Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

[Kasper Daniel Hansen]

Thanks for checking; minfi reads some (but not this exact one) of these
IDATs as part of the build process.

On Mon, Apr 11, 2016 at 8:18 PM, Henrik Bengtsson <
henrik.bengts...@gmail.com> wrote:

> No worries. Glad to hear it WS just a hiccup.
>
> Henrik
> On Apr 11, 2016 4:53 PM, "Dan Tenenbaum"  wrote:
>
> > I upgraded to r70462 and I cannot reproduce it now either. I guess it was
> > an issue in R-alpha, since fixed.
> > Sorry for the trouble.
> >
> > Dan
> >
> >
> > - Original Message -
> > > From: "Henrik Bengtsson" 
> > > To: "Dan Tenenbaum" 
> > > Cc: "Maarten van Iterson" , "bioc-devel" <
> > bioc-devel@r-project.org>
> > > Sent: Monday, April 11, 2016 4:01:05 PM
> > > Subject: Re: [Bioc-devel] moscato2 Windows build error reading IDAT
> file
> >
> > > I *cannot* reproduce this:
> > >
> > > % R --vanilla
> > > ## The IDAT file
> > >> pathname <- system.file(package="minfiData", "extdata", "5723646053",
> > >> "5723646053_R05C02_Grn.idat")
> > >> file.info(pathname)$size
> > > [1] 8091452
> > >> unname(tools::md5sum(pathname))
> > > [1] "dfc33fdaf3e91d872be896643a0c837f"
> > >> packageVersion("minfiData")
> > > [1] '0.13.0'
> > >
> > > ## Parsing it
> > >> data <- illuminaio:::readIDAT_nonenc(pathname)
> > >> str(data)
> > > List of 12
> > > $ fileSize : num 8091452
> > > $ versionNumber: int 3
> > > $ nFields  : int 19
> > > $ fields   : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401
> > 402 ...
> > >  ..- attr(*, "dimnames")=List of 2
> > >  .. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
> > >  .. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
> > > $ nSNPsRead: int 622399
> > > $ Quants   : int [1:622399, 1:3] 455 12883 2451 7650 4579 4955
> > > 1665 1953 5689 264 ...
> > >  ..- attr(*, "dimnames")=List of 2
> > >  .. ..$ : chr [1:622399] "10600313" "10600322" "10600328" "10600336"
> ...
> > >  .. ..$ : chr [1:3] "Mean" "SD" "NBeads"
> > > $ MidBlock : int [1:622399] 10600313 10600322 10600328 10600336
> > > 10600345 10600353 10600357 10600364 10600366 10600369 ...
> > > $ RedGreen : int 0
> > > $ Barcode  : chr "5723646053"
> > > $ ChipType : chr "BeadChip 12x8"
> > > $ RunInfo  : chr[0 , 1:5]
> > >  ..- attr(*, "dimnames")=List of 2
> > >  .. ..$ : NULL
> > >  .. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
> > > $ Unknowns :List of 7
> > >  ..$ MostlyNull: chr ""
> > >  ..$ MostlyA   : chr "R05C02"
> > >  ..$ Unknown.1 : chr ""
> > >  ..$ Unknown.2 : chr ""
> > >  ..$ Unknown.3 : chr ""
> > >  ..$ Unknown.4 : chr ""
> > >  ..$ Unknown.5 : chr ""
> > >
> > >> sessionInfo()
> > > R version 3.3.0 beta (2016-04-08 r70447)
> > > Platform: x86_64-w64-mingw32/x64 (64-bit)
> > > Running under: Windows 7 x64 (build 7601) Service Pack 1
> > >
> > > locale:
> > > [1] LC_COLLATE=English_United States.1252
> > > [2] LC_CTYPE=English_United States.1252
> > > [3] LC_MONETARY=English_United States.1252
> > > [4] LC_NUMERIC=C
> > > [5] LC_TIME=English_United States.1252
> > >
> > > attached base packages:
> > > [1] stats graphics  grDevices utils datasets  methods   base
> > >
> > > loaded via a namespace (and not attached):
> > > [1] base64_1.1illuminaio_0.13.1
> > >
> > > % R CMD config COMPILED_BY
> > > gcc-4.9.3
> > >
> > > /Henrik
> > >
> > > On Mon, Apr 11, 2016 at 9:21 AM, Dan Tenenbaum  >
> > wrote:
> > >> The problem seems to have to do with illuminaio and possibly
> minfiData;
> > it can
> > >> be reduced to / reproduced by the following:
> > >>
> > >> library(illuminaio)
> > >> file <-
> > >>
> >
> "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat"
> > >> illuminaio:::readIDAT_nonenc(file)
> > >>
> > >> Specifically the error occurs on line 59 of
> > illuminaio/R/readIDAT_nonenc.R, in
> > >> the readString() function inside readIDAT_nonenc().
> > >>
> > >> I'll leave it to the maintainer(s) of those packages to trobuleshoot
> > further
> > >> what the problem is.
> > >>
> > >>> traceback()
> > >> 5: readString(con = con)
> > >> 4: readField(con = con, field = xx)
> > >> 3: FUN(X[[i]], ...)
> > >> 2: lapply(res, function(xx) {
> > >>where <- fields[xx, "byteOffset"]
> > >>seek(con, where = where, origin = "start")
> > >>readField(con = con, field = xx)
> > >>})
> > >> 1: illuminaio:::readIDAT_nonenc(file)
> > >>
> > >>
> > >>> sessionInfo()
> > >> R version 3.3.0 alpha (2016-03-28 r70390)
> > >> Platform: x86_64-w64-mingw32/x64 (64-bit)
> > >> Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1
> > >>
> > >> locale:
> > >> [1] LC_COLLATE=English_United States.1252
> > >> [2] LC_CTYPE=English_United States.1252
> > >> [3] LC_MONETARY=English_United States.1252
> > >> [4] LC_NUMERIC=C
> > >> [5] LC_TIME=English_United States.1252
> > >>
> > >> attached base packages:
> > >> [1] stats4   

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

[Henrik Bengtsson]

No worries. Glad to hear it WS just a hiccup.

Henrik
On Apr 11, 2016 4:53 PM, "Dan Tenenbaum"  wrote:

> I upgraded to r70462 and I cannot reproduce it now either. I guess it was
> an issue in R-alpha, since fixed.
> Sorry for the trouble.
>
> Dan
>
>
> - Original Message -
> > From: "Henrik Bengtsson" 
> > To: "Dan Tenenbaum" 
> > Cc: "Maarten van Iterson" , "bioc-devel" <
> bioc-devel@r-project.org>
> > Sent: Monday, April 11, 2016 4:01:05 PM
> > Subject: Re: [Bioc-devel] moscato2 Windows build error reading IDAT file
>
> > I *cannot* reproduce this:
> >
> > % R --vanilla
> > ## The IDAT file
> >> pathname <- system.file(package="minfiData", "extdata", "5723646053",
> >> "5723646053_R05C02_Grn.idat")
> >> file.info(pathname)$size
> > [1] 8091452
> >> unname(tools::md5sum(pathname))
> > [1] "dfc33fdaf3e91d872be896643a0c837f"
> >> packageVersion("minfiData")
> > [1] '0.13.0'
> >
> > ## Parsing it
> >> data <- illuminaio:::readIDAT_nonenc(pathname)
> >> str(data)
> > List of 12
> > $ fileSize : num 8091452
> > $ versionNumber: int 3
> > $ nFields  : int 19
> > $ fields   : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401
> 402 ...
> >  ..- attr(*, "dimnames")=List of 2
> >  .. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
> >  .. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
> > $ nSNPsRead: int 622399
> > $ Quants   : int [1:622399, 1:3] 455 12883 2451 7650 4579 4955
> > 1665 1953 5689 264 ...
> >  ..- attr(*, "dimnames")=List of 2
> >  .. ..$ : chr [1:622399] "10600313" "10600322" "10600328" "10600336" ...
> >  .. ..$ : chr [1:3] "Mean" "SD" "NBeads"
> > $ MidBlock : int [1:622399] 10600313 10600322 10600328 10600336
> > 10600345 10600353 10600357 10600364 10600366 10600369 ...
> > $ RedGreen : int 0
> > $ Barcode  : chr "5723646053"
> > $ ChipType : chr "BeadChip 12x8"
> > $ RunInfo  : chr[0 , 1:5]
> >  ..- attr(*, "dimnames")=List of 2
> >  .. ..$ : NULL
> >  .. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
> > $ Unknowns :List of 7
> >  ..$ MostlyNull: chr ""
> >  ..$ MostlyA   : chr "R05C02"
> >  ..$ Unknown.1 : chr ""
> >  ..$ Unknown.2 : chr ""
> >  ..$ Unknown.3 : chr ""
> >  ..$ Unknown.4 : chr ""
> >  ..$ Unknown.5 : chr ""
> >
> >> sessionInfo()
> > R version 3.3.0 beta (2016-04-08 r70447)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> > Running under: Windows 7 x64 (build 7601) Service Pack 1
> >
> > locale:
> > [1] LC_COLLATE=English_United States.1252
> > [2] LC_CTYPE=English_United States.1252
> > [3] LC_MONETARY=English_United States.1252
> > [4] LC_NUMERIC=C
> > [5] LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] stats graphics  grDevices utils datasets  methods   base
> >
> > loaded via a namespace (and not attached):
> > [1] base64_1.1illuminaio_0.13.1
> >
> > % R CMD config COMPILED_BY
> > gcc-4.9.3
> >
> > /Henrik
> >
> > On Mon, Apr 11, 2016 at 9:21 AM, Dan Tenenbaum 
> wrote:
> >> The problem seems to have to do with illuminaio and possibly minfiData;
> it can
> >> be reduced to / reproduced by the following:
> >>
> >> library(illuminaio)
> >> file <-
> >>
> "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat"
> >> illuminaio:::readIDAT_nonenc(file)
> >>
> >> Specifically the error occurs on line 59 of
> illuminaio/R/readIDAT_nonenc.R, in
> >> the readString() function inside readIDAT_nonenc().
> >>
> >> I'll leave it to the maintainer(s) of those packages to trobuleshoot
> further
> >> what the problem is.
> >>
> >>> traceback()
> >> 5: readString(con = con)
> >> 4: readField(con = con, field = xx)
> >> 3: FUN(X[[i]], ...)
> >> 2: lapply(res, function(xx) {
> >>where <- fields[xx, "byteOffset"]
> >>seek(con, where = where, origin = "start")
> >>readField(con = con, field = xx)
> >>})
> >> 1: illuminaio:::readIDAT_nonenc(file)
> >>
> >>
> >>> sessionInfo()
> >> R version 3.3.0 alpha (2016-03-28 r70390)
> >> Platform: x86_64-w64-mingw32/x64 (64-bit)
> >> Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1
> >>
> >> locale:
> >> [1] LC_COLLATE=English_United States.1252
> >> [2] LC_CTYPE=English_United States.1252
> >> [3] LC_MONETARY=English_United States.1252
> >> [4] LC_NUMERIC=C
> >> [5] LC_TIME=English_United States.1252
> >>
> >> attached base packages:
> >> [1] stats4parallel  stats graphics  grDevices utils datasets
> >> [8] methods   base
> >>
> >> other attached packages:
> >>  [1] illuminaio_0.13.1
> >>  [2] minfiData_0.13.0
> >>  [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
> >>  [4] IlluminaHumanMethylation450kmanifest_0.4.0
> >>  [5] minfi_1.17.10
> >>  [6] bumphunter_1.11.5
> >>  [7] locfit_1.5-9.1
> >>  [8] iterators_1.0.8
> >>  [9] foreach_1.4.3
> >> [10] Biostrings_2.39.12
> >> [11] XVector_0.11.8
> >> [12] 

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

[Dan Tenenbaum]

I upgraded to r70462 and I cannot reproduce it now either. I guess it was an 
issue in R-alpha, since fixed.
Sorry for the trouble.

Dan


- Original Message -
> From: "Henrik Bengtsson" 
> To: "Dan Tenenbaum" 
> Cc: "Maarten van Iterson" , "bioc-devel" 
> 
> Sent: Monday, April 11, 2016 4:01:05 PM
> Subject: Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

> I *cannot* reproduce this:
> 
> % R --vanilla
> ## The IDAT file
>> pathname <- system.file(package="minfiData", "extdata", "5723646053",
>> "5723646053_R05C02_Grn.idat")
>> file.info(pathname)$size
> [1] 8091452
>> unname(tools::md5sum(pathname))
> [1] "dfc33fdaf3e91d872be896643a0c837f"
>> packageVersion("minfiData")
> [1] '0.13.0'
> 
> ## Parsing it
>> data <- illuminaio:::readIDAT_nonenc(pathname)
>> str(data)
> List of 12
> $ fileSize : num 8091452
> $ versionNumber: int 3
> $ nFields  : int 19
> $ fields   : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401 402 ...
>  ..- attr(*, "dimnames")=List of 2
>  .. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
>  .. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
> $ nSNPsRead: int 622399
> $ Quants   : int [1:622399, 1:3] 455 12883 2451 7650 4579 4955
> 1665 1953 5689 264 ...
>  ..- attr(*, "dimnames")=List of 2
>  .. ..$ : chr [1:622399] "10600313" "10600322" "10600328" "10600336" ...
>  .. ..$ : chr [1:3] "Mean" "SD" "NBeads"
> $ MidBlock : int [1:622399] 10600313 10600322 10600328 10600336
> 10600345 10600353 10600357 10600364 10600366 10600369 ...
> $ RedGreen : int 0
> $ Barcode  : chr "5723646053"
> $ ChipType : chr "BeadChip 12x8"
> $ RunInfo  : chr[0 , 1:5]
>  ..- attr(*, "dimnames")=List of 2
>  .. ..$ : NULL
>  .. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
> $ Unknowns :List of 7
>  ..$ MostlyNull: chr ""
>  ..$ MostlyA   : chr "R05C02"
>  ..$ Unknown.1 : chr ""
>  ..$ Unknown.2 : chr ""
>  ..$ Unknown.3 : chr ""
>  ..$ Unknown.4 : chr ""
>  ..$ Unknown.5 : chr ""
> 
>> sessionInfo()
> R version 3.3.0 beta (2016-04-08 r70447)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] base64_1.1illuminaio_0.13.1
> 
> % R CMD config COMPILED_BY
> gcc-4.9.3
> 
> /Henrik
> 
> On Mon, Apr 11, 2016 at 9:21 AM, Dan Tenenbaum  wrote:
>> The problem seems to have to do with illuminaio and possibly minfiData; it 
>> can
>> be reduced to / reproduced by the following:
>>
>> library(illuminaio)
>> file <-
>> "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat"
>> illuminaio:::readIDAT_nonenc(file)
>>
>> Specifically the error occurs on line 59 of illuminaio/R/readIDAT_nonenc.R, 
>> in
>> the readString() function inside readIDAT_nonenc().
>>
>> I'll leave it to the maintainer(s) of those packages to trobuleshoot further
>> what the problem is.
>>
>>> traceback()
>> 5: readString(con = con)
>> 4: readField(con = con, field = xx)
>> 3: FUN(X[[i]], ...)
>> 2: lapply(res, function(xx) {
>>where <- fields[xx, "byteOffset"]
>>seek(con, where = where, origin = "start")
>>readField(con = con, field = xx)
>>})
>> 1: illuminaio:::readIDAT_nonenc(file)
>>
>>
>>> sessionInfo()
>> R version 3.3.0 alpha (2016-03-28 r70390)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats4parallel  stats graphics  grDevices utils datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] illuminaio_0.13.1
>>  [2] minfiData_0.13.0
>>  [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
>>  [4] IlluminaHumanMethylation450kmanifest_0.4.0
>>  [5] minfi_1.17.10
>>  [6] bumphunter_1.11.5
>>  [7] locfit_1.5-9.1
>>  [8] iterators_1.0.8
>>  [9] foreach_1.4.3
>> [10] Biostrings_2.39.12
>> [11] XVector_0.11.8
>> [12] SummarizedExperiment_1.1.24
>> [13] GenomicRanges_1.23.26
>> [14] GenomeInfoDb_1.7.6
>> [15] IRanges_2.5.43
>> [16] S4Vectors_0.9.46
>> [17] lattice_0.20-33
>> [18] Biobase_2.31.3
>> [19] BiocGenerics_0.17.5
>> [20] MethylAid_1.5.4
>>
>> loaded via a namespace (and not attached):
>>  [1] mclust_5.2   base64_1.1   Rcpp_0.12.4
>>  [4] Rsamtools_1.23.8 digest_0.6.9   

Re: [Bioc-devel] import except on Window Machine

[Michael Lawrence]

On Mon, Apr 11, 2016 at 2:54 PM, Hervé Pagès  wrote:
> Hi Michael,
>
> On 04/11/2016 01:23 PM, Michael Lawrence wrote:
>>
>> Yes, you're right, sorry. I didn't realize that the generic is always
>> exported from a package defining methods on the generic.
>
>
> What's the rationale behind this feature?

As stated in Writing R Extensions, it is to ensure that the user sees
the generic for the exported methods, even when the package defining
the generic is not attached. I guess another way would be to have the
package with the generic be partially attached, only exposing the
generics with exported methods.

> It seems to be a recurrent
> source of surprise and confusion. In the last couple of years I must
> have fixed dozens (maybe 100+) of NAMESPACEs that import things from
> the wrong place, that is, what the maintainer of the package actually
> needs and should import is the foo() generic from package A, but s/he
> imports a particular method from package B instead. Sometimes that
> method is not even the one that they actually need. *Unfortunately*
> things work for a while but break later when the random method they
> import disappears from package B.
>
> One almost always calls the generic, not a particular method directly.
> So personally I never use importMethodsFrom. Don't see the need for it.
> I don't even know what it does i.e. what importing a method means
> exactly. AFAIK when I call the generic, dispatch on the appropriate
> method works, whether I "import" that method or not...

I agree that explicitly importing and exporting methods may not be very useful.

exportMethods() and importMethodsFrom() do help when making generics
internal, because export(generic)/import(generic) would end up
importing/exporting a base function (since a compatible setGeneric()
is a no-op). But there's basically one person who makes generics
internal, and he's not doing so very often.

>
> Getting the NAMESPACE right has always been a source of struggle
> for developers. Simplifying and clarifying some of the concepts
> involved would help make the process a little more straightforward.
>

> Thanks,
> H.
>
>
>> That can make
>> the exceptions more difficult to maintain. A better syntax for this
>> case might have been:
>>
>> import(cranPackage, override=values)
>>
>> But we have to live with except= for now.
>>
>> Michael
>>
>> On Mon, Apr 11, 2016 at 12:25 PM, Zhu, Lihua (Julie)
>>  wrote:
>>>
>>> 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"  wrote:
>>>
 On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum 
 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" 
>> To: "Dan Tenenbaum" 
>> Cc: "Lihua Zhu" , "Michael Lawrence"
>> , "bioc-devel"
>> 
>> 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
>> * 

Re: [Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

[Henrik Bengtsson]

I'm not an OS X user, but two things you might look into/help you troubleshoot:

1. Because you said it only happens when you try to overwrite an
existing PDF, could it be that there is another process holding onto
(=locking) the PDF file that you're trying to write to?  For instance,
are you viewing it at the same time?

2. What happens if you create a dummy dummy.txt file, and then try to
overwrite that (with the same name - so no *.pdf)?  Does that work/not
work?  If it works, it means there's something special with *.pdf
files.  If not, then ... ?!?.

My $.02

/Henrik

PS. I think Wolfgang's point is that few people will spent time
troubleshooting obsolete versions of R (unless they're on the same
version), meaning the chances for feedback/troubleshooting on this is
much smaller than if it could be confirmed we a more up-to-date
version of R.  Because if it does given a problem in a new version,
there is nothing really to fix.  Having said this, any feedback that
might >= 1 person is always useful.


On Mon, Apr 11, 2016 at 2:35 PM, Neil French Collier
 wrote:
> Dear Wolfgang,
>
> Thanks for your response.
>
> No, I haven't tried doing the complete reinstallation as you suggest. If I
> recall correctly, this has happened on previous occasions but like I said
> in my email it's not all that disruptive to my workflow. It's more like a
> 'first world problem'.
>
> I was encouraged to submit the query because I had correspondence with
> someone involved with R development: "this shouldn't be happening" was the
> advice I received. I use R a lot but I'm not deeply knowledgable about it's
> inner workings.
>
> To be frank, I really don't care if this is resolved. I was just trying to
> help the R development group after receiving advice that it might be
> important.
>
> Again, thanks for your help.
>
> Cheers
>
> Neil
>
> On Mon, Apr 11, 2016 at 6:41 PM, Wolfgang Huber  wrote:
>
>> Dear Neil
>>
>> Have you tried with completely uninstalling your R, and reinstalling a
>> more recent version (e.g. 3.2.4 right now).
>> And then the same with your operating system - OS X is currently at
>> 10.11.4.
>> There is likely not much interest (or benefit) in chasing such things in
>> obsolete versions.
>>
>> And I think R-help would be the more appropriate place for this kind of
>> question.
>> Wolfgang
>>
>> > On Apr 11, 2016, at 18:37 GMT+2, Neil French Collier <
>> neilander...@gmail.com> wrote:
>> >
>> > Dear colleagues,
>> >
>> > I wish to report a problem I encounter when trying to save a graphic to
>> > file. When I produce a graphic and try to save it R becomes unresponsive
>> > and I must force quit, and then restart R. The problem occurs when I try
>> to
>> > overwrite an existing graphic: for example when I made changes to the
>> > graphic and want to save the graphic using the original file name. It
>> only
>> > happens when I use the menus to save files, not using script. It doesn't
>> > happen when I save it as a new file. So, like this:
>> >
>> > 1. Make the graphic
>> > 2. Click File -> Save -> click on existing file name
>> > 3. Colour wheel appears and R is unresponsive.
>> >
>> > Reproducible example:
>> >
>> > x <- seq(1,10)
>> > y <- x^2
>> > plot(x,y, type="l") # Save as new file, all fine.
>> >
>> > #Change plot and save as old plot file name:
>> >
>> > plot(x,y, type="l", col=2)
>> >
>> > # Click File -> Save
>> > # 'Save quartz to PDF file' box opens
>> > # Click on existing file name
>> > # Colour wheel
>> >
>> > Here is the sessionInfo():
>> >
>> > R version 3.2.2 (2015-08-14)
>> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> > Running under: OS X 10.11.1 (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
>> >
>> > attached base packages:
>> > [1] stats graphics  grDevices utils datasets  methods   base
>> >
>> > I'm not sure if this is worthy of reporting but I was encouraged to
>> submit
>> > a report. It doesn't really make a huge impact on my workflow, but it can
>> > be annoying.
>> >
>> > --
>> > Cheers,
>> >
>> > Neil
>> >
>> > Neil French Collier, PhD
>> > Faculty of Sustainability
>> > Leuphana University Lüneburg
>> > Rotenbleicher Weg 67
>> > 21335 Lueneburg
>> > Germany
>> >
>> > Twitter: @foodsecbio
>> > email: coll...@leuphana.de
>> > Google Scholar
>> > <
>> https://scholar.google.com.au/citations?hl=en=xVdc-dsJ_op=list_works=pubdate
>> >
>> > Ideas for Sustainability 
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > __
>> > R-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> Wolfgang
>>
>> Wolfgang Huber
>> Principal Investigator, EMBL Senior Scientist
>> Genome Biology Unit
>> European Molecular Biology Laboratory (EMBL)
>> Heidelberg, Germany
>>
>> wolfgang.hu...@embl.de
>> http://www.huber.embl.de
>>
>>
>>
>>
>>
>>
>>
>>

Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

[Henrik Bengtsson]

I *cannot* reproduce this:

% R --vanilla
## The IDAT file
> pathname <- system.file(package="minfiData", "extdata", "5723646053", 
> "5723646053_R05C02_Grn.idat")
> file.info(pathname)$size
[1] 8091452
> unname(tools::md5sum(pathname))
[1] "dfc33fdaf3e91d872be896643a0c837f"
> packageVersion("minfiData")
[1] '0.13.0'

## Parsing it
> data <- illuminaio:::readIDAT_nonenc(pathname)
> str(data)
List of 12
 $ fileSize : num 8091452
 $ versionNumber: int 3
 $ nFields  : int 19
 $ fields   : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401 402 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
  .. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
 $ nSNPsRead: int 622399
 $ Quants   : int [1:622399, 1:3] 455 12883 2451 7650 4579 4955
1665 1953 5689 264 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:622399] "10600313" "10600322" "10600328" "10600336" ...
  .. ..$ : chr [1:3] "Mean" "SD" "NBeads"
 $ MidBlock : int [1:622399] 10600313 10600322 10600328 10600336
10600345 10600353 10600357 10600364 10600366 10600369 ...
 $ RedGreen : int 0
 $ Barcode  : chr "5723646053"
 $ ChipType : chr "BeadChip 12x8"
 $ RunInfo  : chr[0 , 1:5]
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
 $ Unknowns :List of 7
  ..$ MostlyNull: chr ""
  ..$ MostlyA   : chr "R05C02"
  ..$ Unknown.1 : chr ""
  ..$ Unknown.2 : chr ""
  ..$ Unknown.3 : chr ""
  ..$ Unknown.4 : chr ""
  ..$ Unknown.5 : chr ""

> sessionInfo()
R version 3.3.0 beta (2016-04-08 r70447)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] base64_1.1illuminaio_0.13.1

% R CMD config COMPILED_BY
gcc-4.9.3

/Henrik

On Mon, Apr 11, 2016 at 9:21 AM, Dan Tenenbaum  wrote:
> The problem seems to have to do with illuminaio and possibly minfiData; it 
> can be reduced to / reproduced by the following:
>
> library(illuminaio)
> file <- 
> "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat"
> illuminaio:::readIDAT_nonenc(file)
>
> Specifically the error occurs on line 59 of illuminaio/R/readIDAT_nonenc.R, 
> in the readString() function inside readIDAT_nonenc().
>
> I'll leave it to the maintainer(s) of those packages to trobuleshoot further 
> what the problem is.
>
>> traceback()
> 5: readString(con = con)
> 4: readField(con = con, field = xx)
> 3: FUN(X[[i]], ...)
> 2: lapply(res, function(xx) {
>where <- fields[xx, "byteOffset"]
>seek(con, where = where, origin = "start")
>readField(con = con, field = xx)
>})
> 1: illuminaio:::readIDAT_nonenc(file)
>
>
>> sessionInfo()
> R version 3.3.0 alpha (2016-03-28 r70390)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats4parallel  stats graphics  grDevices utils datasets
> [8] methods   base
>
> other attached packages:
>  [1] illuminaio_0.13.1
>  [2] minfiData_0.13.0
>  [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
>  [4] IlluminaHumanMethylation450kmanifest_0.4.0
>  [5] minfi_1.17.10
>  [6] bumphunter_1.11.5
>  [7] locfit_1.5-9.1
>  [8] iterators_1.0.8
>  [9] foreach_1.4.3
> [10] Biostrings_2.39.12
> [11] XVector_0.11.8
> [12] SummarizedExperiment_1.1.24
> [13] GenomicRanges_1.23.26
> [14] GenomeInfoDb_1.7.6
> [15] IRanges_2.5.43
> [16] S4Vectors_0.9.46
> [17] lattice_0.20-33
> [18] Biobase_2.31.3
> [19] BiocGenerics_0.17.5
> [20] MethylAid_1.5.4
>
> loaded via a namespace (and not attached):
>  [1] mclust_5.2   base64_1.1   Rcpp_0.12.4
>  [4] Rsamtools_1.23.8 digest_0.6.9 gridBase_0.4-7
>  [7] mime_0.4 R6_2.1.2 plyr_1.8.3
> [10] chron_2.3-47 RSQLite_1.0.0ggplot2_2.1.0
> [13] zlibbioc_1.17.1  GenomicFeatures_1.23.29  data.table_1.9.6
> [16] annotate_1.49.1  hexbin_1.27.1preprocessCore_1.33.0
> [19] splines_3.3.0BiocParallel_1.5.21  stringr_1.0.0
> [22] RCurl_1.95-4.8   biomaRt_2.27.2   munsell_0.4.3
> [25] shiny_0.13.2 httpuv_1.3.3 rtracklayer_1.31.10
> [28] multtest_2.27.0  pkgmaker_0.22htmltools_0.3.5
> [31] GEOquery_2.37.0  quadprog_1.5-5  

Re: [Bioc-devel] import except on Window Machine

[Hervé Pagès]

Hi Michael,

On 04/11/2016 01:23 PM, Michael Lawrence wrote:

Yes, you're right, sorry. I didn't realize that the generic is always
exported from a package defining methods on the generic.


What's the rationale behind this feature? It seems to be a recurrent
source of surprise and confusion. In the last couple of years I must
have fixed dozens (maybe 100+) of NAMESPACEs that import things from
the wrong place, that is, what the maintainer of the package actually
needs and should import is the foo() generic from package A, but s/he
imports a particular method from package B instead. Sometimes that
method is not even the one that they actually need. *Unfortunately*
things work for a while but break later when the random method they
import disappears from package B.

One almost always calls the generic, not a particular method directly.
So personally I never use importMethodsFrom. Don't see the need for it.
I don't even know what it does i.e. what importing a method means
exactly. AFAIK when I call the generic, dispatch on the appropriate
method works, whether I "import" that method or not...

Getting the NAMESPACE right has always been a source of struggle
for developers. Simplifying and clarifying some of the concepts
involved would help make the process a little more straightforward.

Thanks,
H.



That can make
the exceptions more difficult to maintain. A better syntax for this
case might have been:

import(cranPackage, override=values)

But we have to live with except= for now.

Michael

On Mon, Apr 11, 2016 at 12:25 PM, Zhu, Lihua (Julie)
 wrote:

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"  wrote:


On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum 
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" 
To: "Dan Tenenbaum" 
Cc: "Lihua Zhu" , "Michael Lawrence"
, "bioc-devel"

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 
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" 
To: "Dan Tenenbaum" 
Cc: "Lihua Zhu" , "Michael Lawrence" <

lawrence.mich...@gene.com>, "bioc-devel"


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



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 

Re: [Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

[Neil French Collier]

Dear Wolfgang,

Thanks for your response.

No, I haven't tried doing the complete reinstallation as you suggest. If I
recall correctly, this has happened on previous occasions but like I said
in my email it's not all that disruptive to my workflow. It's more like a
'first world problem'.

I was encouraged to submit the query because I had correspondence with
someone involved with R development: "this shouldn't be happening" was the
advice I received. I use R a lot but I'm not deeply knowledgable about it's
inner workings.

To be frank, I really don't care if this is resolved. I was just trying to
help the R development group after receiving advice that it might be
important.

Again, thanks for your help.

Cheers

Neil

On Mon, Apr 11, 2016 at 6:41 PM, Wolfgang Huber  wrote:

> Dear Neil
>
> Have you tried with completely uninstalling your R, and reinstalling a
> more recent version (e.g. 3.2.4 right now).
> And then the same with your operating system - OS X is currently at
> 10.11.4.
> There is likely not much interest (or benefit) in chasing such things in
> obsolete versions.
>
> And I think R-help would be the more appropriate place for this kind of
> question.
> Wolfgang
>
> > On Apr 11, 2016, at 18:37 GMT+2, Neil French Collier <
> neilander...@gmail.com> wrote:
> >
> > Dear colleagues,
> >
> > I wish to report a problem I encounter when trying to save a graphic to
> > file. When I produce a graphic and try to save it R becomes unresponsive
> > and I must force quit, and then restart R. The problem occurs when I try
> to
> > overwrite an existing graphic: for example when I made changes to the
> > graphic and want to save the graphic using the original file name. It
> only
> > happens when I use the menus to save files, not using script. It doesn't
> > happen when I save it as a new file. So, like this:
> >
> > 1. Make the graphic
> > 2. Click File -> Save -> click on existing file name
> > 3. Colour wheel appears and R is unresponsive.
> >
> > Reproducible example:
> >
> > x <- seq(1,10)
> > y <- x^2
> > plot(x,y, type="l") # Save as new file, all fine.
> >
> > #Change plot and save as old plot file name:
> >
> > plot(x,y, type="l", col=2)
> >
> > # Click File -> Save
> > # 'Save quartz to PDF file' box opens
> > # Click on existing file name
> > # Colour wheel
> >
> > Here is the sessionInfo():
> >
> > R version 3.2.2 (2015-08-14)
> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
> > Running under: OS X 10.11.1 (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
> >
> > attached base packages:
> > [1] stats graphics  grDevices utils datasets  methods   base
> >
> > I'm not sure if this is worthy of reporting but I was encouraged to
> submit
> > a report. It doesn't really make a huge impact on my workflow, but it can
> > be annoying.
> >
> > --
> > Cheers,
> >
> > Neil
> >
> > Neil French Collier, PhD
> > Faculty of Sustainability
> > Leuphana University Lüneburg
> > Rotenbleicher Weg 67
> > 21335 Lueneburg
> > Germany
> >
> > Twitter: @foodsecbio
> > email: coll...@leuphana.de
> > Google Scholar
> > <
> https://scholar.google.com.au/citations?hl=en=xVdc-dsJ_op=list_works=pubdate
> >
> > Ideas for Sustainability 
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> Wolfgang
>
> Wolfgang Huber
> Principal Investigator, EMBL Senior Scientist
> Genome Biology Unit
> European Molecular Biology Laboratory (EMBL)
> Heidelberg, Germany
>
> wolfgang.hu...@embl.de
> http://www.huber.embl.de
>
>
>
>
>
>
>
>
>
>


-- 
Cheers,

Neil

Neil French Collier, PhD
Faculty of Sustainability
Leuphana University Lüneburg
Rotenbleicher Weg 67
21335 Lueneburg
Germany

Twitter: @foodsecbio
email: coll...@leuphana.de
Google Scholar

Ideas for Sustainability 

[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Bioc-devel] Using Git with Bioconductor SVN repositories

[Dan Tenenbaum]

>From your git log excerpt it looks like there has been some non-linear commit 
>history. svn does not like this.
You may need to follow the instructions here:

https://www.bioconductor.org/developers/how-to/git-mirrors/#dealing-with-prior-history--merge-conflicts

Dan


- Original Message -
> From: "Maarten van Iterson" 
> To: "bioc-devel" 
> Sent: Friday, April 8, 2016 11:26:16 PM
> Subject: [Bioc-devel] Using Git with Bioconductor SVN repositories

> Dear all,
> 
> I'm struggling with using git and the Bioconductor SVN repo of my packages.
> 
> For example, I have a package in devel (bacon) and managed to push changes
> to the svn/trunk of my package using the steps described at:
> 
> https://www.bioconductor.org/developers/how-to/git-mirrors/
> 
> following scenario 2, but after
> 
> git checkout master
> git merge devel
> 
> the decorate output of git log is:
> 
> *   e8e3752 - (HEAD, master) Merge branch 'devel' (22 seconds ago)
> 
>|\
>| * fe340af - (git-svn-devel, devel) fix bug meta-analysis and add trimming
> of test-statistics (in the future) 
> * | 73921c7 - (origin/master, origin/HEAD) fix bug meta-analysis and add
> trimming of test-statistics (15 minutes ago) 
>|/
> * 693fdba - (bioc/master) add ggplot versions of hist and qq add topTable
> function and updating vignette (2 weeks ago) 
> * fc2436f - update markdown file (2 weeks ago) 
> * 52a7818 - add ggplot versions of hist and qq add topTable function and
> updating vignette (2 weeks ago) 
> * 92ed414 - fix typo and add URL and BugReports to DESCR. (2 weeks ago)
> 
> * b45332b - Adding doppelgangR, EpiCluster, PCAN, bacon, SwathXtend (3
> weeks ago) 
> 
> whereas I expect every branch should be in sync.
> The state of my fork is: 1 commit ahead, 1 commit behind
> Bioconductor-mirror:master.  What should I do at this point?
> 
> If followed this scenario before and commit to git and push to GitHub as
> normally but ended up in a state that I only could solve by removing my
> fork from github and start all over again.
> 
> Cheers,
> Maarten
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] package submission - problem with vignette

[Lara Urban]

Dear Dan,

Many thanks, apparently I just had to update one of the knitr-associated
components.

I hope it will go through now.

Many thanks again and enjoy your evening,
Lara

2016-04-11 17:39 GMT+01:00 Dan Tenenbaum :

>
>
> - Original Message -
> > From: "Dan Tenenbaum" 
> > To: "Lara Urban" 
> > Cc: "bioc-devel" 
> > Sent: Monday, April 11, 2016 9:29:30 AM
> > Subject: Re: [Bioc-devel] package submission - problem with vignette
>
> > It means that when you run R CMD build YourPackageName, the vignette is
> not
> > built.
> >
> > It simply looks in the output of R CMD build for a line that starts:
> >
> >* creating vignettes ...
> >
> > If this line is present, it means `R` has not detected that a vignette
> > needs to be built.
>
> Oops, that should say: "If this line is NOT present..."
>
> Dan
>
> >
> > It's `REQUIRED` that the vignette be built.
> >
> > If you have vignette sources yet still get this message, there could
> > be several causes:
> >
> > * Missing or invalid `VignetteBuilder` line in the `DESCRIPTION` file.
> > * Missing or invalid `VignetteEngine` line in the vignette source.
> >
> > See `knitr`'s [package vignette](http://yihui.name/knitr/demo/vignette/)
> > page, or the
> > [Non-Sweave
> > vignettes](
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes
> )
> > section of "Writing R Extensions" for more information.
> >
> > Dan
> >
> >
> > - Original Message -
> >> From: "Lara Urban" 
> >> To: "bioc-devel" 
> >> Sent: Monday, April 11, 2016 8:58:14 AM
> >> Subject: [Bioc-devel] package submission - problem with vignette
> >
> >> Dear BiocDevel,
> >>
> >> I have a question regarding the submission of my package; thank you very
> >> much in advance.
> >>
> >> I have submitted my package to Bioconductor a few days ago and it passed
> >> build, check and bioccheck. Now, that I had to change just one line in
> my R
> >> code and submitted it again, I get an error on all three platforms,
> because
> >> it is required that my vignette is built by R CMD build; however, I
> still
> >> have my Rmd file in the order vignettes as before. Shouldn't it build
> >> automatically? Do you have any ideas what is going wrong here?
> >>
> >> Many thanks and kind regards,
> >> Lara
> >>
> >>
> >> --
> >> Lara Urban
> >>
> >> Predoctoral Fellow
> >> EMBL-European Bioinformatics Institute
> >> Wellcome Trust Genome Campus
> >> Hinxton, Cambridge
> >> CB10 1SD
> >> United Kingdom
> >>
> >> PhD Student
> >> Wolfson College
> >> University of Cambridge
> >>
> >> phone:  + 49 (0) 176 76 37 99 03
> <%2B%2044%20%280%29%201223%20494%20655>
> >> email: lara.h.ur...@ebi.ac.uk 
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Lara Urban

Predoctoral Fellow
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom

PhD Student
Wolfson College
University of Cambridge

phone:  + 49 (0) 176 76 37 99 03 <%2B%2044%20%280%29%201223%20494%20655>
email: lara.h.ur...@ebi.ac.uk 

[[alternative HTML version deleted]]

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Re: [Bioc-devel] import except on Window Machine

[Zhu, Lihua (Julie)]

Michael,

Thanks for confirming!

