Closed alexg9010 closed 7 months ago
The build failed during rebuilding the vignette, failing at the following chunk:
The error message "Stoping here." comes from the readMethylDB
function, indicating the tabix file contains no header:
Running the code chunk in R version 4.3.1 (2023-06-16) worked without any problems, but running in R Under development (unstable) (2024-01-09 r85796) failed:
> data(methylKit)
baseDB.obj <- makeMethylDB(methylBase.obj,"my/path")
> baseDB.obj <- makeMethylDB(methylBase.obj,"my/path")
mydbpath <- getDBPath(baseDB.obj)
rm(baseDB.obj)
methylKit:::checkTabixHeader(mydbpath)
readMethylDB(mydbpath)
compressing the file with bgzip...
making tabix index...
flatfile located at: my/path/methylBase_949590f63.txt.bgz
> mydbpath <- getDBPath(baseDB.obj)
> rm(baseDB.obj)
>
> methylKit:::checkTabixHeader(mydbpath)
Could not read header of file my/path/methylBase_949590f63.txt.bgz
NULL
> readMethylDB(mydbpath)
No Tabix Header Found,
Please provide tabix file with header created from methylKit version >=1.13.1.
Error in readMethylDB(mydbpath) : Stopping here.
>
Further inspecting the checkTabixHeader
function, we see that another function readTabixHeader
is called.
Running this function directly, we see that isEmpty
at line 391 is failing:
> methylKit:::readTabixHeader(mydbpath)
Error in FUN(X[[i]], ...) :
isEmpty() is not defined for objects of class NULL
On 11.01.2024, 17:42 we received a mail from bioconductor that the build failed.
The build failed for all platforms and the logs show the same message: