[med-svn] [r-bioc-ensembldb] branch upstream updated (0f017c8 -> cc1e361)
Andreas Tille
tille at debian.org
Thu Oct 19 20:57:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-bioc-ensembldb.
from 0f017c8 New upstream version 1.6.2
new cc1e361 New upstream version 2.0.4
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
DESCRIPTION | 39 +-
NAMESPACE | 275 ++++-
R/Classes.R | 722 ++++++------
R/Deprecated.R | 182 +++
R/Generics.R | 211 ++--
R/Methods-Filter.R | 1173 +++++--------------
R/Methods.R | 1207 ++++++++++++--------
R/dbhelpers.R | 629 ++++++----
R/functions-Filter.R | 324 ++++++
R/{EnsDbFromGTF.R => functions-create-EnsDb.R} | 880 +++++++++++---
R/functions-utils.R | 176 ++-
R/loadEnsDb.R | 5 -
R/makeEnsemblDbPackage.R | 213 ----
R/runEnsDbApp.R | 10 -
R/select-methods.R | 220 ++--
build/vignette.rds | Bin 325 -> 367 bytes
inst/NEWS | 121 +-
inst/doc/MySQL-backend.R | 4 +-
inst/doc/MySQL-backend.Rmd | 18 +-
inst/doc/MySQL-backend.html | 137 ++-
inst/doc/ensembldb.R | 204 ++--
inst/doc/ensembldb.Rmd | 569 +++++----
inst/doc/ensembldb.html | 744 +++++++-----
inst/doc/proteins.R | 94 ++
inst/doc/proteins.Rmd | 273 +++++
inst/doc/proteins.html | 369 ++++++
inst/extended_tests/extended_tests.R | 855 ++++++++++++++
inst/extended_tests/performance_tests.R | 173 +++
inst/gff/Devosia_geojensis.ASM96941v1.32.gff3.gz | Bin 0 -> 272773 bytes
inst/gtf/Devosia_geojensis.ASM96941v1.32.gtf.gz | Bin 0 -> 269508 bytes
inst/perl/get_gene_transcript_exon_tables.pl | 122 +-
inst/perl/test_script.pl | 78 ++
inst/scripts/checkEnsDbs.R | 22 +
inst/scripts/generate-EnsDBs.R | 321 ++++++
inst/shinyHappyPeople/server.R | 6 +-
inst/test/testFunctionality.R | 293 -----
inst/test/testInternals.R | 146 ---
inst/unitTests/test_Filters.R | 241 ----
inst/unitTests/test_Functionality.R | 507 --------
inst/unitTests/test_GFF.R | 179 ---
inst/unitTests/test_GRangeFilter.R | 102 --
inst/unitTests/test_SymbolFilter.R | 58 -
inst/unitTests/test_buildEdb.R | 45 -
inst/unitTests/test_getGenomeFaFile.R | 49 -
inst/unitTests/test_get_sequence.R | 189 ---
inst/unitTests/test_mysql.R | 24 -
inst/unitTests/test_ordering.R | 280 -----
inst/unitTests/test_performance.R | 62 -
inst/unitTests/test_select.R | 229 ----
inst/unitTests/test_transcript_lengths.R | 140 ---
inst/unitTests/test_ucscChromosomeNames.R | 508 --------
inst/unitTests/test_validity.R | 11 -
inst/unitTests/test_xByOverlap.R | 102 --
man/Deprecated.Rd | 92 ++
man/EnsDb-AnnotationDbi.Rd | 62 +-
man/EnsDb-class.Rd | 69 +-
man/EnsDb-exonsBy.Rd | 217 ++--
man/EnsDb-lengths.Rd | 40 +-
man/EnsDb-seqlevels.Rd | 11 +-
man/EnsDb-sequences.Rd | 3 +-
man/EnsDb-utils.Rd | 28 +-
man/EnsDb.Rd | 1 -
man/Filter-classes.Rd | 350 ++++++
man/GeneidFilter-class.Rd | 451 --------
man/ProteinFunctionality.Rd | 115 ++
man/SeqendFilter.Rd | 237 ----
man/hasProteinData-EnsDb-method.Rd | 32 +
man/listEnsDbs.Rd | 7 +-
man/makeEnsemblDbPackage.Rd | 10 +-
man/useMySQL-EnsDb-method.Rd | 3 +-
readme.md | 16 +
tests/runTests.R | 1 -
tests/testthat.R | 6 +
tests/testthat/test_Classes.R | 85 ++
tests/testthat/test_Methods-Filter.R | 515 +++++++++
.../test_Methods-with-returnFilterColumns.R | 276 ++---
tests/testthat/test_Methods.R | 893 +++++++++++++++
tests/testthat/test_Protein-related-tests.R | 253 ++++
tests/testthat/test_SymbolFilter.R | 99 ++
tests/testthat/test_dbhelpers.R | 405 +++++++
tests/testthat/test_extractTranscriptSeqs.R | 65 ++
tests/testthat/test_functions-Filter.R | 226 ++++
tests/testthat/test_functions-create-EnsDb.R | 234 ++++
tests/testthat/test_functions-utils.R | 106 ++
tests/testthat/test_select-methods.R | 414 +++++++
tests/testthat/test_seqLevelStyle.R | 445 ++++++++
tests/testthat/test_validity.R | 20 +
vignettes/MySQL-backend.Rmd | 18 +-
vignettes/MySQL-backend.org | 29 +-
vignettes/ensembldb.Rmd | 569 +++++----
vignettes/ensembldb.org | 1187 +++++++++++++++----
vignettes/images/dblayout.png | Bin 444031 -> 204300 bytes
vignettes/proteins.Rmd | 273 +++++
vignettes/proteins.org | 485 ++++++++
94 files changed, 13852 insertions(+), 8037 deletions(-)
create mode 100644 R/Deprecated.R
create mode 100644 R/functions-Filter.R
rename R/{EnsDbFromGTF.R => functions-create-EnsDb.R} (55%)
delete mode 100644 R/loadEnsDb.R
delete mode 100644 R/makeEnsemblDbPackage.R
delete mode 100644 R/runEnsDbApp.R
create mode 100644 inst/doc/proteins.R
create mode 100644 inst/doc/proteins.Rmd
create mode 100644 inst/doc/proteins.html
create mode 100644 inst/extended_tests/extended_tests.R
create mode 100644 inst/extended_tests/performance_tests.R
create mode 100644 inst/gff/Devosia_geojensis.ASM96941v1.32.gff3.gz
create mode 100644 inst/gtf/Devosia_geojensis.ASM96941v1.32.gtf.gz
create mode 100644 inst/perl/test_script.pl
create mode 100644 inst/scripts/checkEnsDbs.R
create mode 100644 inst/scripts/generate-EnsDBs.R
delete mode 100644 inst/test/testFunctionality.R
delete mode 100644 inst/test/testInternals.R
delete mode 100644 inst/unitTests/test_Filters.R
delete mode 100644 inst/unitTests/test_Functionality.R
delete mode 100644 inst/unitTests/test_GFF.R
delete mode 100644 inst/unitTests/test_GRangeFilter.R
delete mode 100644 inst/unitTests/test_SymbolFilter.R
delete mode 100644 inst/unitTests/test_buildEdb.R
delete mode 100644 inst/unitTests/test_getGenomeFaFile.R
delete mode 100644 inst/unitTests/test_get_sequence.R
delete mode 100644 inst/unitTests/test_mysql.R
delete mode 100644 inst/unitTests/test_ordering.R
delete mode 100644 inst/unitTests/test_performance.R
delete mode 100644 inst/unitTests/test_select.R
delete mode 100644 inst/unitTests/test_transcript_lengths.R
delete mode 100644 inst/unitTests/test_ucscChromosomeNames.R
delete mode 100644 inst/unitTests/test_validity.R
delete mode 100644 inst/unitTests/test_xByOverlap.R
create mode 100644 man/Deprecated.Rd
create mode 100644 man/Filter-classes.Rd
delete mode 100644 man/GeneidFilter-class.Rd
create mode 100644 man/ProteinFunctionality.Rd
delete mode 100644 man/SeqendFilter.Rd
create mode 100644 man/hasProteinData-EnsDb-method.Rd
create mode 100644 readme.md
delete mode 100644 tests/runTests.R
create mode 100644 tests/testthat.R
create mode 100644 tests/testthat/test_Classes.R
create mode 100644 tests/testthat/test_Methods-Filter.R
rename inst/unitTests/test_returnCols.R => tests/testthat/test_Methods-with-returnFilterColumns.R (56%)
create mode 100644 tests/testthat/test_Methods.R
create mode 100644 tests/testthat/test_Protein-related-tests.R
create mode 100644 tests/testthat/test_SymbolFilter.R
create mode 100644 tests/testthat/test_dbhelpers.R
create mode 100644 tests/testthat/test_extractTranscriptSeqs.R
create mode 100644 tests/testthat/test_functions-Filter.R
create mode 100644 tests/testthat/test_functions-create-EnsDb.R
create mode 100644 tests/testthat/test_functions-utils.R
create mode 100644 tests/testthat/test_select-methods.R
create mode 100644 tests/testthat/test_seqLevelStyle.R
create mode 100644 tests/testthat/test_validity.R
create mode 100644 vignettes/proteins.Rmd
create mode 100644 vignettes/proteins.org
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