[Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
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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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
On 10/23/2017 09:47 AM, 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...
A little bit more helpfully, at least on Linux R CMD build evaluates the
script R_HOME/bin/build, which launches R as
echo 'tools:::.build_packages()' | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" --no-restore --slave --args ${args}
It's actually very tedious to figure out how the R process that builds
the vignette is launched.
Martin
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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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
> 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
On 10/23/2017 09:59 AM, Elizabeth Purdom wrote:
On Oct 23, 2017, at 3:47 PM, Martin Morgan
mailto:martin.mor...@roswellpark.org>>
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?
>
> 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?
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,
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Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
FYI, that seems to be a locale issue, as the locale defines the sort order.
The first one is sorting alphabetically in a case-insensitive manner, eg
aAbBcC etc, the second is sorting in a case sensitive manner, where capital
letters all come before lower-case letters, e.g. ABC...YZabc...
You can see what locale you're in via Sys.getlocale() or see it in your
sessionInfo under the locale heading.
Best,
~G
On Mon, Oct 23, 2017 at 1:06 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 <
> martin.mor...@roswellpark.org> wrote:
> >
> > On 10/23/2017 09:59 AM, Elizabeth Purdom wrote:
> >>> On Oct 23, 2017, at 3:47 PM, Martin Morgan <
> martin.mor...@roswellpark.org >
> 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
Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
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.
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 mailto:martin.mor...@roswellpark.org>> 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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Bioc-devel@r-project.o
Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
Hi Hervé, Thanks for the suggestion. I actually checked first that they were
the same length, but identical() would be safer and simplify my code. Elizabeth
> On Oct 23, 2017, at 10:40 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.
>
> 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)
>>
Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
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)
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
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
Re: [Bioc-devel] How to recreate R CMD BUILD environment in interactive session?
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
mailto:martin.mor...@roswellpark.org>> 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
