Re: [Bioc-devel] Object not found in vignette

I put in the anamiR/data/ Just like other data I used in the vignette. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:45 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette On 04/20/2017 02:36 PM, 王棣台

Re: [Bioc-devel] Object not found in vignette

I find that my data file will not change after I did any commit. That might be the problem. Is there anything I forget to do? Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 06:00 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel]

Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:50 PM, 王棣台 wrote: I put in the anamiR/data/ Just like other data I used in the vignette. As I said, I don't see it there. According to data(package="anamiR"), the data sets available in your package are: Data sets in package ‘anamiR’: egSymb A table with

Re: [Bioc-devel] Vignette update after change in git mirror repo

Hi, Maia. The git mirror is not used for building packages. Instead, you will need to commit to svn for changes to show up on Bioconductor. See here for details of working with git and svn together. https://www.bioconductor.org/developers/how-to/git-mirrors/ If I misunderstood what you are

[Bioc-devel] Object not found in vignette

Hi all, I kept getting the same Error from BUILD REPORT: Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: object 'table_pre' not found However, I did confirm my package with R CMD BUILD and CHECK before committing, and there was no errors and warnings. I really

Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:36 PM, 王棣台 wrote: That missing object is a list format data generated by myself, so I don't think it would be about Depends, Imports, or Suggests. Except this one, other generated data can be found. And where did you put this data set so that data(table_pre) can find it? H.

Re: [Bioc-devel] Object not found in vignette

it should be in my package since anamiR version 1.1.8 That is weird. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:49 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette On 04/20/2017 02:45 PM, Hervé

Re: [Bioc-devel] Object not found in vignette

Hi, The name of my package is anamiR. it is an object which I try to use in vignette as an example data. Ti-Tai Wang ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:16 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found

Re: [Bioc-devel] Object not found in vignette

That missing object is a list format data generated by myself, so I don't think it would be about Depends, Imports, or Suggests. Except this one, other generated data can be found. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:16 至:

Re: [Bioc-devel] Object not found in vignette

Also recently you bumped the version from 1.1.* to 1.2.* then went back to 1.1.* again. As a result the version that is available via biocLite() is 1.2.2, as reflected on the package landing page: https://bioconductor.org/packages/3.5/bioc/html/anamiR.html Any change you do to your package

[Bioc-devel] Vignette update after change in git mirror repo

How long does it take for the html vignette to update after a change in the git mirror has taken place? I changed my code in the git mirror a few days ago, and the html vignette hasn't incorporated these changes yet. Thanks in advance for your help. Maia [[alternative HTML version

Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:45 PM, Hervé Pagès wrote: On 04/20/2017 02:36 PM, 王棣台 wrote: That missing object is a list format data generated by myself, so I don't think it would be about Depends, Imports, or Suggests. Except this one, other generated data can be found. And where did you put this data

Re: [Bioc-devel] xps build problem on veracruz2

Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see: https://support.bioconductor.org/p/90056/#90247 This means, that users of xps seem to be willing to

Re: [Bioc-devel] Object not found in vignette

Okay, I will try to commit it again. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 06:00 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette Also recently you bumped the version from 1.1.* to 1.2.* then

Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look at it? I suspect something is missing in your Depends, Imports, or Suggests field. Works for you because you have the missing package installed on your machine but not on the build machine because the package is missing there. The

Re: [Bioc-devel] Object not found in vignette

No, I definitely have committed it since version 1.1.8 and I can see it right now in my anamiR/data files. Ti-Tai ��: Hervé Pagès [hpa...@fredhutch.org] 寄件日期: 2017年4月21日 上午 05:53 至: 王棣台; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in

Re: [Bioc-devel] xps build problem on veracruz2

On 04/20/2017 03:01 PM, cstrato wrote: Dear Herve, Doing 'csrutil disable' does indeed solve the problem, since: 1, in this way I was able to build xps on Mac OS Sierra 2, in this way I could already help one user of xps, see:

Re: [Bioc-devel] xps build problem on veracruz2

Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and has been discouraged for years. xps is the only Bioconductor package that relies on these variables for its configure/build process. H. On 04/20/2017 03:24 PM, Dan Tenenbaum wrote: Disabling SIP should not be done anywhere.

Re: [Bioc-devel] Object not found in vignette

Did you "svn add" the file? On Thu, Apr 20, 2017 at 3:10 PM, 王棣台 wrote: > I find that my data file will not change after I did any commit. > That might be the problem. > Is there anything I forget to do? > > Ti-Tai > > 從: Hervé Pagès

Re: [Bioc-devel] Object not found in vignette

Oh... I think I forget to add... Thanks a lot. Ti-Tai ��: Michael Lawrence [lawrence.mich...@gene.com] 寄件日期: 2017年4月21日 上午 06:12 至: 王棣台 副本: Hervé Pagès; bioc-devel@r-project.org 主旨: Re: [Bioc-devel] Object not found in vignette Did you "svn add" the

Re: [Bioc-devel] xps build problem on veracruz2

Disabling SIP should not be done anywhere. Every page I've read on this topic strongly discourages doing this. - Original Message - > From: "Hervé Pagès" > To: "cstrato" , "Dan Tenenbaum" > Cc: "bioc-devel"

Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

Hi Roel, Thank you for working on the package. The builds start at 5pm EST daily. If it's helpful, you can see which R version, compilers and compiler flags are used for each build machine by clicking the name at the top left of the report:

Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

On 04/20/2017 03:08 AM, Michael Stadler wrote: Dear Martin, I've now spend a day trying to resolve this. To make a long story short: I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile and work under macOS Sierra. I tried updating bowtie, but: - bowtie 1.2 has a bug that

Re: [Bioc-devel] xps build problem on veracruz2

Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that won't help your end users. I'm no expert in developing a package on Mac but other people on this list are. Also R-SIG-Mac might be a good place to seek help for this. Cheers, H. On 04/20/2017 10:53 AM, cstrato

Re: [Bioc-devel] xps build problem on veracruz2

On 04/20/2017 10:59 AM, Hervé Pagès wrote: Hi Christian, Disabling 'csrutil disable' might help xps on veracruz2 but that ^^ oops, no double negative intended here. I meant, doing 'csrutil disable' might help... etc H. won't help your end users. I'm no expert in

Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

Dear Martin, I've now spend a day trying to resolve this. To make a long story short: I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile and work under macOS Sierra. I tried updating bowtie, but: - bowtie 1.2 has a bug that prevents it from using multiple threads, which I

Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

Dear Valerie, We're working on MutationalPatterns as you can see (we've had our last changes pushed into the SVN repository just two days ago). Due to the timezone differences between Europe and the US, we seem to be missing out the starting point of a new build round. So, at which time do you