[R-pkg-devel] Trying to remove dot file

[Adrian Cunningham]

Hello Everyone,


I am trying to eliminate a warning from my package so that it will pass the
devtools check.

* checking package subdirectories ... WARNING
Subdirectory 'man' contains invalid file names:
  '._PlotMDS.Rd'
Please remove or rename the files.


I tried using "dot_clean -m --keep=mostrecent /PlotMDS/man" and that didn't
seem to remove the file. I am not able to view the file (tried using sudo
ls).

Does anyone have any suggestions to help me? Any suggestions would be most
welcome and appreciated, thank you!


-- 
Adrian Cunningham

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Re: [Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment

[Vincent Carey]

no answers yet?  would it work to put your matrices as separate assays in a
SummarizedExperiment?
as long as they are conformant in dimensions and dimnames I think that
would work.  That
SummarizedExperiment would then work well in an MAE.

On Mon, Oct 23, 2017 at 1:00 PM, Francesco Napolitano 
wrote:

> Hi,
>
> I'm trying to build a MultiAssayExperiment. However, in my case each
> assay should ideally include two matrices: one with a statistic and
> another one with the corresponding p-value. I'm currently managing
> each of them simply as a list of two matrices, but assay class expects
> table-like data. I must also be able to quickly extract entire rows or
> columns from each matrix.
>
> Is there a suitable way to model this into a MultiAssayExperiment?
>
> Thank you,
> Francesco
>
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>

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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Hervé Pagès]

On 10/23/2017 01:42 PM, Martin Morgan wrote:

On 10/23/2017 04:40 PM, Hervé Pagès wrote:

Hi Elizabeth,

Thanks for troubleshooting this.

Note that testing with identical()/checkIdentical() is safer than with
'any(sort(colnames1) != sort(colnames2))'. The latter won't do the
right thing if 'colnames1' and 'colnames2' have different lengths.


...but in this case it sounds like you're aiming for a set comparison,

   setequal(colnames1, colnames2)


Still not 100% safe though. Will give a false positive in the rare
situation where some columns are duplicated ;-)

> setequal(c("a", "b", "a"), c("b", "a"))
[1] TRUE

H.



Martin



Cheers,
H.


On 10/23/2017 01:06 PM, Elizabeth Purdom wrote:

Dear Martin,

Just for completeness, I figured out the discrepancy and solved my
problem. In my check, I check that the column names contain the
expected names and I didn’t want to make the order required in a
certain way so I used sort -- but only of one side because I naively
assumed the other side would be fixed:

any(sort(colnames(object@merge_nodeMerge)) !=
c('Contrast','isMerged','mergeClusterId','Node’)

But the different environments are sorting differently!

In my normal interactive R session:

sort(c("Contrast", "isMerged", "mergeClusterId", "Node"))

[1] "Contrast"   "isMerged"   "mergeClusterId" "Node"

In the build version of R however:
Browse[2]> sort(c("Contrast", "isMerged", "mergeClusterId", "Node"))
[1] "Contrast"   "Node"   "isMerged"   "mergeClusterId"

Thank you very much for your help in getting an interactive session
in the build environment!

Elizabeth


On Oct 23, 2017, at 4:35 PM, Martin Morgan
 wrote:

On 10/23/2017 09:59 AM, Elizabeth Purdom wrote:

On Oct 23, 2017, at 3:47 PM, Martin Morgan
> wrote:

On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:

Hello,
I am updating an existing package and I am getting an error in
running my vignette (and a similar error in an example in help
pages) but ONLY when I run R CMD BUILD. I can’t recreate the
error in any session where I can debug and figure out what is
happening. So my question is how can I recreate the exact
environment of R CMD BUILD that runs the vignette but in an
interactive session so that I can figure out what is going on?
I have tried reproducing the error in other environments:
* Running R —vanilla interactively and trying the code manually
* running purl on my vignette to get pure R code and running just
the R code with R CMD BATCH —vanilla


hint on the specific package and / or error message?

My approach would be to install the package, Stangle / purl the
vignette, and R -f vignette.R, then trim the vignette to a fast
reproducible case. But it sounds like you're doing that...

Martin


Yes, that is what I tried but did not get the error from the R code.
And I apologize, it’s the `clusterExperiment` package. My error was
so specific to the class created by my package that I didn’t think
it would be useful, but here is the relevant error message:
Quitting from lines 271-272 (clusterExperimentTutorial.Rmd)
Error: processing vignette 'clusterExperimentTutorial.Rmd' failed
with diagnostics:
invalid class "ClusterExperiment" object: merge_nodeMerge must have
4 columns and column names equal to:
'Node','Contrast','isMerged','mergeClusterId'
Execution halted
I would note that my vignette calls an object that is saved as a
data object as part of my package to speed up compilation. But I
experimented and you can also switch it so that it creates the
object from scratch and doesn’t load the object, and it runs into
the same error. There is a `LazyData: false` in my DESCRIPTION
File, because I was having problems with my R data object, because
it is of the class I make with my package, and without the package
loaded there was some problem loading it.


I can reproduce the error with

clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C
R -f clusterExperimentTutorial.R

leading to


##
recallRSEC

rsecFluidigm<-RSEC(rsecFluidigm,isCount=TRUE,combineProportion=0.6,mergeMethod="JC",mergeCutoff=0.05)


Error in validObject(.Object) :
  invalid class "ClusterExperiment" object: merge_nodeMerge must be
data.frame with 4 columns and column names equal to:
'Node','Contrast','isMerged','mergeClusterId'
Calls: RSEC ... .local -> new -> initialize -> initialize ->
validObject
Execution halted

and then for work inside R


clusterExperiment/vignettes$ R_DEFAULT_PACKAGES= LC_COLLATE=C R
Bioconductor version 3.6 (BiocInstaller 1.27.7), ?biocLite for help

source("clusterExperimentTutorial.R", echo=TRUE, max=Inf)


Does that set you down the right path?

Martin



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message 

[Bioc-devel] cellbaseR build

[mohammed Elsiddieg]

Hi All

I am the maintainer of cellbaseR, a client for the CellBase Annotation
database, Unfortunately,
The web services are down at the moment which results in build errors, but
this is not due to a fault in R package, I hope this does not disqualify my
package from Bioconductor release as I know Today is deadline for passing
build

Best regards

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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Elizabeth Purdom]

Dear Martin,

Just for completeness, I figured out the discrepancy and solved my problem. In 
my check, I check that the column names contain the expected names and I didn’t 
want to make the order required in a certain way so I used sort -- but only of 
one side because I naively assumed the other side would be fixed:

any(sort(colnames(object@merge_nodeMerge)) != 
c('Contrast','isMerged','mergeClusterId','Node’)

But the different environments are sorting differently!

In my normal interactive R session:
> sort(c("Contrast", "isMerged", "mergeClusterId", "Node"))
[1] "Contrast"   "isMerged"   "mergeClusterId" "Node"  

In the build version of R however:
Browse[2]> sort(c("Contrast", "isMerged", "mergeClusterId", "Node"))
[1] "Contrast"   "Node"   "isMerged"   "mergeClusterId"

Thank you very much for your help in getting an interactive session in the 
build environment!

Elizabeth

> On Oct 23, 2017, at 4:35 PM, Martin Morgan  
> wrote:
> 
> On 10/23/2017 09:59 AM, Elizabeth Purdom wrote:
>>> On Oct 23, 2017, at 3:47 PM, Martin Morgan >> > wrote:
>>> 
>>> On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:
 Hello,
 I am updating an existing package and I am getting an error in running my 
 vignette (and a similar error in an example in help pages) but ONLY when I 
 run R CMD BUILD. I can’t recreate the error in any session where I can 
 debug and figure out what is happening. So my question is how can I 
 recreate the exact environment of R CMD BUILD that runs the vignette but 
 in an interactive session so that I can figure out what is going on?
 I have tried reproducing the error in other environments:
 * Running R —vanilla interactively and trying the code manually
 * running purl on my vignette to get pure R code and running just the R 
 code with R CMD BATCH —vanilla
>>> 
>>> hint on the specific package and / or error message?
>>> 
>>> My approach would be to install the package, Stangle / purl the vignette, 
>>> and R -f vignette.R, then trim the vignette to a fast reproducible case. 
>>> But it sounds like you're doing that...
>>> 
>>> Martin
>>> 
>> Yes, that is what I tried but did not get the error from the R code.
>> And I apologize, it’s the `clusterExperiment` package. My error was so 
>> specific to the class created by my package that I didn’t think it would be 
>> useful, but here is the relevant error message:
>> Quitting from lines 271-272 (clusterExperimentTutorial.Rmd)
>> Error: processing vignette 'clusterExperimentTutorial.Rmd' failed with 
>> diagnostics:
>> invalid class "ClusterExperiment" object: merge_nodeMerge must have 4 
>> columns and column names equal to: 
>> 'Node','Contrast','isMerged','mergeClusterId'
>> Execution halted
>> I would note that my vignette calls an object that is saved as a data object 
>> as part of my package to speed up compilation. But I experimented and you 
>> can also switch it so that it creates the object from scratch and doesn’t 
>> load the object, and it runs into the same error. There is a `LazyData: 
>> false` in my DESCRIPTION File, because I was having problems with my R data 
>> object, because it is of the class I make with my package, and without the 
>> package loaded there was some problem loading it.
> 
> I can reproduce the error with
> 
> clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C R -f 
> clusterExperimentTutorial.R
> 
> leading to
> 
> > ## 
> > recallRSEC
> > rsecFluidigm<-RSEC(rsecFluidigm,isCount=TRUE,combineProportion=0.6,mergeMethod="JC",mergeCutoff=0.05)
> Error in validObject(.Object) :
>  invalid class "ClusterExperiment" object: merge_nodeMerge must be data.frame 
> with 4 columns and column names equal to: 
> 'Node','Contrast','isMerged','mergeClusterId'
> Calls: RSEC ... .local -> new -> initialize -> initialize -> validObject
> Execution halted
> 
> and then for work inside R
> 
> 
> clusterExperiment/vignettes$ R_DEFAULT_PACKAGES= LC_COLLATE=C R
> Bioconductor version 3.6 (BiocInstaller 1.27.7), ?biocLite for help
> > source("clusterExperimentTutorial.R", echo=TRUE, max=Inf)
> 
> Does that set you down the right path?
> 
> Martin
> 
> 
> 
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
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[Bioc-devel] Modeling (statistic, p-value) pairs in MultiAssayExperiment

[Francesco Napolitano]

Hi,

I'm trying to build a MultiAssayExperiment. However, in my case each
assay should ideally include two matrices: one with a statistic and
another one with the corresponding p-value. I'm currently managing
each of them simply as a list of two matrices, but assay class expects
table-like data. I must also be able to quickly extract entire rows or
columns from each matrix.

Is there a suitable way to model this into a MultiAssayExperiment?

Thank you,
Francesco

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Re: [Rd] range function with finite=T and logical parameters

[Martin Maechler]

> Lukas Stadler 
> on Mon, 23 Oct 2017 15:56:55 +0200 writes:

> Hi!
> I was wondering about the behavior of the range function wrt. logical NAs:

>> range(c(0L, 1L, NA), finite=T)
> [1] 0 1
>> range(c(F, T, NA), finite=T)
> [1] NA NA

> The documentation is quite clear that "finite = TRUE includes na.rm = 
TRUE”, so that I would have assumed that these two snippets would produce the 
same result.

> - Lukas


I agree.  Further, another informal "rule" would require that the two calls

 range(L, *)  
 range(as.numeric(L), *)

are equivalent for logical vectors L without attributes.
I'll look into fixing this by an obvious change to (R-level)
range.default().

--

Note for the more advanced ones -- i.e. typical R-devel readers :

T and F are variables in R.  For that reason, using the language
keywords TRUE and FALSE is much preferred in such cases.  For
some tests we'd even use

T <- FALSE

or even

delayedAssign("F", stop("do not use 'F'  when programming with R"))

before running the tests -- just do ensure that the code to be
tested does not use these short forms.


Thank you, Lukas,  for the report!

Best,
Martin

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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Elizabeth Purdom]

> 
> I can reproduce the error with
> 
> clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C R -f 
> clusterExperimentTutorial.R
> 
> leading to
> 
> > ## 
> > recallRSEC
> > rsecFluidigm<-RSEC(rsecFluidigm,isCount=TRUE,combineProportion=0.6,mergeMethod="JC",mergeCutoff=0.05)
> Error in validObject(.Object) :
>  invalid class "ClusterExperiment" object: merge_nodeMerge must be data.frame 
> with 4 columns and column names equal to: 
> 'Node','Contrast','isMerged','mergeClusterId'
> Calls: RSEC ... .local -> new -> initialize -> initialize -> validObject
> Execution halted
> 
> and then for work inside R
> 
> 
> clusterExperiment/vignettes$ R_DEFAULT_PACKAGES= LC_COLLATE=C R
> Bioconductor version 3.6 (BiocInstaller 1.27.7), ?biocLite for help
> > source("clusterExperimentTutorial.R", echo=TRUE, max=Inf)
> 
> Does that set you down the right path?
> 
> Martin
> 

Yes, thank you!!! I can get it in the interactive session now.
Elizabeth

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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Martin Morgan]

On 10/23/2017 09:59 AM, Elizabeth Purdom wrote:


On Oct 23, 2017, at 3:47 PM, Martin Morgan 
> 
wrote:


On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:

Hello,
I am updating an existing package and I am getting an error in 
running my vignette (and a similar error in an example in help pages) 
but ONLY when I run R CMD BUILD. I can’t recreate the error in any 
session where I can debug and figure out what is happening. So my 
question is how can I recreate the exact environment of R CMD BUILD 
that runs the vignette but in an interactive session so that I can 
figure out what is going on?

I have tried reproducing the error in other environments:
* Running R —vanilla interactively and trying the code manually
* running purl on my vignette to get pure R code and running just the 
R code with R CMD BATCH —vanilla


hint on the specific package and / or error message?

My approach would be to install the package, Stangle / purl the 
vignette, and R -f vignette.R, then trim the vignette to a fast 
reproducible case. But it sounds like you're doing that...


Martin



Yes, that is what I tried but did not get the error from the R code.

And I apologize, it’s the `clusterExperiment` package. My error was so 
specific to the class created by my package that I didn’t think it would 
be useful, but here is the relevant error message:


Quitting from lines 271-272 (clusterExperimentTutorial.Rmd)
Error: processing vignette 'clusterExperimentTutorial.Rmd' failed with 
diagnostics:
invalid class "ClusterExperiment" object: merge_nodeMerge must have 4 
columns and column names equal to: 
'Node','Contrast','isMerged','mergeClusterId'

Execution halted

I would note that my vignette calls an object that is saved as a data 
object as part of my package to speed up compilation. But I experimented 
and you can also switch it so that it creates the object from scratch 
and doesn’t load the object, and it runs into the same error. There is a 
`LazyData: false` in my DESCRIPTION File, because I was having problems 
with my R data object, because it is of the class I make with my 
package, and without the package loaded there was some problem loading it.


I can reproduce the error with

clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C R 
-f clusterExperimentTutorial.R


leading to

> ## 
recallRSEC
> 
rsecFluidigm<-RSEC(rsecFluidigm,isCount=TRUE,combineProportion=0.6,mergeMethod="JC",mergeCutoff=0.05)

Error in validObject(.Object) :
  invalid class "ClusterExperiment" object: merge_nodeMerge must be 
data.frame with 4 columns and column names equal to: 
'Node','Contrast','isMerged','mergeClusterId'

Calls: RSEC ... .local -> new -> initialize -> initialize -> validObject
Execution halted

and then for work inside R


clusterExperiment/vignettes$ R_DEFAULT_PACKAGES= LC_COLLATE=C R
Bioconductor version 3.6 (BiocInstaller 1.27.7), ?biocLite for help
> source("clusterExperimentTutorial.R", echo=TRUE, max=Inf)

Does that set you down the right path?

Martin








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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Elizabeth Purdom]

> On Oct 23, 2017, at 3:47 PM, Martin Morgan  
> wrote:
> 
> On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:
>> Hello,
>> I am updating an existing package and I am getting an error in running my 
>> vignette (and a similar error in an example in help pages) but ONLY when I 
>> run R CMD BUILD. I can’t recreate the error in any session where I can debug 
>> and figure out what is happening. So my question is how can I recreate the 
>> exact environment of R CMD BUILD that runs the vignette but in an 
>> interactive session so that I can figure out what is going on?
>> I have tried reproducing the error in other environments:
>> * Running R —vanilla interactively and trying the code manually
>> * running purl on my vignette to get pure R code and running just the R code 
>> with R CMD BATCH —vanilla
> 
> hint on the specific package and / or error message?
> 
> My approach would be to install the package, Stangle / purl the vignette, and 
> R -f vignette.R, then trim the vignette to a fast reproducible case. But it 
> sounds like you're doing that...
> 
> Martin
> 

Yes, that is what I tried but did not get the error from the R code. 

