[Bioc-devel] import except on Window Machine

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Mon Apr 11 21:25:22 CEST 2016 

Thanks Michael!

FYI, I would get a warning message if I did not use import(IRanges,
except=values).

Best,

Julie

On 4/11/16 2:40 PM, "Michael Lawrence" <lawrence.michael at gene.com> wrote:

>On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
>wrote:
>> In that output you sent me, it's still using roxygen (via devtools) to
>>create the namespace. Try creating it manually and see if you still get
>>the same error.
>>
>> What does your NAMESPACE look like anyway?
>>
>> Looking at the NAMESPACE for CRISPRseek, the instances of the 'except'
>>syntax look like this:
>>
>> import(S4Vectors, except=c(fold, values))
>> import(IRanges, except=values)
>
>Unrelated note: should be no need to exclude values from IRanges. It
>is S4Vectors that exports the generic.
>
>>
>> So maybe make sure the objects to be excepted are not quoted?
>>
>> Dan
>>
>>
>>
>> ----- Original Message -----
>>> 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 10:21:42 AM
>>> Subject: Re: [Bioc-devel] import except on Window Machine
>>
>>> ##### ##    BUILT &   RELOAD
>>> ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
>>>
>>> * installing to library
>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹
>>> ERROR: failed to lock directory
>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹ for
>>> modifying
>>> Try removing
>>> 
>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-b
>>>ioCancer¹
>>>
>>> Exited with status 3.
>>>
>>> ######## BUILT SOURCE PACKAGE
>>> ==> devtools::document(roclets=c('rd', 'collate', 'namespace'))
>>>
>>> Updating bioCancer documentation
>>> Loading bioCancer
>>> Documentation completed
>>>
>>> ==> devtools::build()
>>>
>>> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
>>> --no-environ  \
>>>  --no-save --no-restore CMD build '/Volumes/DATA/radiant/bioCancer'  \
>>>  --no-resave-data --no-manual
>>>
>>> * checking for file Œ/Volumes/DATA/radiant/bioCancer/DESCRIPTION¹ ...
>>>OK
>>> * preparing ŒbioCancer¹:
>>> * checking DESCRIPTION meta-information ... OK
>>> * checking for LF line-endings in source and make files
>>> * checking for empty or unneeded directories
>>> * building ŒbioCancer_0.99.0.tar.gz¹
>>>
>>> [1] "/Volumes/DATA/radiant/bioCancer_0.99.0.tar.gz"
>>>
>>> Source package written to /Volumes/DATA/radiant
>>>
>>> On Mon, Apr 11, 2016 at 6:10 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
>>> wrote:
>>>
>>>> roxygen2 does not support the new syntax. Do you still get the same
>>>>error
>>>> if you write your NAMESPACE manually?
>>>>
>>>> ----- Original Message -----
>>>> > 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
>>>> >> > Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹
>>>> >> > * installing *source* package ŒbioCancer¹ ...
>>>> >> > ** R
>>>> >> > ** inst
>>>> >> > ** preparing package for lazy loading
>>>> >> > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>>>> >> vI[[i]])
>>>> >> > :
>>>> >> >  there is no package called Œc("dataTableOutput",
>>>>"renderDataTable")¹
>>>> >> > ERROR: lazy loading failed for package ŒbioCancer¹
>>>> >> > * removing
>>>> >> >
>>>> >>
>>>> 
>>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCanc
>>>>er¹
>>>> >> > * restoring previous
>>>> >> >
>>>> >>
>>>> 
>>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCanc
>>>>er¹
>>>> >> >
>>>> >> > 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_ch
>>>>ec
>>>> >> >>
>>>> >>
>>>> 
>>>>>>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQ
>>>>>>ICaQ
>>>> >> >>
>>>> >>
>>>> 
>>>>>>&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2b
>>>>>>gmPH
>>>> >> >>
>>>> >>
>>>> 
>>>>>>hwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw&s=l
>>>>>>EJWy
>>>> >> >> >>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]]
>>>> >> >> >>
>>>> >> >> >> _______________________________________________
>>>> >> >> >> Bioc-devel at r-project.org mailing list
>>>> >> >> >>
>>>> >> >> >>
>>>> >> >>
>>>> >>
>>>> 
>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm
>>>>an
>>>> >> >>
>>>> >>
>>>> 
>>>>>>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D
>>>>>>erPl
>>>> >> >>
>>>> >>
>>>> 
>>>>>>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B
>>>>>>-0yS
>>>> >> >>
>>>> >>
>>>> 
>>>>>>t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g
>>>>>>&e=
>>>> >> >>
>>>> >> >> _______________________________________________
>>>> >> >> Bioc-devel at r-project.org mailing list
>>>> >> >> 
>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm
>>>>an_listinfo_bioc-2Ddevel&d=BQIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D
>>>>erPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=p3WrsvoaEWYRGX
>>>>1hHvBYdHyfl3qSnDlhimrlUmhWc78&s=3y16NmxUwgAm1KDxESsjtgLdg1qSZ5EWMfbHqPx
>>>>x7Go&e=

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