[Bioc-devel] import except on Window Machine

[Zhu, Lihua (Julie)]

Dear Karim,

I edit NAMESPACE manually and here is my R sessionInfo.

R Under development (unstable) (2016-04-03 r70416)
Platform: x86_64-apple-darwin12.5.0 (64-bit)
Running under: OS X 10.8.5 (Mountain Lion)

Best regards,

Julie

From: Karim Mezhoud <kmezhoud at gmail.com<mailto:kmezhoud at gmail.com>>
Date: Monday, April 11, 2016 1:03 PM
To: Lihua Julie Zhu <julie.zhu at umassmed.edu<mailto:julie.zhu at umassmed.edu>>
Cc: Dan Tenenbaum <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>>, Michael Lawrence <lawrence.michael at gene.com<mailto:lawrence.michael at gene.com>>, "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: Re: [Bioc-devel] import except on Window Machine

Dear Julie,
Are you using roxigen2 to edit NAMESPACE file?
Are you using R 3.4?
Thanks

In my case, When I used R 3.3 I get this error:


==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer

* installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘bioCancer’ ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called ‘c("dataTableOutput", "renderDataTable")’
ERROR: lazy loading failed for package ‘bioCancer’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’

Exited with status 1

When I used R 3.4, I get :

unfortunately,

Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
Bioconductor does not yet support R version 3.4.0



On Mon, Apr 11, 2016 at 5:30 PM, Zhu, Lihua (Julie) <Julie.Zhu at umassmed.edu<mailto:Julie.Zhu at umassmed.edu>> wrote:
Thanks, Dan!

Best,

Julie

On 4/11/16 12:22 PM, "Dan Tenenbaum" <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>> wrote:

>The windows machine is still running an older version of R that does not
>support this NAMESPACE syntax. I will update it this week.
>Dan
>
>
>----- Original Message -----
>> From: "Lihua Zhu" <Julie.Zhu at umassmed.edu<mailto:Julie.Zhu at umassmed.edu>>
>> To: "bioc-devel" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
>> Cc: "Michael Lawrence" <lawrence.michael at gene.com<mailto:lawrence.michael at gene.com>>
>> Sent: Monday, April 11, 2016 9:18:31 AM
>> Subject: [Bioc-devel] import except on Window Machine
>
>> Michael,
>>
>> For some reason,  adding except clause in import in the NAMESPACE file
>>gives
>> error on window server, although it runs fine on Linux and Mac OS X.
>>
>>https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_chec
>>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQICaQ
>>&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPH
>>hwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw&s=lEJWy
>>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA&e=
>>
>> Here is the line that gives error.
>> import(S4Vectors, except=c(fold, values))
>>
>> Did I miss something? Thank!
>>
>> Best regards,
>>
>> Julie
>>
>>
>>
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>>
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>>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
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