- HDF5Array and beachmat in Imports rather than Suggests
... | ... |
@@ -8,7 +8,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"), |
8 | 8 |
email = "kasperdanielhansen@gmail.com"), |
9 | 9 |
person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com")) |
10 | 10 |
Depends: |
11 |
- R (>= 3.3), |
|
11 |
+ R (>= 3.5), |
|
12 | 12 |
methods, |
13 | 13 |
BiocGenerics, |
14 | 14 |
GenomicRanges (>= 1.29.14), |
... | ... |
@@ -25,25 +25,25 @@ Imports: |
25 | 25 |
data.table, |
26 | 26 |
S4Vectors, |
27 | 27 |
R.utils (>= 2.0.0), |
28 |
- DelayedMatrixStats (>= 1.1.12), |
|
28 |
+ DelayedMatrixStats (>= 1.3.1), |
|
29 | 29 |
permute, |
30 | 30 |
limma, |
31 |
- DelayedArray (>= 0.5.34), |
|
31 |
+ DelayedArray (>= 0.7.6), |
|
32 | 32 |
Rcpp, |
33 | 33 |
BiocParallel, |
34 | 34 |
readr, |
35 | 35 |
BSgenome, |
36 | 36 |
Biostrings, |
37 |
- utils |
|
37 |
+ utils, |
|
38 |
+ HDF5Array, |
|
39 |
+ beachmat |
|
38 | 40 |
Suggests: |
39 | 41 |
testthat, |
40 | 42 |
bsseqData, |
41 | 43 |
BiocStyle, |
42 | 44 |
rmarkdown, |
43 | 45 |
knitr, |
44 |
- beachmat, |
|
45 | 46 |
Matrix, |
46 |
- HDF5Array, |
|
47 | 47 |
doParallel |
48 | 48 |
Collate: |
49 | 49 |
utils.R |
... | ... |
@@ -3,6 +3,14 @@ |
3 | 3 |
## |
4 | 4 |
|
5 | 5 |
import(methods) |
6 |
+import(S4Vectors) |
|
7 |
+import(IRanges) |
|
8 |
+import(GenomicRanges) |
|
9 |
+import(SummarizedExperiment) |
|
10 |
+import(DelayedArray) |
|
11 |
+import(HDF5Array) |
|
12 |
+import(BiocParallel) |
|
13 |
+import(limma) |
|
6 | 14 |
importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames", |
7 | 15 |
"combine", "density", "intersect", "lapply", "ncol", |
8 | 16 |
"nrow", "order", "paste", "pmax", "pmin", "rbind", |
... | ... |
@@ -18,9 +26,7 @@ import(parallel) |
18 | 26 |
importFrom(locfit, "locfit", "lp") |
19 | 27 |
importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2", |
20 | 28 |
"rowSums2", "rowMeans2", "rowAlls") |
21 |
-import(IRanges) |
|
22 |
-import(GenomicRanges) |
|
23 |
-import(SummarizedExperiment) |
|
29 |
+ |
|
24 | 30 |
importFrom(scales, "alpha") |
25 | 31 |
importClassesFrom(Biobase, "AnnotatedDataFrame") |
26 | 32 |
importMethodsFrom(Biobase, "annotatedDataFrameFrom", |
... | ... |
@@ -31,15 +37,11 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", |
31 | 37 |
"seqinfo<-", "seqnames", "seqnames<-", "seqlevels", |
32 | 38 |
"seqlevels<-", "sortSeqlevels") |
33 | 39 |
importFrom(GenomeInfoDb, "Seqinfo") |
34 |
-import(S4Vectors) |
|
35 | 40 |
importFrom(gtools, "combinations") |
36 | 41 |
# NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor, |
37 | 42 |
# e.g., shift(). If new ones are discovered, add them to this list. |
38 | 43 |
import(data.table, except = c(shift, first, second)) |
39 |
-import(limma) |
|
40 | 44 |
importFrom(permute, "shuffleSet", "how") |
41 |
-import(DelayedArray) |
|
42 |
-import(BiocParallel) |
|
43 | 45 |
importFrom(readr, "cols", "cols_only", "col_character", "col_integer", |
44 | 46 |
"col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv") |
45 | 47 |
importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement") |
... | ... |
@@ -226,11 +226,7 @@ BSmooth <- function(BSseq, |
226 | 226 |
se.coef_sink <- NULL |
227 | 227 |
sink_lock <- NULL |
228 | 228 |
} else if (BACKEND == "HDF5Array") { |
229 |
- if (!requireNamespace("HDF5Array", quietly = TRUE)) { |
|
230 |
- stop("HDF5Array package required for HDF5Array backend", |
|
231 |
- call. = FALSE) |
|
232 |
- } |
|
233 |
- coef_sink <- HDF5Array::HDF5RealizationSink( |
|
229 |
+ coef_sink <- HDF5RealizationSink( |
|
234 | 230 |
dim = dim(M), |
235 | 231 |
# NOTE: Never allow dimnames. |
236 | 232 |
dimnames = NULL, |
... | ... |
@@ -241,13 +241,7 @@ |
241 | 241 |
Cov_sink <- NULL |
242 | 242 |
sink_lock <- NULL |
243 | 243 |
} else if (BACKEND == "HDF5Array") { |
244 |
- if (!requireNamespace("HDF5Array", quietly = TRUE)) { |
|
245 |
- stop("HDF5Array package required for HDF5Array backend", |
|
246 |
- call. = FALSE) |
|
247 |
- } |
|
248 |
- # TODO: HDF5Array is only in suggests, so need to qualify the use of |
|
249 |
- # HDF5RealizationSink() |
|
250 |
- M_sink <- HDF5Array::HDF5RealizationSink( |
|
244 |
+ M_sink <- HDF5RealizationSink( |
|
251 | 245 |
dim = c(ans_nrow, ans_ncol), |
252 | 246 |
# NOTE: Never allow dimnames. |
253 | 247 |
dimnames = NULL, |