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Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 16 Sep 2021 14:05:49 +0200
Description: Despite the fact that r-bioc-org.hs.eg.db is explicitly in
Test-Depends the test suite fails with:
> AnnotationDbi:::.test()
Loading required package: RSQLite
Loading required package: GO.db
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'dbconn': object 'org.Hs.eg.db' not found
'select()' returned many:many mapping between keys and columns
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'x' not found
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'org.Hs.eg.db' not found
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': unable to find an inherited method for function ‘keys’ for signature ‘"standardGeneric"’
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 's' not found
Timing stopped at: 0 0 0
Error in quiet(select(x, keys, cols, keytype = "ENTREZID")) :
could not find function "quiet"
Timing stopped at: 0 0 0
Error in quiet(select(x, sym, "PFAM", keytype = "ALIAS")) :
could not find function "quiet"
Timing stopped at: 0.001 0 0.001
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'hgu95av2.db' not found
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'x' not found
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'hgu95av2.db' not found
'select()' returned 1:1 mapping between keys and columns
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 'org.Hs.eg.db' not found
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 'org.Hs.eg.db' not found
Timing stopped at: 0 0 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 'org.Hs.eg.db' not found
RUNIT TEST PROTOCOL -- Thu Sep 16 12:14:58 2021
***********************************************
Number of test functions: 16
Number of errors: 13
Number of failures: 0
1 Test Suite :
AnnotationDbi RUnit Tests - 16 test functions, 13 errors, 0 failures
ERROR in test_dbconn_and_dbfile: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'dbconn': object 'org.Hs.eg.db' not found
ERROR in test_select_NAsInNAsOut: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'x' not found
ERROR in test_select_XtoX: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'org.Hs.eg.db' not found
ERROR in test_select10: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': unable to find an inherited method for function ‘keys’ for signature ‘"standardGeneric"’
ERROR in test_select11: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 's' not found
ERROR in test_select12: Error in quiet(select(x, keys, cols, keytype = "ENTREZID")) :
could not find function "quiet"
ERROR in test_select13: Error in quiet(select(x, sym, "PFAM", keytype = "ALIAS")) :
could not find function "quiet"
ERROR in test_select14: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'hgu95av2.db' not found
ERROR in test_select15: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'x' not found
ERROR in test_select16: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'select': object 'hgu95av2.db' not found
ERROR in test_select7: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 'org.Hs.eg.db' not found
ERROR in test_select8: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 'org.Hs.eg.db' not found
ERROR in test_select9: Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': error in evaluating the argument 'x' in selecting a method for function 'keys': object 'org.Hs.eg.db' not found
see:
https://salsa.debian.org/r-pkg-team/r-bioc-annotationdbi/-/jobs/1952020#L1174
@@ -198,115 +198,6 @@
checkIdentical(c("UNIPROT","SYMBOL","PATH"), colnames(res))
}
-test_select10 <- function(){
- ## What about when we have to get data from Arabidopsis using various
- ## keytypes?
- cols <- c("SYMBOL","CHR")
- keys <- head(keys(t,"TAIR"))
- res <- quiet(select(t, keys, cols, keytype="TAIR"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("TAIR","SYMBOL","CHR"), colnames(res))
-
- keys <- head(keys(t,"ENTREZID"))
- res <- quiet(select(t, keys, cols, keytype="ENTREZID"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("ENTREZID","SYMBOL","CHR"), colnames(res))
-
- keys=head(keys(t,"REFSEQ"))
- res <- quiet(select(t, keys, cols , keytype="REFSEQ"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("REFSEQ","SYMBOL","CHR"), colnames(res))
-}
-
-test_select11 <- function(){
- ## how about different keytypes for yeast?
- keys <- head(keys(s, "REFSEQ"))
- cols <- c("CHR","PFAM")
- res <- quiet(select(s, keys, cols, keytype="REFSEQ"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("REFSEQ","CHR","PFAM"), colnames(res))
-
- keys <- head(keys(s, "ENTREZID"))
- cols <- c("CHR","PATH")
- res <- quiet(select(s, keys, cols, keytype="ENTREZID"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("ENTREZID","CHR","PATH"), colnames(res))
-
- keys <- head(keys(s, "ORF"))
- cols <- c("CHR","SGD")
- res <- select(s, keys, cols, keytype="ORF")
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("ORF","CHR","SGD"), colnames(res))
-
- ## And if you flip things the other way
- cols <- c("SGD","CHR")
- res <- select(s, keys, cols, keytype="ORF")
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("ORF","SGD","CHR"), colnames(res))
-
- ## Martins bug discoveries
- keys <- keys(s, keytype="GENENAME")
- checkTrue(length(keys) > 0)
- checkTrue(is.character(keys))
- keys <- keys(s, keytype="CHRLOC")
- checkTrue(length(keys) > 0)
- checkTrue(is.character(keys))
-
- res <- select(s, "YAL003W", "GENENAME")
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("ORF","SGD","GENENAME"), colnames(res))
-
- ## This works but is slow (therefore it's tested elsewhere)
- ## res <- select(s, keys="YAL003W", columns(s))
-
- ## Another test to make sure we can join up to ORF properly
- keys <- keys(s,"ENTREZID")
- res <- select(s, columns="ORF", keys=keys, keytype="ENTREZID")
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==3)
- checkIdentical(c("ENTREZID","ORF","SGD"), colnames(res))
-}
-
-test_select12 <- function(){
- ## what happens when we use GO as an ID?
- keys <- "1"
- cols <- c("GO","ENTREZID")
- res <- quiet(select(x, keys, cols, keytype="ENTREZID"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==4)
- checkIdentical(c("ENTREZID","GO","EVIDENCE","ONTOLOGY"), colnames(res))
-
- keys <- "GO:0000018"
- cols <- c("GO","ENTREZID")
- res <- quiet(select(x, keys, cols, keytype="GO"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==4)
- checkIdentical(c("GO","EVIDENCE","ONTOLOGY","ENTREZID"), colnames(res))
-
- keys <- "GO:0000023"
- cols <- c("GO","ENTREZID")
- res <- quiet(select(t, keys, cols, keytype="GO"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==4)
- checkIdentical(c("GO","EVIDENCE","ONTOLOGY","ENTREZID"), colnames(res))
-
- keys <- "GO:0000023"
- cols <- c("ENTREZID","TAIR","GO")
- res <- quiet(select(t, keys, cols, keytype="GO"))
- checkTrue(dim(res)[1]>0)
- checkTrue(dim(res)[2]==5)
- checkIdentical(c("GO","EVIDENCE","ONTOLOGY","ENTREZID","TAIR"),
- colnames(res))
-}
-
test_select13 <- function(){
## what happens with dropping unwanted rows?
sym <- "ITGA7"
@@ -334,6 +225,7 @@
}
}
+
## NA values are now OK for legacySelect (in order to be consistent
## with other select methods which have greater respect for incoming NA values
test_select_NAsInNAsOut <- function(){
|
