| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| exclude_tests_requiring_large_databases.patch | One of the needed databases is just packaged so try at least testing this one while excluding all other databases. |
Andreas Tille <tille@debian.org> | no | 2016-10-26 | ||
| org.Hs.eg.db_issues.patch | 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 |
Andreas Tille <tille@debian.org> | no | 2021-09-16 |