[Bioc-devel] Object not found in vignette

[Hervé Pagès]

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