And I apologize, it’s the `clusterExperiment` package. My error was so specific 
to the class created by my package that I didn’t think it would be useful, but 
here is the relevant error message:

Quitting from lines 271-272 (clusterExperimentTutorial.Rmd) 
Error: processing vignette 'clusterExperimentTutorial.Rmd' failed with 
diagnostics:
invalid class "ClusterExperiment" object: merge_nodeMerge must have 4 columns 
and column names equal to: 'Node','Contrast','isMerged','mergeClusterId'
Execution halted

I would note that my vignette calls an object that is saved as a data object as 
part of my package to speed up compilation. But I experimented and you can also 
switch it so that it creates the object from scratch and doesn’t load the 
object, and it runs into the same error. There is a `LazyData: false` in my 
DESCRIPTION File, because I was having problems with my R data object, because 
it is of the class I make with my package, and without the package loaded there 
was some problem loading it. 




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[Rd] range function with finite=T and logical parameters

[Lukas Stadler]

Hi!

I was wondering about the behavior of the range function wrt. logical NAs:

> range(c(0L, 1L, NA), finite=T)
[1] 0 1
> range(c(F, T, NA), finite=T)
[1] NA NA

The documentation is quite clear that "finite = TRUE includes na.rm = TRUE”, so 
that I would have assumed that these two snippets would produce the same result.

- Lukas
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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Martin Morgan]

On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:

Hello,

I am updating an existing package and I am getting an error in running my 
vignette (and a similar error in an example in help pages) but ONLY when I run 
R CMD BUILD. I can’t recreate the error in any session where I can debug and 
figure out what is happening. So my question is how can I recreate the exact 
environment of R CMD BUILD that runs the vignette but in an interactive session 
so that I can figure out what is going on?

I have tried reproducing the error in other environments:

* Running R —vanilla interactively and trying the code manually
* running purl on my vignette to get pure R code and running just the R code 
with R CMD BATCH —vanilla


hint on the specific package and / or error message?

My approach would be to install the package, Stangle / purl the 
vignette, and R -f vignette.R, then trim the vignette to a fast 
reproducible case. But it sounds like you're doing that...


Martin


* Running R —vanilla interactively and compiling the vignette

But all of the above runs the code without any error.

Furthermore, for some reason TravisCI can build the package without problem nor 
does it hit any error in R CMD CHECK with TravisCI so for a long time I assumed 
it was some local file or environment on my machine and forgot about it. But 
now that I have pushed the changes to Bioconductor, they are getting the same 
error about the vignette not building.

By the way, I can’t slowly take back my commands to see what broke it, because 
the change was a dramatic one involving redefining my S4 class, so a large 
number of things had to be adapted before any code would work and there’s no 
way to slowly roll that back.

Most of the posts I have seen about debugging discrepancies between R CMD BUILD 
(or equivalently R CMD CHECK) seem to be about namespace issues with other 
packages. Of course I can’t be sure since I have a pretty terse error from R 
CMD BUILD, but the error that is given is my own error (it’s a check I wrote as 
part of the validity check when I updated the class) so it seems unclear how it 
would be a namespace error.

Thanks for any suggestions,
Elizabeth Purdom
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[Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

[Elizabeth Purdom]

Hello,

I am updating an existing package and I am getting an error in running my 
vignette (and a similar error in an example in help pages) but ONLY when I run 
R CMD BUILD. I can’t recreate the error in any session where I can debug and 
figure out what is happening. So my question is how can I recreate the exact 
environment of R CMD BUILD that runs the vignette but in an interactive session 
so that I can figure out what is going on?

I have tried reproducing the error in other environments:

* Running R —vanilla interactively and trying the code manually
* running purl on my vignette to get pure R code and running just the R code 
with R CMD BATCH —vanilla
* Running R —vanilla interactively and compiling the vignette

But all of the above runs the code without any error.

Furthermore, for some reason TravisCI can build the package without problem nor 
does it hit any error in R CMD CHECK with TravisCI so for a long time I assumed 
it was some local file or environment on my machine and forgot about it. But 
now that I have pushed the changes to Bioconductor, they are getting the same 
error about the vignette not building. 

By the way, I can’t slowly take back my commands to see what broke it, because 
the change was a dramatic one involving redefining my S4 class, so a large 
number of things had to be adapted before any code would work and there’s no 
way to slowly roll that back. 

Most of the posts I have seen about debugging discrepancies between R CMD BUILD 
(or equivalently R CMD CHECK) seem to be about namespace issues with other 
packages. Of course I can’t be sure since I have a pretty terse error from R 
CMD BUILD, but the error that is given is my own error (it’s a check I wrote as 
part of the validity check when I updated the class) so it seems unclear how it 
would be a namespace error. 

Thanks for any suggestions,
Elizabeth Purdom
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[Bioc-devel] Cannot reproduce Bioc build server errors for annotatr package

[Raymond Cavalcante]

Hello all,

I’m getting some CHECK errors in the examples and tests for the annotatr 
package (http://bioconductor.org/checkResults/devel/bioc-LATEST/annotatr/ 
) that I 
cannot reproduce using the bioconductor/devel_core2 Docker image + most 
up-to-date packages. I think the issue is coming from rtracklayer while reading 
in a BED (or BED-like) file that has '.' in the strand column instead of '+', 
'-', or '*'.

Here is the error on the build system for all three platforms:

> Running examples in ‘annotatr-Ex.R’ failed
> The error most likely occurred in:
> 
> > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> > ### Name: annotate_regions
> > ### Title: A function to intersect user region data with annotation data
> > ### Aliases: annotate_regions
> > 
> > ### ** Examples
> > 
> >r_file = system.file('extdata', 'test_read_multiple_data_nohead.bed', 
> > package='annotatr')
> >extraCols = c(pval = 'numeric', mu1 = 'integer', mu0 = 'integer', 
> > diff_exp = 'character')
> >r = read_regions(con = r_file, extraCols = extraCols, rename_score = 
> > 'coverage')
> Error in .local(x, ...) : strand values must be in '+' '-' '*'
> Calls: read_regions ... GenomicData -> normStrand -> strand -> strand -> 
> .local
> Execution halted

Below is my sessionInfo() for the Docker image based on the 
https://hub.docker.com/r/bioconductor/devel_core2/ 
 image. I suppose I could 
change all of my example data to use '*' for the strand, but many peak callers 
(macs2 being one of the most popular) use the '.' convention for no strand in 
their BED output, and I think rtracklayer should respect this.

Thanks, Raymond

> > sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 9 (stretch)
> 
> Matrix products: default
> BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=C 
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C 
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C   
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base 
> 
> other attached packages:
> [1] annotatr_1.3.2   BiocInstaller_1.27.6
> 
> loaded via a namespace (and not attached):
>  [1] Biobase_2.37.2   
>  [2] httr_1.3.1   
>  [3] regioneR_1.9.2   
>  [4] org.Rn.eg.db_3.4.2   
>  [5] bit64_0.9-7  
>  [6] AnnotationHub_2.9.21 
>  [7] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 
>  [8] shiny_1.0.5  
>  [9] assertthat_0.2.0 
> [10] interactiveDisplayBase_1.15.0
> [11] stats4_3.4.1 
> [12] blob_1.1.0   
> [13] BSgenome_1.45.3  
> [14] GenomeInfoDbData_0.99.1  
> [15] Rsamtools_1.29.1 
> [16] yaml_2.1.14  
> [17] progress_1.1.2   
> [18] RSQLite_2.0  
> [19] lattice_0.20-35  
> [20] glue_1.1.1   
> [21] digest_0.6.12
> [22] GenomicRanges_1.29.15
> [23] XVector_0.17.2   
> [24] colorspace_1.3-2 
> [25] htmltools_0.3.6  
> [26] httpuv_1.3.5 
> [27] Matrix_1.2-11
> [28] plyr_1.8.4   
> [29] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0  
> [30] XML_3.98-1.9 
> [31] pkgconfig_2.0.1  
> [32] TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1  
> [33] biomaRt_2.33.4   
> [34] org.Mm.eg.db_3.4.2   
> [35] zlibbioc_1.23.0  
> [36] xtable_1.8-2 
> [37] scales_0.5.0 
> [38] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
> [39] org.Dm.eg.db_3.4.2   
> [40] BiocParallel_1.11.13 
> [41] tibble_1.3.4 
> [42] IRanges_2.11.19  
> [43] ggplot2_2.2.1
> [44] SummarizedExperiment_1.7.10  
> [45] GenomicFeatures_1.29.13  
> [46] BiocGenerics_0.23.4  
> [47] lazyeval_0.2.0   
> [48] magrittr_1.5 
> [49] mime_0.5 
> [50] 

Re: [R-pkg-devel] Add appveyor in package with RcppGSL dependency

[Julio Trecenti]

@Dirk, yes, we checked the revdeps but only SimInf seems to have appveyor
working. Thank you for the advices.

@Jenny Thank you! Now we'll do our homework and return with feedback,
hopefully having a complete solution :)

Julio

On Sun, Oct 22, 2017 at 7:51 PM Jennifer Bryan 
wrote:

> On travis, you're installing libgsl0-dev yet I don't see anything similar
> in your appveyor config. If you look at install.out in your AppVeyor build
> artefacts:
>
> https://ci.appveyor.com/project/brsantos/baquantreg/build/artifacts
>
> that seems to be why compilation is failing.
>
> That seems like a lead worth pursuing.
>
> Jenny
>
> * installing *source* package 'baquantreg' ...
> ** libs
> C:/Rtools/mingw_32/bin/g++  -I"c:/R/include" -DNDEBUG -I/include
> -I../inst/include -I"c:/RLibrary/Rcpp/include"
> -I"c:/RLibrary/RcppArmadillo/include" -I"c:/RLibrary/RcppGSL/include"
> -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall  -mtune=core2 -c
> BayesQR.cpp -o BayesQR.o
> In file included from c:/RLibrary/RcppGSL/include/RcppGSL.h:25:0,
>  from BayesQR.cpp:2:
> c:/RLibrary/RcppGSL/include/RcppGSLForward.h:26:29: fatal error:
> gsl/gsl_vector.h: No such file or directory
>  #include 
>  ^
> compilation terminated.
> make: *** [BayesQR.o] Error 1
> Warning: running command 'make -f "Makevars.win" -f
> "c:/R/etc/i386/Makeconf" -f "c:/R/share/make/winshlib.mk"
> SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)'
> SHLIB="baquantreg.dll" OBJECTS="BayesQR.o RcppExports.o TwoPartBayesQR.o
> ZItobitBayesQR.o helper1.o helperAlpha.o helperGIG.o helperLV.o helperRD.o
> helperTN.o spBayesQR.o sppBayesQR.o"' had status 2
> ERROR: compilation failed for package 'baquantreg'
> * removing 'C:/projects/baquantreg/baquantreg.Rcheck/baquantreg'
>
>
>
> On Sun, Oct 22, 2017 at 11:37 AM, Julio Trecenti  > wrote:
>
>> Hi!
>>
>> We are trying to add CI to this package
>> https://github.com/brsantos/baquantreg.
>>
>> We are trying to do add appveyor to work with our package based on @stewid
>> solution here: https://github.com/stewid/SimInf.
>>
>> However, our shell knowledge is limited and we did not manage to do it.
>>
>> Would you have any thoughts on this?
>>
>> Thanks!
>>
>> PS: thanks Dirk for the valuable advices!
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
>
>

