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
<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
<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 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.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=3O1928D4_siHrVAZeKxKOXOeKeLFslkcQGPRdXb_YSk&s=_-4eL50gxWxWGFjisSH08OY5LgD1bmPVPvowL13m7_E&e=
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
