Can't load an example regionDB.
lining-yuan opened this issue · comments
No problem with the path.
regionDB = loadRegionDB(dbLocation=dbPath)
Reading collection annotations:
ucsc_example: found collection annotation:C:/Program Files/R/R-3.6.0/library/LOLA/extdata/hg19/ucsc_example/collection.txt
Reading region annotations...
C:/Program Files/R/R-3.6.0/library/LOLA/extdata/hg19//ucsc_example/regions
In 'ucsc_example', found index file:C:/Program Files/R/R-3.6.0/library/LOLA/extdata/hg19/ucsc_example/index.txt
Collection: ucsc_example. Creating size file...
Error in system(paste("wc -l ", filename), intern = TRUE) :
'wc' not found
In addition: Warning message:
In readRegionSetAnnotation(dbLocation, collections) :
You don't have simpleCache installed, so you won't be able to cache the
regionDB after reading it in. Install simpleCache to speed up later database
loading.
Hi all,
I have the same problem as OP. First I was trying to make my own custom regionsDB, but as that didn't work I tried the one provided with the package, but that didn't work either.
dbPath = system.file("extdata", "hg19", package="LOLA")
RegionsDB = loadRegionDB(dbPath)
Reading collection annotations:
ucsc_example: found collection annotation:C:/Documents/R/R-3.6.2/library/LOLA/extdata/hg19/ucsc_example/collection.txt
Reading region annotations...
::Creating cache:: C:/Documents/R/R-3.6.2/library/LOLA/extdata/hg19/ucsc_example//ucsc_example_files.RData
C:/Documents/R/R-3.6.2/library/LOLA/extdata/hg19//ucsc_example/regions
In 'ucsc_example', found index file:C:/Documents/R/R-3.6.2/library/LOLA/extdata/hg19/ucsc_example/index.txt
Collection: ucsc_example. Creating size file...
Error in system(paste("wc -l ", filename), intern = TRUE) :
'wc' not found
In addition: Warning message:
In dir.create(cacheDir, recursive = TRUE) :
'C:\Documents\R\R-3.6.2\library\LOLA\extdata\hg19\ucsc_example' already exists
It seems wc shouldn't even be needed if the collectionAnnoDT[,size] was assigned correctly.
on line 218 of loadRegionDB.R:
collectionAnnoDT[groupSizes, size:=size_int]
Here is my sessionInfo():
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=Finnish_Finland.1252 LC_CTYPE=Finnish_Finland.1252 LC_MONETARY=Finnish_Finland.1252
[4] LC_NUMERIC=C LC_TIME=Finnish_Finland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] LOLA_1.16.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 IRanges_2.20.2 bitops_1.0-6 GenomeInfoDb_1.22.0
[5] plyr_1.8.5 magrittr_1.5 stats4_3.6.2 stringi_1.4.5
[9] zlibbioc_1.32.0 reshape2_1.4.3 XVector_0.26.0 data.table_1.12.8
[13] S4Vectors_0.24.3 tools_3.6.2 stringr_1.4.0 RCurl_1.98-1.1
[17] parallel_3.6.2 compiler_3.6.2 simpleCache_0.4.1 BiocGenerics_0.32.0
[21] GenomicRanges_1.38.0 GenomeInfoDbData_1.2.2
Any help would be appreciated!
-Konsta
Are you by chance using windows? It doesn't have wc and so that causes problems. I fixed this in this commit but maybe I forgot to push this to bioc -- can you try with the version on github?
you can install it with devtools::install_github("nsheff/LOLA")
let me know if that solves it and if so I will push the update to bioconductor...
Hello, Nathan
I'm indeed using Windows. I tested to installing from devtools, and now it seems to be working.
regionDB = loadRegionDB(dbPath)
Reading collection annotations:
ucsc_example: found collection annotation:C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/collection.txt
Reading region annotations...
::Creating cache:: C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example//ucsc_example_files.RData
C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19//ucsc_example/regions
In 'ucsc_example', found index file:C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/index.txt
Collection: ucsc_example. Creating size file...
ucsc_example
::Creating cache:: C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/ucsc_example.RData
Reading 5 files...
1: C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/regions/cpgIslandExt.bed
2: C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/regions/laminB1Lads.bed
3: C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/regions/numtSAssembled.bed
4: C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed
5: C:/Users/Documents/R/win-library/3.6/LOLA/extdata/hg19/ucsc_example/regions/vistaEnhancers_colNames.bed
Warning message:
In dir.create(cacheDir, recursive = TRUE) :
'C:\Users\Documents\R\win-library\3.6\LOLA\extdata\hg19\ucsc_example' already exists
Like you see, I still get that one warning, but the database gets build.
Thank you!
-Konsta