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Re: [R-pkg-devel] Fw: [CRAN-pretest-archived] CRAN submission nnfor 0.9

[Thierry Onkelinx]

Dear Nikos,

Your examples are taking too much time. Make them run faster. Or
remove some of them.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Kliniekstraat 25, B-1070 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///


Van 14 tot en met 19 december 2017 verhuizen we uit onze vestiging in
Brussel naar het Herman Teirlinckgebouw op de site Thurn & Taxis.
Vanaf dan ben je welkom op het nieuwe adres: Havenlaan 88 bus 73, 1000 Brussel.

///



2017-10-23 9:09 GMT+02:00 Nikos Kourentzes :
> Dear all,
> I am facing a problem with a package I am trying to submit.
> I am getting three notes, for which I am not sure what could be done.
> Any help is greatly appreciated. Please here for the summary:
> https://win-builder.r-project.org/incoming_pretest/171023_084642_nnfor_09/00check.log
> or look for the details at the forwarded email.
>
> Thank you,Nikos
>  Associate Professor, Dept. Management Science Lancaster University 
> Management School, UK Lancaster Centre for Forecastingblog: 
> http://nikolaos.kourentzes.com twitter: @nkourentzNew Book: Ord, Fildes & 
> Kourentzes (2017) Principles of Business Forecasting (2nd ed.), Wessex.
>
>
> - Forwarded Message -
>  From: "uwe.lig...@r-project.org" 
>  To: nikol...@kourentzes.com
> Cc: cran-submissi...@r-project.org
>  Sent: Monday, 23 October 2017, 7:58
>  Subject: [CRAN-pretest-archived] CRAN submission nnfor 0.9
>
> Dear maintainer,
>
> package nnfor_0.9.tar.gz does not pass the incoming checks automatically, 
> please see the pre-test at:
> 
> Status: 3 NOTEs
>
>
> Please fix all problems and resubmit a fixed version via the webform.
> If you are not sure how to fix the problems shown, please ask for help on the 
> R-package-devel mailing list:
> 
> If you are fairly certain the rejection is a false positive, please reply-all 
> to this message and explain.
>
> More details are given in the directory:
> 
> The files will be removed after roughly 7 days.
>
>
> Best regards,
> CRAN teams' auto-check service
>
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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[R-pkg-devel] Fw: [CRAN-pretest-archived] CRAN submission nnfor 0.9

[Nikos Kourentzes]

Dear all,
I am facing a problem with a package I am trying to submit. 
I am getting three notes, for which I am not sure what could be done. 
Any help is greatly appreciated. Please here for the summary:
https://win-builder.r-project.org/incoming_pretest/171023_084642_nnfor_09/00check.log
or look for the details at the forwarded email. 

Thank you,Nikos
 Associate Professor, Dept. Management Science Lancaster University Management 
School, UK Lancaster Centre for Forecastingblog: http://nikolaos.kourentzes.com 
twitter: @nkourentzNew Book: Ord, Fildes & Kourentzes (2017) Principles of 
Business Forecasting (2nd ed.), Wessex.

 
- Forwarded Message -
 From: "uwe.lig...@r-project.org" 
 To: nikol...@kourentzes.com 
Cc: cran-submissi...@r-project.org
 Sent: Monday, 23 October 2017, 7:58
 Subject: [CRAN-pretest-archived] CRAN submission nnfor 0.9
   
Dear maintainer,
 
package nnfor_0.9.tar.gz does not pass the incoming checks automatically, 
please see the pre-test at:

Status: 3 NOTEs
 

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:

If you are fairly certain the rejection is a false positive, please reply-all 
to this message and explain.
 
More details are given in the directory:

The files will be removed after roughly 7 days.
 
 
Best regards,
CRAN teams' auto-check service



   
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Re: [Bioc-devel] EXTERNAL: Re: IMPCdata push permissions to git repo

[Shepherd, Lori]

What are the packages you are trying to access?


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Carles 
Hernández 
Sent: Friday, October 20, 2017 5:29:36 AM
To: bioc-devel
Subject: EXTERNAL: Re: [Bioc-devel] IMPCdata push permissions to git repo

Hi all,


In my case I got the same error:

$ git fetch --all
Fetching origin
Fetching upstream
The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
established.
ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream


But I'm working with a new data-package, accepted joint with a new package
for the current devel version of Bioconductor.



Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
*ISGlobal*
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22
carles.hernan...@isglobal.org
www.isglobal.org | 
www.carleshf.com

*We are pleased to tell you that after three years of a strategic alliance
between ISGlobal and CREAL, both institutions have merged. The resulting
institution, which retains the ISGlobal name, will build upon the existing
areas of excellence to become a world-class player in research, education
and innovation in Global Health. More info at http://ow.ly/krQd301Nj3w
*

On 19 October 2017 at 13:17, jmason  wrote:

> confirmed, thanks!
>
> On 19/10/2017 12:09, Martin Morgan wrote:
>
>> On 10/19/2017 07:04 AM, jmason wrote:
>>
>>> Hi bioc-devel,
>>>
>>>
>>> I am maintainer of the IMPCdata package.  I can clone the package, but
>>> when I push I get:
>>>
>>> ➜  IMPCdata git:(master) ✗ git push
>>> FATAL: W any packages/IMPCdata jmason DENIED by fallthru
>>> (or you mis-spelled the reponame)
>>> fatal: Could not read from remote repository.
>>>
>>> Please make sure you have the correct access rights
>>> and the repository exists.
>>>
>>> Can you please enable me to push to:
>>>g...@git.bioconductor.org:packages/IMPCdata
>>>
>>
>> you provided the incorrect svn id
>>
>> This has been fixed and you should now have access.
>>
>> Martin
>>
>>
>>>
>>> thanks,
>>> Jeremy
>>>
>>>
>>
>> This email message may contain legally privileged and/or confidential
>> information.  If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited.  If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

--


This message is intended exclusively for its addressee and may contain
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PROTECCIÓN DE DATOS. Sus datos de carácter personal 

Re: [Bioc-devel] EXTERNAL: R version dependence of a new package

[Yaoyong Li]

Dear Lori,

many thanks for your detailed explanations. I think that it makes sense
from Bioconductor maintenance's point of view to require that the R version
of a package should be the same of the R version in a Bioconductor release
which includes the package, because it's the safest option. On the other
hand, I still think that this requirement put some unnecessary limit on the
scope of the R version which a package can be used with. For example, as
the package creator I know that my package can work with R from 2.3.0 and
upward, including the version 3.4 that the current Bioconductor used, then
why should I have to restrict the R version to 3.4 and upward. I guess that
it's the package creator's responsibility to determine which R version(s)
their packages depend on? It seems to me that there is a R version problem
between the package and the Biocondonctor only when the R versions that a
package specifies does not include the R version of a Bioconductor release
which the package is supposed to be included in.

I think that it probably makes no much difference in practice between what
I think it should be and the current practice in Bioconductor, as one can
easily upgrade the R to the latest version with no cost. But I hope you can
see the difference in theory.

Best regards,

Yaoyong

On Fri, Oct 20, 2017 at 1:02 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> We strongly recommend the version of R that is used on our builders when
> building and checking your package.  This is also to ensure that the
> package dependencies are also in a version that is compatible with a new
> package.  We can't guarantee that a package will work with a previous
> version of a dependency so the best practice is to use the current version
> of R as we check against the most recent and current versions of packages
> for the version of R and Bioconductor.  This is also why we have biocValid
> and biocLite to make sure packages are up-to-date and valid for a
> particular version of R and Bioconductor.  Package can change over time and
> cause compatibility issues that are unforseen; R also can change from
> version to version and cause unforseen problems.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of
> Yaoyong Li 
> *Sent:* Friday, October 20, 2017 7:54:16 AM
> *To:* bioc-devel@r-project.org
> *Subject:* EXTERNAL: [Bioc-devel] R version dependence of a new package
>
> Hello,
>
> may I ask a question about the R version dependence?
>
> Currently I am trying to submit a package to Bioconductor repository. When
> my package was built at bioconductor.org, I got a warning message
>
> "* WARNING: Update R version dependency from 2.3.0 to 3.4."
>
> So I changed the R dependency to 3.4 in my DESCRIPTION file, and
> consequently the warning message disappeared. However, as one result of the
> change, my package cannot be loaded and run in R whose version is earlier
> than 3.4. On the other hand, my package actually doesn't need the R version
> >= 3.4. For example, it works perfectly with R version 3.2.2 which was
> installed in my computer. S my question is why the package builder at
> bioconductor.org wanted my package to update the R version to 3.4.
>
> Best regards,
>
> Yaoyong
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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Re: [Rd] Illegal Logical Values

[Tomas Kalibera]

On 10/21/2017 04:14 PM, Radford Neal wrote:

On Fri, 2017-10-20 at 14:01 +, brodie gaslam via R-devel wrote:

I'm thinking of this passage:


Logical values are sent as 0 (FALSE), 1 (TRUE) or INT_MIN =
-2147483648 (NA, but only if NAOK is true), and the compiled code
should return one of these three values. (Non-zero values other
than INT_MIN are mapped to TRUE.)

The parenthetical seems to suggest that something like 'LOGICAL(x)[0]
= 2;' will be treated as TRUE, which it sometimes is, and sometimes
isn't:

From: Martyn Plummer 
The title of Section 5.2 is "Interface functions .C and .Fortran" and
the text above refers to those interfaces. It explains how logical
vectors are mapped to C integer arrays on entry and back again on exit.

This does work as advertised.


Not always.  As I reported on bugzilla three years ago (PR#15878), it
only works if the logical argument does not have to be copied.  The
bug has been fixed in pqR since pqR-2014-09-30.

Radford Neal

Thanks, that's indeed a bug - now fixed in 73583.
Tomas



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Re: [Bioc-devel] Package failure due to GenomicFeatures update

[bora.u...@mdc-berlin.de]

Thank you Herve! Then, I will pull the code from github to update my code, too. 

Hopefully my package will also go through by 24th :)

Best,
Bora


From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Monday, October 23, 2017 6:17 AM
To: Uyar, Bora; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Package failure due to GenomicFeatures update

Hi Bora,

I just fixed this in GenomicFeatures 1.29.15. The error on the build
report won't clear until Tuesday Oct 24 though.

Cheers,
H.


On 10/22/2017 02:59 PM, bora.u...@mdc-berlin.de wrote:
> Hi,
>
> I am the maintainer of the RCAS package. Currently, my package build report 
> shows errors related to the latest commit to GenomicFeatures package (See 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_GenomicFeatures_commit_22b2ea0a81bc064b8554400ce8f7e13e2c833d38=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q=bz4mjLoa7FjycKUx_wCB7Ic1b2nOpTJt0J69fXSaasQ=).
>  GenomicFeatures is showing errors because of the same reason.
>
> This is an excerpt from the GenomicFeatures build report:
> "# Creation time: 2017-10-22 00:29:43 -0400 (Sun, 22 Oct 2017)
>
> # GenomicFeatures version at creation time: 1.29.14
> # RSQLite version at creation time: 2.0
> # DBSCHEMAVERSION: 1.2
>>
>> ## Reverse operation:
>> gr2 <- asGFF(txdb)
>>
>> ## Sanity check:
>> stopifnot(identical(as.list(txdb), as.list(makeTxDbFromGRanges(gr2
> Error in .get_cds_IDX(type, phase) :
>when 'gr' contains CDS features, it must have a "phase" metadata column
>and the phase must be 0, 1, or 2, for all the CDS features
> Calls: stopifnot ... identical -> as.list -> makeTxDbFromGRanges -> 
> .get_cds_IDX
> Execution halted”
>
> The build report for RCAS shows the same error. However, I cannot fix this 
> problem because I can only install GenomicFeatures version 1.29.13, but the 
> bioc-build system is using GenomicFeatures v1.29.14.
>
> Do you know when this will be solved?
>
> Best,
> Bora
>
> _
>
> Dr. Bora Uyar
>
> Bioinformatics Scientist
> Scientific Bioinformatics Platform
> The Berlin Institute for Medical Systems Biology (BIMSB)
> Max Delbrueck Center (MDC) for Molecular Medicine
>
> Robert-Rössle-Str. 10, 13125, Berlin, Germany
> Building 89, Room 1.08
>
> web: 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinformatics.mdc-2Dberlin.de_team.html-23bora-2Duyar-2Dphd=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q=9gkC_jhjUe4nWpERCOvchonLiz90IwwrayNY4zEsYSE=
> email: bora.u...@mdc-berlin.de
> office tel: +49 30 9406 1802
>
>
>   [[alternative HTML version deleted]]
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Re: [Bioc-devel] IMPCdata push permissions to git repo

[Carles Hernández]

Hi all,


In my case I got the same error:

$ git fetch --all
Fetching origin
Fetching upstream
The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
established.
ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream


But I'm working with a new data-package, accepted joint with a new package
for the current devel version of Bioconductor.



Carles Hernandez-Ferrer
Bioinformatic Analyst / PhD Student
*ISGlobal*
Barcelona Institute for Global Health - Campus Mar
Barcelona Biomedical Research Park (PRBB) (office 183.01 A)
Doctor Aiguader, 88
08003 Barcelona, Spain
Tel. +34 93 214 73 22
carles.hernan...@isglobal.org
www.isglobal.org | www.carleshf.com

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On 19 October 2017 at 13:17, jmason  wrote:

> confirmed, thanks!
>
> On 19/10/2017 12:09, Martin Morgan wrote:
>
>> On 10/19/2017 07:04 AM, jmason wrote:
>>
>>> Hi bioc-devel,
>>>
>>>
>>> I am maintainer of the IMPCdata package.  I can clone the package, but
>>> when I push I get:
>>>
>>> ➜  IMPCdata git:(master) ✗ git push
>>> FATAL: W any packages/IMPCdata jmason DENIED by fallthru
>>> (or you mis-spelled the reponame)
>>> fatal: Could not read from remote repository.
>>>
>>> Please make sure you have the correct access rights
>>> and the repository exists.
>>>
>>> Can you please enable me to push to:
>>>g...@git.bioconductor.org:packages/IMPCdata
>>>
>>
>> you provided the incorrect svn id
>>
>> This has been fixed and you should now have access.
>>
>> Martin
>>
>>
>>>
>>> thanks,
>>> Jeremy
>>>
>>>
>>
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Re: [Bioc-devel] Superscript in BiocStyle 2.5.39 html document seems to be not working

[Andrzej Oleś]

Hi Stefan,

thanks for reporting this. Should be fixed in BiocStyle 2.5.42.

Best,
Andrzej

On Mon, Oct 23, 2017 at 7:55 AM, Stefan Mutter 
wrote:

> Hi,
>
>
> I am currently writing a vignette for a package that we want to submit to
> Bioconductor. I am using BiocStyle 2.5.39 and create a html_document.
>
>
> In the vignette, I want to use superscript for meter square and I used the
> notation m^2^. However, the html output does not produce a superscript.
> Subscripting works. I have attached an example and added my sessionInfo
> below. I was wondering whether I am doing something wrong or if there is a
> problem with the style?
>
>
> Thanks a lot for your help.
>
>
> Cheers,
>
> Stefan
>
>
> Session Info:
>
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
>
> Matrix products: default
> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/
> A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods
> [7] base
>
> other attached packages:
> [1] Numero_0.99.0
>
> loaded via a namespace (and not attached):
>  [1] compiler_3.4.1   backports_1.1.1  BiocStyle_2.5.39 magrittr_1.5
>  [5] rprojroot_1.2htmltools_0.3.6  tools_3.4.1  yaml_2.1.14
>  [9] Rcpp_0.12.13 stringi_1.1.5rmarkdown_1.6knitr_1.17
> [13] stringr_1.2.0digest_0.6.12evaluate_0.10.1 ?
>
>
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