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

2017-10-23 Thread 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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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

2017-10-23 Thread 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
> 
> 
> 
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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

2017-10-23 Thread 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?

2017-10-23 Thread 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?

2017-10-23 Thread 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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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

2017-10-23 Thread 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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