[Bioc-devel] Object not found in vignette

[Michael Lawrence]

Looking here:
https://github.com/Bioconductor-mirror/anamiR/commits/master

While I see some commits related to table_pre, none of them appear to
change anything in the "data" directory.


On Thu, Apr 20, 2017 at 2:57 PM, 王棣台 <r04945002 at ntu.edu.tw> wrote:
> 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
> ________________________________________
> 從: Hervé Pagès [hpages at fredhutch.org]
> 寄件日期: 2017年4月21日 上午 05:53
> 至: 王棣台; bioc-devel at r-project.org
> 主旨: 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 information of gene symbol and
>                          gene ID
> kegg.gs                 KEGG pathways with gene set information
> mirna                   miRNA expression data about breast cancer
> mrna                    mRNA expression data about breast cancer
> pheno.mirna             phenotype data of 'mirna' about breast cancer
> pheno.mrna              phenotype data of 'mrna' about breast cancer
>
> So again, did you forget to commit it to svn, or did you add it to the
> wrong place?
>
> H.
>
>>
>> Ti-Tai
>> ________________________________________
>> 從: Hervé Pagès [hpages at fredhutch.org]
>> 寄件日期: 2017年4月21日 上午 05:45
>> 至: 王棣台; bioc-devel at r-project.org
>> 主旨: 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.
>>
>>>
>>> Ti-Tai
>>>
>>> ________________________________________
>>> 從: Hervé Pagès [hpages at fredhutch.org]
>>> 寄件日期: 2017年4月21日 上午 05:16
>>> 至: 王棣台; bioc-devel at r-project.org
>>> 主旨: 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 build system (and your
>>> users) doesn't have this package so the vignette fails there.
>>> By adding the package to Depends, Imports, or Suggests, you let
>>> the build system know that this package needs to be installed
>>> before it tries to build the vignette.
>>>
>>> H.
>>>
>>> On 04/20/2017 01:51 PM, 王棣台 wrote:
>>>> 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 don't know what is the problem.
>>>>
>>>> Does anyone have the same error before?
>>>>
>>>> Many Thanks,
>>>>
>>>> Ti-Tai Wang
>>>>
>>>>       [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU&s=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg&e=
>>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fredhutch.org
>>> Phone:  (206) 667-5791
>>> Fax:    (206) 667-1319
>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel