On 03/30/2017 05:21 AM, Sokratis Kariotis wrote:
Hey all,
Thanks for the input! I followed Marcel's advice and included the library
in my vignette. Also, I replaced lazyData with a datalist. The datalist
file includes "compressed_result : result" which is in turn loaded in the
vignette using "data(compressed_result)". However, I got:
Warning in data(compressed_result) :
data set ‘compressed_result’ not found
Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics:
chunk 1
Error in assays(result) : object 'result' not found
I Stangle'd the vignette
cd pathprintGEOData/vignettes
R CMD Stangle usingPathprintGEOData.Rnw
and then walked through the lines of R code. I got to
> data(compressed_result)
Warning message:
In data(compressed_result) : data set 'compressed_result' not found
The data 'compressed_result' is not found, because it is in the
pathprintGEOData package, and the pathprintGEOData package is not on the
search path.
> search()
[1] ".GlobalEnv" "package:SummarizedExperiment"
[3] "package:DelayedArray" "package:matrixStats"
[5] "package:Biobase" "package:GenomicRanges"
[7] "package:GenomeInfoDb" "package:IRanges"
[9] "package:S4Vectors" "package:BiocGenerics"
[11] "package:parallel" "package:stats4"
[13] "package:pathprint" "ESSR"
[15] "package:BiocInstaller" "package:stats"
[17] "package:graphics" "package:grDevices"
[19] "package:utils" "package:datasets"
[21] "package:methods" "Autoloads"
[23] "package:base"
It is not on the search path because, originally, pathprint had Depends:
pathprintGEOData, but that was modified, as you know, to Suggests:
pathprintGEOData, to avoid circular dependencies that thwart our build
system. So previously library(pathprint) was enough to make the data
available, but now you must either load the package
library(pathprintGEOData)
data(compressed_result)
or tell data() where the data set is
data(compressed_result, package="pathprintGEOData")
One would still like to use an informative name for the data (first
argument of data) and presumably an identical name for the object that
is loaded.
Martin
So the dataset is still not loaded (again, these errors did not exist
prior to package acceptance). I have been using devtools to
build/check the package (since the github issue was closed) and these
warnings/errors dont show up, which imakes it difficult for me to fix
them. Thanks again for any input!
Regards,
Sokratis
On 27 March 2017 at 19:58, Michael Lawrence <lawrence.mich...@gene.com>
wrote:
Actually, I don't see where the package itself is loaded in the
vignette. If it were, this error would not occur.
Unsurprisingly, I get this when trying to run the vignette code:
Warning message:
In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found
I noticed that pathprintGEOData just provides compressed_result, not
the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
You might also consider turning off lazy data and using a datalist
file for that package since the file is somewhat large.
I also think that the datalist file for pathprint is out of date.
Michael
On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
<marcel.ramospe...@roswellpark.org> wrote:
Hi Sokratis,
You can resolve this issue by moving `SummarizedExperiment` to the
Suggests field and
including a `library(SummarizedExperiment)` call in your vignette.
Best regards,
Marcel
On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
<s.kario...@sheffield.ac.uk <mailto:s.kario...@sheffield.ac.uk>> wrote:
Hey,
I have submitted the package pathprintGEOData, which got accepted,
but the
build/check report is now producing the following error:
*Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
diagnostics: chunk 1 Error in assays(result) : could not find
function
"assays"*
*assays *is a function from the SummarizedExperiment package which I
have
added on my Depends in DESCRIPTION. This error was not present during
building/checking before this package was accepted. Besides adding
SummarizedExperiment
to my Imports what else might be responsible for that error?
Thank you for any help on the matter!
-Sokratis
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