Best,

Julie

On 4/11/16 4:23 PM, "Michael Lawrence"  wrote:

>Yes, you're right, sorry. I didn't realize that the generic is always
>exported from a package defining methods on the generic. That can make
>the exceptions more difficult to maintain. A better syntax for this
>case might have been:
>
>import(cranPackage, override=values)
>
>But we have to live with except= for now.
>
>Michael
>
>On Mon, Apr 11, 2016 at 12:25 PM, Zhu, Lihua (Julie)
> wrote:
>> 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" 
>>wrote:
>>
>>>On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum 
>>>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" 
> To: "Dan Tenenbaum" 
> Cc: "Lihua Zhu" , "Michael Lawrence"
>, "bioc-devel"
> 
> 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
>
> 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" 
>> > To: "Dan Tenenbaum" 
>> > Cc: "Lihua Zhu" , "Michael Lawrence" <
>> lawrence.mich...@gene.com>, "bioc-devel"
>> > 
>> > 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
>>
>> > 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" 
>> >> > To: "Lihua Zhu" 
>> >> > Cc: "Dan Tenenbaum" , "Michael
>>Lawrence"
>><
>> >> lawrence.mich...@gene.com>, "bioc-devel"
>> >> > 
>> >> > Sent: Monday, April 11, 2016 10:03:52 AM
>> >> > Subject: Re: 

Re: [Bioc-devel] import except on Window Machine

[Michael Lawrence]

Yes, you're right, sorry. I didn't realize that the generic is always
exported from a package defining methods on the generic. That can make
the exceptions more difficult to maintain. A better syntax for this
case might have been:

import(cranPackage, override=values)

But we have to live with except= for now.

Michael

On Mon, Apr 11, 2016 at 12:25 PM, Zhu, Lihua (Julie)
 wrote:
> 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"  wrote:
>
>>On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum 
>>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" 
 To: "Dan Tenenbaum" 
 Cc: "Lihua Zhu" , "Michael Lawrence"
, "bioc-devel"
 
 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 
 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" 
> > To: "Dan Tenenbaum" 
> > Cc: "Lihua Zhu" , "Michael Lawrence" <
> lawrence.mich...@gene.com>, "bioc-devel"
> > 
> > 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
>
> > 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" 
> >> > To: "Lihua Zhu" 
> >> > Cc: "Dan Tenenbaum" , "Michael Lawrence"
><
> >> lawrence.mich...@gene.com>, "bioc-devel"
> >> > 
> >> > 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 

Re: [Rd] Understanding POSIXct creation on different OSes.

[Dirk Eddelbuettel]

Bumping this up to the front again ... because it exhibits a difference in
behaviour of R across OSs.  Such a 'feature' may not be desirable.

On 4 April 2016 at 18:00, Arunkumar Srinivasan wrote:
| Hello,
| 
| Following Dirk's post here: 
https://github.com/Rdatatable/data.table/issues/1619
| we would like to clarify if this is the right behaviour, and if so,
| the rationale behind it.
| 
| Here's the summary (thanks to Dirk and Joshua):
| 
| Sys.setenv("TZ"="America/Chicago")
| dates = as.Date("2016-03-02") + (0:3)*7 # four Wednesdays
| # [1] "2016-03-02" "2016-03-09" "2016-03-16" "2016-03-23"
| 
| # on OS X and Windows 10 -- expected result
| as.POSIXct(as.POSIXlt(dates), tz = "America/Chicago")
| # [1] "2016-03-02 CST" "2016-03-09 CST" "2016-03-16 CDT" "2016-03-23 CDT"
| 
| # On Linux (tested on Ubuntu 14.04) -- not as expected
| as.POSIXct(as.POSIXlt(dates), tz = "America/Chicago")
| # [1] "2016-03-02 00:00:00 CST" "2016-03-09 00:00:00 CST" "2016-03-16
| 01:00:00 CDT" "2016-03-23 01:00:00 CDT"
|
| # 'isdst' attribute is identical on OS X / Windows / Ubuntu, as expected
| # since dates don't have timezones, as pointed out by @JoshuaUlrich under
| # issue #1619.
| lt = as.POSIXlt(dates)
| lt$isdst
| # [1] 0 0 0 0
| 
| # However, as Dirk points out, setting isdst to -1 on Ubuntu returns
| expected results
| lt$isdst = -1
| as.POSIXct(lt, tz = "America/Chicago")
| # [1] "2016-03-02 CST" "2016-03-09 CST" "2016-03-16 CDT" "2016-03-23 CDT"
| 
| # Note that setting isdst to -1 on OS X / Windows has no effect, i.e.,
| the result is always as expected.
| 
| As Dirk points out, from ?POSIXlt:
| "Where possible the platform limits are detected, and outside the
| limits we use our own C code. This uses the offset from GMT in
| use either for 1902 (when there was no DST) or that predicted for
| one of 2030 to 2037 (chosen so that the likely DST transition days
| are Sundays), and uses the alternate (daylight-saving) time zone
| only if ‘isdst’ is positive or (if ‘-1’) if DST was predicted to
| be in operation in the 2030s on that day."
| 
| It's not clear what this exactly means, and if it is related to the
| behaviour shown above. It'd be nice to know if a) this behaviour of
| non-identical result is as expected, and if so, b) can we rely on
| setting 'isdst' to -1 returning the expected result always?

Could someone from R Core please comment, or would you prefer us to file a
bug report?

Thanks!

Dirk



| Thank you,
| Arun.
| 
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [Bioc-devel] import except on Window Machine

[Zhu, Lihua (Julie)]

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"  wrote:

>On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum 
>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" 
>>> To: "Dan Tenenbaum" 
>>> Cc: "Lihua Zhu" , "Michael Lawrence"
>>>, "bioc-devel"
>>> 
>>> 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 
>>> 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" 
 > To: "Dan Tenenbaum" 
 > Cc: "Lihua Zhu" , "Michael Lawrence" <
 lawrence.mich...@gene.com>, "bioc-devel"
 > 
 > 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

 > 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" 
 >> > To: "Lihua Zhu" 
 >> > Cc: "Dan Tenenbaum" , "Michael Lawrence"
<
 >> lawrence.mich...@gene.com>, "bioc-devel"
 >> > 
 >> > 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 

Re: [Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

[Wolfgang Huber]

Dear Neil

Have you tried with completely uninstalling your R, and reinstalling a more 
recent version (e.g. 3.2.4 right now).
And then the same with your operating system - OS X is currently at 10.11.4.
There is likely not much interest (or benefit) in chasing such things in 
obsolete versions.

And I think R-help would be the more appropriate place for this kind of 
question.
Wolfgang

> On Apr 11, 2016, at 18:37 GMT+2, Neil French Collier  
> wrote:
> 
> Dear colleagues,
> 
> I wish to report a problem I encounter when trying to save a graphic to
> file. When I produce a graphic and try to save it R becomes unresponsive
> and I must force quit, and then restart R. The problem occurs when I try to
> overwrite an existing graphic: for example when I made changes to the
> graphic and want to save the graphic using the original file name. It only
> happens when I use the menus to save files, not using script. It doesn't
> happen when I save it as a new file. So, like this:
> 
> 1. Make the graphic
> 2. Click File -> Save -> click on existing file name
> 3. Colour wheel appears and R is unresponsive.
> 
> Reproducible example:
> 
> x <- seq(1,10)
> y <- x^2
> plot(x,y, type="l") # Save as new file, all fine.
> 
> #Change plot and save as old plot file name:
> 
> plot(x,y, type="l", col=2)
> 
> # Click File -> Save
> # 'Save quartz to PDF file' box opens
> # Click on existing file name
> # Colour wheel
> 
> Here is the sessionInfo():
> 
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.11.1 (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
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> I'm not sure if this is worthy of reporting but I was encouraged to submit
> a report. It doesn't really make a huge impact on my workflow, but it can
> be annoying.
> 
> -- 
> Cheers,
> 
> Neil
> 
> Neil French Collier, PhD
> Faculty of Sustainability
> Leuphana University Lüneburg
> Rotenbleicher Weg 67
> 21335 Lueneburg
> Germany
> 
> Twitter: @foodsecbio
> email: coll...@leuphana.de
> Google Scholar
> 
> Ideas for Sustainability 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Wolfgang

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.hu...@embl.de
http://www.huber.embl.de

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Re: [Bioc-devel] import except on Window Machine

[Michael Lawrence]

On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum  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" 
>> To: "Dan Tenenbaum" 
>> Cc: "Lihua Zhu" , "Michael Lawrence" 
>> , "bioc-devel"
>> 
>> 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
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
>> ERROR: failed to lock directory
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ for
>> modifying
>> Try removing
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-bioCancer’
>>
>> 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 ‘/Volumes/DATA/radiant/bioCancer/DESCRIPTION’ ... OK
>> * preparing ‘bioCancer’:
>> * checking DESCRIPTION meta-information ... OK
>> * checking for LF line-endings in source and make files
>> * checking for empty or unneeded directories
>> * building ‘bioCancer_0.99.0.tar.gz’
>>
>> [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 
>> 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" 
>>> > To: "Dan Tenenbaum" 
>>> > Cc: "Lihua Zhu" , "Michael Lawrence" <
>>> lawrence.mich...@gene.com>, "bioc-devel"
>>> > 
>>> > 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 
>>> > 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" 
>>> >> > To: "Lihua Zhu" 
>>> >> > Cc: "Dan Tenenbaum" , "Michael Lawrence" <
>>> >> lawrence.mich...@gene.com>, "bioc-devel"
>>> >> > 
>>> >> > 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 :
>>> >> >
>>> 

Re: [Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

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)

So maybe make sure the objects to be excepted are not quoted?

Dan



- Original Message -
> From: "Karim Mezhoud" 
> To: "Dan Tenenbaum" 
> Cc: "Lihua Zhu" , "Michael Lawrence" 
> , "bioc-devel"
> 
> 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
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
> ERROR: failed to lock directory
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ for
> modifying
> Try removing
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-bioCancer’
> 
> 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 ‘/Volumes/DATA/radiant/bioCancer/DESCRIPTION’ ... OK
> * preparing ‘bioCancer’:
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building ‘bioCancer_0.99.0.tar.gz’
> 
> [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 
> 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" 
>> > To: "Dan Tenenbaum" 
>> > Cc: "Lihua Zhu" , "Michael Lawrence" <
>> lawrence.mich...@gene.com>, "bioc-devel"
>> > 
>> > 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 
>> > 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" 
>> >> > To: "Lihua Zhu" 
>> >> > Cc: "Dan Tenenbaum" , "Michael Lawrence" <
>> >> lawrence.mich...@gene.com>, "bioc-devel"
>> >> > 
>> >> > 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@umassmed.edu>
>> >> > wrote:
>> >> >
>> >> >> Thanks, Dan!
>> >> >>

Re: [Bioc-devel] import except on Window Machine

[Karim Mezhoud]

# ##BUILT &   RELOAD
==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer

* installing to library
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
ERROR: failed to lock directory
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ for
modifying
Try removing
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-bioCancer’

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 ‘/Volumes/DATA/radiant/bioCancer/DESCRIPTION’ ... OK
* preparing ‘bioCancer’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘bioCancer_0.99.0.tar.gz’

[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 
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" 
> > To: "Dan Tenenbaum" 
> > Cc: "Lihua Zhu" , "Michael Lawrence" <
> lawrence.mich...@gene.com>, "bioc-devel"
> > 
> > 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 
> > 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" 
> >> > To: "Lihua Zhu" 
> >> > Cc: "Dan Tenenbaum" , "Michael Lawrence" <
> >> lawrence.mich...@gene.com>, "bioc-devel"
> >> > 
> >> > 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@umassmed.edu>
> >> > wrote:
> >> >
> >> >> Thanks, Dan!
> >> >>
> >> >> Best,
> >> >>
> >> >> Julie
> >> >>
> >> >> On 4/11/16 12:22 PM, "Dan Tenenbaum"  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" 
> >> >> >> To: "bioc-devel" 
> >> >> >> Cc: "Michael Lawrence" 
> >> >> >> 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.
> >> >> >>
> >> >> >>
> >> >>
> >>
> 

Re: [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 >
Date: Monday, April 11, 2016 1:03 PM
To: Lihua Julie Zhu >
Cc: Dan Tenenbaum >, 
Michael Lawrence >, 
"bioc-devel@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) 
> wrote:
Thanks, Dan!

Best,

Julie

On 4/11/16 12:22 PM, "Dan Tenenbaum" 
> 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" >
>> To: "bioc-devel" >
>> Cc: "Michael Lawrence" 
>> >
>> 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=BQICaQ
>>=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPH
>>hwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw=lEJWy
>>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA=
>>
>> 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@r-project.org mailing list
>>
>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
>>_listinfo_bioc-2Ddevel=BQICaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>>OmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0yS
>>t37UGJMdDhnwk0JFoVzS5Cw=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g=

___
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[[alternative HTML version deleted]]

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Re: [Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

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" 
> To: "Dan Tenenbaum" 
> Cc: "Lihua Zhu" , "Michael Lawrence" 
> , "bioc-devel"
> 
> 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 
> 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" 
>> > To: "Lihua Zhu" 
>> > Cc: "Dan Tenenbaum" , "Michael Lawrence" <
>> lawrence.mich...@gene.com>, "bioc-devel"
>> > 
>> > 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@umassmed.edu>
>> > wrote:
>> >
>> >> Thanks, Dan!
>> >>
>> >> Best,
>> >>
>> >> Julie
>> >>
>> >> On 4/11/16 12:22 PM, "Dan Tenenbaum"  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" 
>> >> >> To: "bioc-devel" 
>> >> >> Cc: "Michael Lawrence" 
>> >> >> 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=BQICaQ
>> >>
>> >>=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPH
>> >>
>> >>hwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw=lEJWy
>> >> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA=
>> >> >>
>> >> >> 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@r-project.org mailing list
>> >> >>
>> >> >>
>> >>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
>> >>
>> >>_listinfo_bioc-2Ddevel=BQICaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>> >>
>> >>OmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0yS
>> >>
>> >>t37UGJMdDhnwk0JFoVzS5Cw=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g=
>> >>
>> >> ___
>> >> Bioc-devel@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] import except on Window Machine

[Karim Mezhoud]

> 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 
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" 
> > To: "Lihua Zhu" 
> > Cc: "Dan Tenenbaum" , "Michael Lawrence" <
> lawrence.mich...@gene.com>, "bioc-devel"
> > 
> > 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@umassmed.edu>
> > wrote:
> >
> >> Thanks, Dan!
> >>
> >> Best,
> >>
> >> Julie
> >>
> >> On 4/11/16 12:22 PM, "Dan Tenenbaum"  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" 
> >> >> To: "bioc-devel" 
> >> >> Cc: "Michael Lawrence" 
> >> >> 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=BQICaQ
> >>
> >>=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPH
> >>
> >>hwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw=lEJWy
> >> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA=
> >> >>
> >> >> 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@r-project.org mailing list
> >> >>
> >> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
> >>
> >>_listinfo_bioc-2Ddevel=BQICaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
> >>
> >>OmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0yS
> >>
> >>t37UGJMdDhnwk0JFoVzS5Cw=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g=
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

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" 
> To: "Lihua Zhu" 
> Cc: "Dan Tenenbaum" , "Michael Lawrence" 
> , "bioc-devel"
> 
> 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) 
> wrote:
> 
>> Thanks, Dan!
>>
>> Best,
>>
>> Julie
>>
>> On 4/11/16 12:22 PM, "Dan Tenenbaum"  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" 
>> >> To: "bioc-devel" 
>> >> Cc: "Michael Lawrence" 
>> >> 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=BQICaQ
>> >>=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPH
>> >>hwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw=lEJWy
>> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA=
>> >>
>> >> 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@r-project.org mailing list
>> >>
>> >>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
>> >>_listinfo_bioc-2Ddevel=BQICaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>> >>OmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0yS
>> >>t37UGJMdDhnwk0JFoVzS5Cw=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g=
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] import except on Window Machine

[Karim Mezhoud]

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) 
wrote:

> Thanks, Dan!
>
> Best,
>
> Julie
>
> On 4/11/16 12:22 PM, "Dan Tenenbaum"  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" 
> >> To: "bioc-devel" 
> >> Cc: "Michael Lawrence" 
> >> 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=BQICaQ
> >>=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPH
> >>hwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw=lEJWy
> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA=
> >>
> >> 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@r-project.org mailing list
> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
> >>_listinfo_bioc-2Ddevel=BQICaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
> >>OmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0yS
> >>t37UGJMdDhnwk0JFoVzS5Cw=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g=
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Rd] R not responding (must force quit) when saving graphic to PDF (bug?)

[Neil French Collier]

Dear colleagues,

I wish to report a problem I encounter when trying to save a graphic to
file. When I produce a graphic and try to save it R becomes unresponsive
and I must force quit, and then restart R. The problem occurs when I try to
overwrite an existing graphic: for example when I made changes to the
graphic and want to save the graphic using the original file name. It only
happens when I use the menus to save files, not using script. It doesn't
happen when I save it as a new file. So, like this:

1. Make the graphic
2. Click File -> Save -> click on existing file name
3. Colour wheel appears and R is unresponsive.

Reproducible example:

x <- seq(1,10)
y <- x^2
plot(x,y, type="l") # Save as new file, all fine.

#Change plot and save as old plot file name:

plot(x,y, type="l", col=2)

# Click File -> Save
# 'Save quartz to PDF file' box opens
# Click on existing file name
# Colour wheel

Here is the sessionInfo():

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (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

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

I'm not sure if this is worthy of reporting but I was encouraged to submit
a report. It doesn't really make a huge impact on my workflow, but it can
be annoying.

-- 
Cheers,

Neil

Neil French Collier, PhD
Faculty of Sustainability
Leuphana University Lüneburg
Rotenbleicher Weg 67
21335 Lueneburg
Germany

Twitter: @foodsecbio
email: coll...@leuphana.de
Google Scholar

Ideas for Sustainability 

[[alternative HTML version deleted]]

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Re: [Bioc-devel] import except on Window Machine

[Zhu, Lihua (Julie)]

Thanks, Dan!

Best,

Julie

On 4/11/16 12:22 PM, "Dan Tenenbaum"  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" 
>> To: "bioc-devel" 
>> Cc: "Michael Lawrence" 
>> 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=BQICaQ
>>=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ=3IbW-yoIQpGZOKgd4i2bgmPH
>>hwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw=lEJWy
>>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA=
>> 
>> 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@r-project.org mailing list
>> 
>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
>>_listinfo_bioc-2Ddevel=BQICaQ=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>>OmhQ=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU=t9rR8WHE_O0PrI0B-0yS
>>t37UGJMdDhnwk0JFoVzS5Cw=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g= 

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Re: [Bioc-devel] package submission - problem with vignette

[Dan Tenenbaum]

It means that when you run R CMD build YourPackageName, the vignette is not 
built.

It simply looks in the output of R CMD build for a line that starts:

* creating vignettes ...

If this line is present, it means `R` has not detected that a vignette
needs to be built.

It's `REQUIRED` that the vignette be built.

If you have vignette sources yet still get this message, there could
be several causes:

* Missing or invalid `VignetteBuilder` line in the `DESCRIPTION` file.
* Missing or invalid `VignetteEngine` line in the vignette source.

See `knitr`'s [package vignette](http://yihui.name/knitr/demo/vignette/)
page, or the
[Non-Sweave 
vignettes](https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes)
section of "Writing R Extensions" for more information.

Dan


- Original Message -
> From: "Lara Urban" 
> To: "bioc-devel" 
> Sent: Monday, April 11, 2016 8:58:14 AM
> Subject: [Bioc-devel] package submission - problem with vignette

> Dear BiocDevel,
> 
> I have a question regarding the submission of my package; thank you very
> much in advance.
> 
> I have submitted my package to Bioconductor a few days ago and it passed
> build, check and bioccheck. Now, that I had to change just one line in my R
> code and submitted it again, I get an error on all three platforms, because
> it is required that my vignette is built by R CMD build; however, I still
> have my Rmd file in the order vignettes as before. Shouldn't it build
> automatically? Do you have any ideas what is going wrong here?
> 
> Many thanks and kind regards,
> Lara
> 
> 
> --
> Lara Urban
> 
> Predoctoral Fellow
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD
> United Kingdom
> 
> PhD Student
> Wolfson College
> University of Cambridge
> 
> phone:  + 49 (0) 176 76 37 99 03 <%2B%2044%20%280%29%201223%20494%20655>
> email: lara.h.ur...@ebi.ac.uk 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] moscato2 Windows build error reading IDAT file

[Dan Tenenbaum]

The problem seems to have to do with illuminaio and possibly minfiData; it can 
be reduced to / reproduced by the following:

library(illuminaio)
file <- 
"e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat"
illuminaio:::readIDAT_nonenc(file)

Specifically the error occurs on line 59 of illuminaio/R/readIDAT_nonenc.R, in 
the readString() function inside readIDAT_nonenc().

I'll leave it to the maintainer(s) of those packages to trobuleshoot further 
what the problem is.

> traceback()
5: readString(con = con)
4: readField(con = con, field = xx)
3: FUN(X[[i]], ...)
2: lapply(res, function(xx) {
   where <- fields[xx, "byteOffset"]
   seek(con, where = where, origin = "start")
   readField(con = con, field = xx)
   })
1: illuminaio:::readIDAT_nonenc(file)


> sessionInfo()
R version 3.3.0 alpha (2016-03-28 r70390)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] illuminaio_0.13.1
 [2] minfiData_0.13.0
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [4] IlluminaHumanMethylation450kmanifest_0.4.0
 [5] minfi_1.17.10
 [6] bumphunter_1.11.5
 [7] locfit_1.5-9.1
 [8] iterators_1.0.8
 [9] foreach_1.4.3
[10] Biostrings_2.39.12
[11] XVector_0.11.8
[12] SummarizedExperiment_1.1.24
[13] GenomicRanges_1.23.26
[14] GenomeInfoDb_1.7.6
[15] IRanges_2.5.43
[16] S4Vectors_0.9.46
[17] lattice_0.20-33
[18] Biobase_2.31.3
[19] BiocGenerics_0.17.5
[20] MethylAid_1.5.4

loaded via a namespace (and not attached):
 [1] mclust_5.2   base64_1.1   Rcpp_0.12.4
 [4] Rsamtools_1.23.8 digest_0.6.9 gridBase_0.4-7
 [7] mime_0.4 R6_2.1.2 plyr_1.8.3
[10] chron_2.3-47 RSQLite_1.0.0ggplot2_2.1.0
[13] zlibbioc_1.17.1  GenomicFeatures_1.23.29  data.table_1.9.6
[16] annotate_1.49.1  hexbin_1.27.1preprocessCore_1.33.0
[19] splines_3.3.0BiocParallel_1.5.21  stringr_1.0.0
[22] RCurl_1.95-4.8   biomaRt_2.27.2   munsell_0.4.3
[25] shiny_0.13.2 httpuv_1.3.3 rtracklayer_1.31.10
[28] multtest_2.27.0  pkgmaker_0.22htmltools_0.3.5
[31] GEOquery_2.37.0  quadprog_1.5-5   codetools_0.2-14
[34] matrixStats_0.50.1   XML_3.98-1.4 reshape_0.8.5
[37] GenomicAlignments_1.7.20 MASS_7.3-45  bitops_1.0-6
[40] grid_3.3.0   nlme_3.1-126 xtable_1.8-2
[43] gtable_0.2.0 registry_0.3 DBI_0.3.1
[46] magrittr_1.5 scales_0.4.0 stringi_1.0-1
[49] genefilter_1.53.3doRNG_1.6limma_3.27.15
[52] nor1mix_1.2-1RColorBrewer_1.1-2   siggenes_1.45.0
[55] tools_3.3.0  rngtools_1.2.4   survival_2.38-3
[58] AnnotationDbi_1.33.8 colorspace_1.2-6 beanplot_1.2

Dan


- Original Message -
> From: "Maarten van Iterson" 
> To: "bioc-devel" 
> Sent: Monday, April 11, 2016 4:01:05 AM
> Subject: [Bioc-devel] moscato2 Windows build error reading IDAT file

> Dear all,
> 
> My package MethylAid does not pass check on moscato2.
> 
> I got
> 
> "Error in while (m%/%128 == 1) { : argument is of length zero
> Calls: summarize ... readIDAT_nonenc -> lapply -> FUN -> readField ->
> readString"
> 
> the summarize function calls read.metharray.exp from minfi which calls
> readIDAT/readIDAT_nonenc
> from illuminaio. However, both packages do pass check on moscato2.
> 
> I don't know how to fix this or if the error is related to the new
> windows toolchain?
> 
> Any idea's or suggestions are welcome!
> 
> Cheers,
> Maarten
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

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" 
> To: "bioc-devel" 
> Cc: "Michael Lawrence" 
> 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.
> http://bioconductor.org/checkResults/devel/bioc-LATEST/CRISPRseek/moscato2-buildsrc.html
> 
> 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]]
> 
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[Bioc-devel] import except on Window Machine

[Zhu, Lihua (Julie)]

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.
http://bioconductor.org/checkResults/devel/bioc-LATEST/CRISPRseek/moscato2-buildsrc.html

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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[Bioc-devel] package submission - problem with vignette

[Lara Urban]

Dear BiocDevel,

I have a question regarding the submission of my package; thank you very
much in advance.

I have submitted my package to Bioconductor a few days ago and it passed
build, check and bioccheck. Now, that I had to change just one line in my R
code and submitted it again, I get an error on all three platforms, because
it is required that my vignette is built by R CMD build; however, I still
have my Rmd file in the order vignettes as before. Shouldn't it build
automatically? Do you have any ideas what is going wrong here?

Many thanks and kind regards,
Lara


-- 
Lara Urban

Predoctoral Fellow
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom

PhD Student
Wolfson College
University of Cambridge

phone:  + 49 (0) 176 76 37 99 03 <%2B%2044%20%280%29%201223%20494%20655>
email: lara.h.ur...@ebi.ac.uk 

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Re: [Bioc-devel] mascato2 check error

[Dan Tenenbaum]

- Original Message -
> From: "Karim Mezhoud" 
> To: "bioc-devel" 
> Sent: Monday, April 11, 2016 5:52:43 AM
> Subject: [Bioc-devel] mascato2 check error

> Dear BioC devel,
> I did not understand the following error check message.
> http://www.bioconductor.org/checkResults/3.3/bioc-LATEST/canceR/moscato2-checksrc.html
> Any suggestion is welcome.

It means some process is holding on to the files and they cannot be removed. 
This happens occasionally. I have manually killed those processes and removed 
those files. The next build should proceed normally.

Dan




> Thank you
> Karim
> 
> ### Running command:
> ###
> ###   rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir
> canceR.buildbin-libdir canceR.Rcheck &&
> E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
> CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir
> canceR_1.3.7.tar.gz >canceR.Rcheck\00install.out 2>&1 &&
> cp canceR.Rcheck\00install.out canceR-install.out  &&
> E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
> CMD check --library=canceR.buildbin-libdir
> --install="check:canceR-install.out" --force-multiarch --no-vignettes
> --timings canceR_1.3.7.tar.gz
> ###
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [R-pkg-devel] [R-SIG-Finance] [VC++ calling R] How to create a real-time interactive ticking time-series chart using dygraph via RInside?

[Joshua Ulrich]

Please choose *one* _relevant_ mailing list.  Spamming 5 (!)
mailing lists fragments the conversation and makes things difficult
for everyone involved.

On Mon, Apr 11, 2016 at 10:03 AM, Mike Deanza  wrote:
> Hi all,
>
>
> I am trying to figure out how to do this in R and I need your help.
>
>
> My journey started from something like the following:
>
>
> http://stackoverflow.com/questions/11365857/real-time-auto-updating-incremental-plot-in-r/1#1
>
>
> n=1000
> df=data.frame(time=1:n,y=runif(n))
> window=100
> for(i in 1:(n©\window)) {
> flush.console()
> plot(df$time,df$y,type='l',xlim=c(i,i+window))
> Sys.sleep(.09)
> }
>
>
> Then I wanted to make it nicer looking so I went to dygraph.
>
>
> And then, I would like to be able to live send tick data from within Visual 
> C++ so I started to investigate RInside.
>
>
> Following the example code here:
>
>
> http://dirk.eddelbuettel.com/papers/useR2009RcppRInside.pdf
>
>
> I can open an RInside object in VC++, and then send some data to it, and then 
> execute some command in it, and then get data back.
>
>
> It is really great.
>
>
> However, is there a way to have the real-time updating ticking plots to be 
> drawn on dygraph inside RInside?
>
>
> It turns out the dygraph package tends to draw onto a browser. That makes the 
> real-time updating pretty slow.
>
>
> Is there a way to set the dygraph to plot to a GUI window in VC++? For 
> example, a QT or MFC GUI window?
>
>
> My working environment is Win7 64bit ,with VS 2013 and VS2015, QT 5.3 32bit.
>
>
> Could anybody please shed some lights on me?
>
>
> Thanks a lot!
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
> ___
> r-sig-fina...@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-finance
> -- Subscriber-posting only. If you want to post, subscribe first.
> -- Also note that this is not the r-help list where general R questions 
> should go.



-- 
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com
R/Finance 2016 | www.rinfinance.com

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Re: [Rd] [R-SIG-Finance] [VC++ calling R] How to create a real-time interactive ticking time-series chart using dygraph via RInside?

[Joshua Ulrich]

Please choose *one* _relevant_ mailing list.  Spamming 5 (!)
mailing lists fragments the conversation and makes things difficult
for everyone involved.

On Mon, Apr 11, 2016 at 10:03 AM, Mike Deanza  wrote:
> Hi all,
>
>
> I am trying to figure out how to do this in R and I need your help.
>
>
> My journey started from something like the following:
>
>
> http://stackoverflow.com/questions/11365857/real-time-auto-updating-incremental-plot-in-r/1#1
>
>
> n=1000
> df=data.frame(time=1:n,y=runif(n))
> window=100
> for(i in 1:(n©\window)) {
> flush.console()
> plot(df$time,df$y,type='l',xlim=c(i,i+window))
> Sys.sleep(.09)
> }
>
>
> Then I wanted to make it nicer looking so I went to dygraph.
>
>
> And then, I would like to be able to live send tick data from within Visual 
> C++ so I started to investigate RInside.
>
>
> Following the example code here:
>
>
> http://dirk.eddelbuettel.com/papers/useR2009RcppRInside.pdf
>
>
> I can open an RInside object in VC++, and then send some data to it, and then 
> execute some command in it, and then get data back.
>
>
> It is really great.
>
>
> However, is there a way to have the real-time updating ticking plots to be 
> drawn on dygraph inside RInside?
>
>
> It turns out the dygraph package tends to draw onto a browser. That makes the 
> real-time updating pretty slow.
>
>
> Is there a way to set the dygraph to plot to a GUI window in VC++? For 
> example, a QT or MFC GUI window?
>
>
> My working environment is Win7 64bit ,with VS 2013 and VS2015, QT 5.3 32bit.
>
>
> Could anybody please shed some lights on me?
>
>
> Thanks a lot!
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
> ___
> r-sig-fina...@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-finance
> -- Subscriber-posting only. If you want to post, subscribe first.
> -- Also note that this is not the r-help list where general R questions 
> should go.



-- 
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com
R/Finance 2016 | www.rinfinance.com

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Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

[Martin Maechler]

> Ravi Varadhan 
> on Mon, 11 Apr 2016 12:42:35 + writes:

> all.equal.eigen() should also accommodate complex vectors, right?
> Ravi

Yes, definitely.   The  ?eigen  help page does nicely mention
that in the complex the eigen vectors are even less determined,
i.e. you could multiply them by any unit length complex number
(of which only two are available in the real case:  +/- 1).

Martin

> 
> From: R-devel  on behalf of Martin 
Maechler 
> Sent: Monday, April 11, 2016 3:08 AM
> To: William Dunlap
> Cc: r-devel; Jeroen Ooms
> Subject: Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0   
on  windows

> William Dunlap via R-devel 
> on Mon, 4 Apr 2016 12:26:38 -0700 writes:

>>> If I recall correctly, some eigen vectors had their
>>> direction flipped (negative values became positive and
>>> vice versa).  Did you notice anything of this kind when
>>> running 'make check' and 'make check recommended' ? It is
>>> important to us that numeric results are reproducible
>>> between versions of R.

>> I think that any code that depends on the direction of an
>> eigenvector should be considered broken.

> I agree [even though I may have fallen into that trap in some of
> the regression tests I had written in the long past!].

>> It is too bad that eigen's output does not have a class so
>> that an all.equal method that know that the vector
>> direction is not relevant could be written for it

> That's an interesting / neat idea.
> So we could give it S3 class "eigen"  iff  only.values is not
> true, which would also "solve" the slightly differently
> structured result of eigen()

> Are you (or others) willing to provide a prototype for
> all.equal.eigen ?

> Martin

>> Bill Dunlap TIBCO Software wdunlap tibco.com

>> On Mon, Apr 4, 2016 at 11:39 AM, Jeroen Ooms
>>  wrote:

>>> On Sun, Apr 3, 2016 at 6:44 PM, Ray Donnelly
>>>  wrote: > I've started to look
>>> into building R for Windows using MSYS2 as both the >
>>> build environment and tools + libraries provider (where
>>> possible).
>>> 
>>> Thanks for your reply, and for the patches.
>>> 
>>> Last time I had a look at this (a few months ago) another
>>> problem was that mingw-w64 v4 was giving different
>>> numeric output for some of the tests in r-base. If I
>>> recall correctly, some eigen vectors had their direction
>>> flipped (negative values became positive and vice versa).
>>> Did you notice anything of this kind when running 'make
>>> check' and 'make check recommended' ? It is important to
>>> us that numeric results are reproducible between versions
>>> of R.

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[Bioc-devel] mascato2 check error

[Karim Mezhoud]

Dear BioC devel,
I did not understand the following error check message.
http://www.bioconductor.org/checkResults/3.3/bioc-LATEST/canceR/moscato2-checksrc.html
Any suggestion is welcome.
Thank you
Karim

### Running command:
###
###   rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir
canceR.buildbin-libdir canceR.Rcheck &&
E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir
canceR_1.3.7.tar.gz >canceR.Rcheck\00install.out 2>&1 &&
cp canceR.Rcheck\00install.out canceR-install.out  &&
E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
CMD check --library=canceR.buildbin-libdir
--install="check:canceR-install.out" --force-multiarch --no-vignettes
--timings canceR_1.3.7.tar.gz
###

[[alternative HTML version deleted]]

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Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

[Ravi Varadhan]

all.equal.eigen() should also accommodate complex vectors, right?

Ravi

From: R-devel  on behalf of Martin Maechler 

Sent: Monday, April 11, 2016 3:08 AM
To: William Dunlap
Cc: r-devel; Jeroen Ooms
Subject: Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0   on  
windows

> William Dunlap via R-devel 
> on Mon, 4 Apr 2016 12:26:38 -0700 writes:

>> If I recall correctly, some eigen vectors had their
>> direction flipped (negative values became positive and
>> vice versa).  Did you notice anything of this kind when
>> running 'make check' and 'make check recommended' ? It is
>> important to us that numeric results are reproducible
>> between versions of R.

> I think that any code that depends on the direction of an
> eigenvector should be considered broken.

I agree [even though I may have fallen into that trap in some of
the regression tests I had written in the long past!].

> It is too bad that eigen's output does not have a class so
> that an all.equal method that know that the vector
> direction is not relevant could be written for it

That's an interesting / neat idea.
So we could give it S3 class "eigen"  iff  only.values is not
true, which would also "solve" the slightly differently
structured result of eigen()

Are you (or others) willing to provide a prototype for
all.equal.eigen ?

Martin

> Bill Dunlap TIBCO Software wdunlap tibco.com

> On Mon, Apr 4, 2016 at 11:39 AM, Jeroen Ooms
>  wrote:

>> On Sun, Apr 3, 2016 at 6:44 PM, Ray Donnelly
>>  wrote: > I've started to look
>> into building R for Windows using MSYS2 as both the >
>> build environment and tools + libraries provider (where
>> possible).
>>
>> Thanks for your reply, and for the patches.
>>
>> Last time I had a look at this (a few months ago) another
>> problem was that mingw-w64 v4 was giving different
>> numeric output for some of the tests in r-base. If I
>> recall correctly, some eigen vectors had their direction
>> flipped (negative values became positive and vice versa).
>> Did you notice anything of this kind when running 'make
>> check' and 'make check recommended' ? It is important to
>> us that numeric results are reproducible between versions
>> of R.
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>

>   [[alternative HTML version deleted]]

> __
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[Bioc-devel] moscato2 Windows build error reading IDAT file

[Maarten van Iterson]

Dear all,

My package MethylAid does not pass check on moscato2.

I got

"Error in while (m%/%128 == 1) { : argument is of length zero
Calls: summarize ... readIDAT_nonenc -> lapply -> FUN -> readField ->
readString"

the summarize function calls read.metharray.exp from minfi which calls
readIDAT/readIDAT_nonenc
 from illuminaio. However, both packages do pass check on moscato2.

I don't know how to fix this or if the error is related to the new
windows toolchain?

Any idea's or suggestions are welcome!

Cheers,
Maarten

[[alternative HTML version deleted]]

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Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

[Martin Maechler]

> William Dunlap via R-devel 
> on Mon, 4 Apr 2016 12:26:38 -0700 writes:

>> If I recall correctly, some eigen vectors had their
>> direction flipped (negative values became positive and
>> vice versa).  Did you notice anything of this kind when
>> running 'make check' and 'make check recommended' ? It is
>> important to us that numeric results are reproducible
>> between versions of R.

> I think that any code that depends on the direction of an
> eigenvector should be considered broken.  

I agree [even though I may have fallen into that trap in some of
the regression tests I had written in the long past!].

> It is too bad that eigen's output does not have a class so
> that an all.equal method that know that the vector
> direction is not relevant could be written for it

That's an interesting / neat idea.
So we could give it S3 class "eigen"  iff  only.values is not
true, which would also "solve" the slightly differently
structured result of eigen() 

Are you (or others) willing to provide a prototype for
all.equal.eigen ?

Martin

> Bill Dunlap TIBCO Software wdunlap tibco.com

> On Mon, Apr 4, 2016 at 11:39 AM, Jeroen Ooms
>  wrote:

>> On Sun, Apr 3, 2016 at 6:44 PM, Ray Donnelly
>>  wrote: > I've started to look
>> into building R for Windows using MSYS2 as both the >
>> build environment and tools + libraries provider (where
>> possible).
>> 
>> Thanks for your reply, and for the patches.
>> 
>> Last time I had a look at this (a few months ago) another
>> problem was that mingw-w64 v4 was giving different
>> numeric output for some of the tests in r-base. If I
>> recall correctly, some eigen vectors had their direction
>> flipped (negative values became positive and vice versa).
>> Did you notice anything of this kind when running 'make
>> check' and 'make check recommended' ? It is important to
>> us that numeric results are reproducible between versions
>> of R.
>> 
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 

>   [[alternative HTML version deleted]]

> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel

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