[Bioc-devel] import except on Window Machine

From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Cc: "Lihua Zhu" <Julie.Zhu at umassmed.edu>, "Michael Lawrence" <lawrence.michael at gene.com>, "bioc-devel"
<bioc-devel at r-project.org>
Sent: Monday, April 11, 2016 10:08:15 AM
Subject: Re: [Bioc-devel] import except on Window Machine

sessionInfo()

R version 3.3.0 beta (2016-04-06 r70435)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

Karim, What is the sessionInfo() in your R-3.3? It might be too old to
have the new feature. It needs to be at svn rev r70426 or newer.

Dan


----- Original Message -----

From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: "Lihua Zhu" <Julie.Zhu at umassmed.edu>
Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Michael Lawrence" <

lawrence.michael at gene.com>, "bioc-devel"

<bioc-devel at r-project.org>
Sent: Monday, April 11, 2016 10:03:52 AM
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>

wrote:

Thanks, Dan!

Best,

Julie

On 4/11/16 12:22 PM, "Dan Tenenbaum" <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>
To: "bioc-devel" <bioc-devel at r-project.org>
Cc: "Michael Lawrence" <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



     [[alternative HTML version deleted]]

https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman

_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl

OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0yS

t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g&e=