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

--- a/inst/unitTests/test_select.R
+++ b/inst/unitTests/test_select.R
@@ -70,232 +70,14 @@ test_select5 <- function(){
   checkIdentical(c("GOID","TERM","ONTOLOGY","DEFINITION"), colnames(res))
 }
 
-test_select7 <- function(){  
-  cols <- c("SYMBOL","ENTREZID") ## 1st of all cols should be 1:1 cols
-  keys <- head(keys(org.Hs.eg.db),n=3)
-  keys <- c(1, keys, keys)
-  res <- select(org.Hs.eg.db, keys, cols)
-  checkTrue(class(res) =="data.frame")
-  checkIdentical(keys, as.character(t(res$ENTREZID)))
-}
-
-test_select8 <- function(){
-  cols <- c("ENTREZID")
-  keys <- head(keys(org.Hs.eg.db),n=3)
-  res <- select(org.Hs.eg.db, keys, cols)
-  checkTrue(class(res) =="data.frame")
-  checkTrue(dim(res)[2] ==1)  
-  checkIdentical(as.character(keys), as.character(t(res$ENTREZID)))
-}
-
-test_select9 <- function(){  
-  ## What about when we need to throw away extra cols?
-  uniKeys <- head(keys(org.Hs.eg.db, keytype="UNIPROT"))
-  cols <- c("SYMBOL", "PATH")
-  res <- quiet(select(org.Hs.eg.db, keys=uniKeys, columns=cols, keytype="UNIPROT"))
-  checkTrue(class(res) =="data.frame")
-  checkTrue(dim(res)[2] ==3)  
-  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"
-  res <- quiet(select(x, sym, "PFAM", keytype="ALIAS"))
-  checkTrue(dim(res)[1]>0)
-  checkTrue(dim(res)[2]==2)
-  ## make sure no NAs are in res$PFAM
-  checkTrue(length(res$PFAM)== length(res$PFAM[!is.na(res$PFAM)]))
-}
-
-test_select14 <- function(){
-  ## what happens when there are no results AT ALL? (should be all NAs)
-  keys <- c("1001_at","1006_at","1007_s_at")
-  res <- select(hgu95av2.db, keys, "PATH", keytype="PROBEID")
-  checkTrue(dim(res)[1]>0)
-  checkTrue(dim(res)[2]==2)
-  ## make sure all of res$PATH ARE NAs
-  ## If this part fails it is a warning that the test is no longer valid,
-  ## which would happen if some of these IDs were to be further annotated for
-  ## PATH (unlikely since PATH is basically dead for this repos)
-  checkTrue(length(res$PATH)== length(res$PATH[is.na(res$PATH)]))
-}
-
-test_select15 <- function(){
-    ## Another bug that seems to happen in post-processing...
-    ## the code that resolves duplicated values is going a bit insane...
-    ## (IOW .replaceValues())
-    if(!all(.Platform$OS.type == "windows", .Platform$r_arch == "i386")){
-        res <- select(x, keys="100008586", columns(x)) 
-        checkTrue(dim(res)[1]>0)
-        checkTrue(dim(res)[2]==26)
-        exp <- c("ENTREZID", "ACCNUM", "ALIAS", "ENSEMBL", "ENSEMBLPROT",
-                 "ENSEMBLTRANS", "ENZYME", "EVIDENCE", "EVIDENCEALL",
-                 "GENENAME", "GENETYPE", "GO", "GOALL", "IPI", "MAP", "OMIM", 
-                 "ONTOLOGY", "ONTOLOGYALL", "PATH", "PFAM", "PMID", "PROSITE",
-                 "REFSEQ", "SYMBOL", "UCSCKG", "UNIPROT")
-        checkIdentical(exp, colnames(res))
-    }
-}
-
-
-test_select16 <- function(){
-    ## What happens if we ask for probes back...
-    ## (and pass in something else as a key)
-    sk = c( 'MAPK3','TIE1' )
-    res <- select(hgu95av2.db, keys=sk, columns = c("PROBEID"), keytype="SYMBOL")
-    checkTrue(dim(res)[1]>0)
-    checkTrue(dim(res)[2]==2)
-    checkIdentical(c('SYMBOL','PROBEID'), colnames(res))
-}
-
 
 ## 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(){
-    ## NAs in should result in NAs out.
-    ## Not that we like NAs but just because if possible: we want to
-    ## preserve the geometry of the keys coming in.
-    k=c('1', NA, NA, '10');
-    res <- select(x, k, 'SYMBOL', 'ENTREZID')
-    checkTrue(dim(res)[1]==4) 
-    checkTrue(dim(res)[2]==2)
-    checkIdentical(c('ENTREZID','SYMBOL'), colnames(res))
-    checkIdentical(k, res$ENTREZID)
-    checkTrue(any(is.na(res$SYMBOL)))
-}
 
 
 ## Some new messages from AnnotationDbi:::.generateExtraRows()
 ## where I am calling it internally...
 ## these tests just make sure the right kinds of messages are being sent...
-test_select_XtoX <- function(){
-    k=c('1','1', NA, '10');
-    res <- tryCatch(select(org.Hs.eg.db, k, 'SYMBOL', 'ENTREZID'),
-                    message = function(x){return(x)})
-    checkTrue(grepl('many:1', res$message))
-    
-    res <- tryCatch(select(org.Hs.eg.db, '1', 'ALIAS', 'ENTREZID'),
-                    message = function(x){return(x)})
-    checkTrue(grepl('1:many', res$message))
-
-    res <- tryCatch(select(org.Hs.eg.db, k, 'ALIAS', 'ENTREZID'),
-                    message = function(x){return(x)})
-    checkTrue(grepl('many:many', res$message))
-
-    res <- tryCatch(select(org.Hs.eg.db, c('1','10'), 'SYMBOL', 'ENTREZID'),
-                    message = function(x){return(x)})
-    checkTrue(grepl('1:1', res$message))
-}
 
 
 ## TODO: deal with any fallout from having new messages in select()
@@ -304,19 +86,6 @@ test_select_XtoX <- function(){
 
 
 
-test_dbconn_and_dbfile <- function(){
-    resc <- dbconn(org.Hs.eg.db)
-    m <- dbGetQuery(resc, "SELECT * FROM metadata")
-    checkTrue(dim(m)[2] ==2)
-    checkTrue(dim(m)[1] > 10)
-              
-    resf <- dbfile(org.Hs.eg.db)
-    mf <- dbGetQuery(dbConnect(SQLite(), resf), "SELECT * FROM metadata")
-    checkTrue(all(mf == m))
-}
-
-
-
 
 ## Fast checking:
 ## BiocGenerics:::testPackage(pattern="^test_select.*\\.R$")