (derfinderHelper.Rmd) > > Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics: > > could not find function "doc_date" > > Execution halted > > doc_date comes from the yaml for the html vignette in which I use: > > date: "r doc_date()" > > The full log for this error message is at: > > > https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3158-L3167 > > I used BiocStyle version 1.8.0 (see > > https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3393) > > and metacran/r-builder with the following Travis configuration file > > > https://github.com/leekgroup/derfinderHelper/blob/86c2f3b38425ee4b089a5aab1716b058926968f7/.travis.yml > > I got the same error with other packages but wasn't able to reproduce > > it locally. I tried with pandoc 1.13.1 instead of 1.12.3 and it didn't > > work either on Travis (using metacran/r-builder). However, switching > > to R Travis v2 (the one with docs on the Travis website) works. > > Here is a full log of a case that works > > > https://travis-ci.org/leekgroup/derfinderHelper/builds/88925326#L1757-L1765 > > using the same BiocStyle version and the following Travis config file > > > https://github.com/leekgroup/derfinderHelper/blob/634aed4148c7bcb69438d0959bd1175ad03bce52/.travis.yml > > It's also the same R version (3.2.2). > > I think that something about the R version in metacran/r-builder could > > be the problem. Before I report this to metacran/r-builder, I was > > wondering if the BiocStyle maintainers had come up with this type of > > error before or have any clues on how to resolve it. > > Thanks, > > Leo > > PS I'd like this to work with metacran/r-builder given the R-devel > > issue with R Travis v2. Although it seems like docker support is on > > the way https://github.com/kasperdanielhansen/bsseq/issues/5 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder
I should add that in my local machine I have pandoc 1.13.1 installed. Also, I just noted that metacran/r-builder uses pandoc 1.12.4.2 at https://github.com/metacran/r-builder/blob/master/pkg-build.sh#L17 So this could be a pandoc issue. On Mon, Nov 2, 2015 at 11:07 PM, Leonardo Collado Torres wrote: > Hi, > I was going to ask this as an issue at the Bioconductor/BiocStyle > repo, but the issue tracker is disabled. > I ran into a bug which I'm not sure where it comes from. It happens > during R CMD build using BiocStyle to generate an html vignette. > For example, here is one such error: > Quitting from lines 2-17 (derfinderHelper.Rmd) > Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics: > could not find function "doc_date" > Execution halted > doc_date comes from the yaml for the html vignette in which I use: > date: "r doc_date()" > The full log for this error message is at: > https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3158-L3167 > I used BiocStyle version 1.8.0 (see > https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3393) > and metacran/r-builder with the following Travis configuration file > https://github.com/leekgroup/derfinderHelper/blob/86c2f3b38425ee4b089a5aab1716b058926968f7/.travis.yml > I got the same error with other packages but wasn't able to reproduce > it locally. I tried with pandoc 1.13.1 instead of 1.12.3 and it didn't > work either on Travis (using metacran/r-builder). However, switching > to R Travis v2 (the one with docs on the Travis website) works. > Here is a full log of a case that works > https://travis-ci.org/leekgroup/derfinderHelper/builds/88925326#L1757-L1765 > using the same BiocStyle version and the following Travis config file > https://github.com/leekgroup/derfinderHelper/blob/634aed4148c7bcb69438d0959bd1175ad03bce52/.travis.yml > It's also the same R version (3.2.2). > I think that something about the R version in metacran/r-builder could > be the problem. Before I report this to metacran/r-builder, I was > wondering if the BiocStyle maintainers had come up with this type of > error before or have any clues on how to resolve it. > Thanks, > Leo > PS I'd like this to work with metacran/r-builder given the R-devel > issue with R Travis v2. Although it seems like docker support is on > the way https://github.com/kasperdanielhansen/bsseq/issues/5 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder
Hi, I was going to ask this as an issue at the Bioconductor/BiocStyle repo, but the issue tracker is disabled. I ran into a bug which I'm not sure where it comes from. It happens during R CMD build using BiocStyle to generate an html vignette. For example, here is one such error: Quitting from lines 2-17 (derfinderHelper.Rmd) Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics: could not find function "doc_date" Execution halted doc_date comes from the yaml for the html vignette in which I use: date: "r doc_date()" The full log for this error message is at: https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3158-L3167 I used BiocStyle version 1.8.0 (see https://travis-ci.org/leekgroup/derfinderHelper/builds/88823566#L3393) and metacran/r-builder with the following Travis configuration file https://github.com/leekgroup/derfinderHelper/blob/86c2f3b38425ee4b089a5aab1716b058926968f7/.travis.yml I got the same error with other packages but wasn't able to reproduce it locally. I tried with pandoc 1.13.1 instead of 1.12.3 and it didn't work either on Travis (using metacran/r-builder). However, switching to R Travis v2 (the one with docs on the Travis website) works. Here is a full log of a case that works https://travis-ci.org/leekgroup/derfinderHelper/builds/88925326#L1757-L1765 using the same BiocStyle version and the following Travis config file https://github.com/leekgroup/derfinderHelper/blob/634aed4148c7bcb69438d0959bd1175ad03bce52/.travis.yml It's also the same R version (3.2.2). I think that something about the R version in metacran/r-builder could be the problem. Before I report this to metacran/r-builder, I was wondering if the BiocStyle maintainers had come up with this type of error before or have any clues on how to resolve it. Thanks, Leo PS I'd like this to work with metacran/r-builder given the R-devel issue with R Travis v2. Although it seems like docker support is on the way https://github.com/kasperdanielhansen/bsseq/issues/5 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
