Changelog
Source:NEWS.md
rpx 2.9
rpx 2.9.1
- Remove the generated subdir in the ftp_url when creating the PXDataset object <2023-09-26 Tue> (see issue #25).
rpx 2.7
rpx 2.7.4
- Delete entries in default cache before running the unit tests. This assures that the instances matche any updates in the class definition.
rpx 2.7.3
- New
px_file_types()andfile_types()functions to infer mass spectrometry and proteomics file types based on their extensions. - New
pxSubmissionDate()andpxPublicationDate()accessor functions.
rpx 2.7.1
- Don’t rely on a PRIDE project’s README.txt files anymore, as it has been discontinued (see issue #21). The files in a project are now listed from the remote ftp directory.
rpx 2.3
rpx 2.3.3
- Don’t run caching example as it replies on PRIDE which is failing too often for the tests to pass on all systems.
rpx 2.3.2
- Provide fix for PRIDE migration and annotation discrepancies (see issue #17). This fix will however lead to re-downloading some cached files due to different URLs. The fix might only be temporary, based on if/how PRIDE will address their inconsistencies.
rpx 2.3.1
- Use
BiocFileCache::bfcrpathto get correct rpath, irrespective of absolute or relative.
rpx 2.1
rpx 2.1.12
- Annotate additional experiments as returning errors (see issues for full list) <2021-10-07 Thu>
rpx 2.1.11
- Annotate PXD012095 as returning an error (see #12) <2021-10-04 Mon>
rpx 2.1.10
- Caching PRIDE sitemap with all PXD projects.
- New
pxinstruments(),pxptms()andpxprotocols()accessors.
rpx 2.1.8
New
PXDataset2class with richer interface and more stable data downloading functions.PXDatasetandPXDataset2work transparently andPXDataset2is now default.Add deprecation notice in
PXDataset()constructor.
rpx 2.1.7
- Improve object creating printout.
- Improve
pxCachedProjects()output.
rpx 2.1.6
- Update installation instruction in
README.md. - Cache location is now also stored inside the
PXDatasetobject. - New
pxCacheInfo()function and use it to show caching info inshow,PXDataset.
rpx 2.1.4
Fix bug in PXDdataset internal data storage.
New
pxCachedProjects()function that return the cached projects.Fixes and improvements in the documentation.
rpx 2.1.3
PXDatasets are also cached upon creation and retrieved from cache next time they are generated.
cache is now returned by
rpxCache().
rpx 2.1.2
- New feature: PXDataset objects now query and store data (ref, tax, files, url) when generated instead of fetching these on the fly every time. This new feature has been added to circumvent the issues with data access (see #5).
rpx 2.1.1
-
pxannouced()paused (see #7).
rpx 1.99.0
rpx 1.99.6
- Switching to
tools::R_user_dir()fromrappdirs::user_cache_dir()to set package cache directory, following changes inBiocFileCache(see for details).
rpx 1.21
Changes in version 1.21.2
- Temporary fix for issue #5 (wrong URL from PRIDE server) <2019-10-02 Wed>
rpx 1.13
Changes in version 1.13.2
- Fix errors due to changes on PX side. PXD000001 reference remains untested - see https://twitter.com/lgatt0/status/885091284142239744 for details. <2017-07-12 Wed>
rpx 1.12
rpx 1.11
Changes in version 1.11.3
-
pxgetgains adestdirargument to specify the destination to which files should be downloaded <2017-01-27 Fri>
rpx 0.99
Changes in version 0.99.9
- In pxref, dealing with cases without any-r pending publications [2014-04-01 Tue]
Changes in version 0.99.5
- Suggestions, biocView and typos reported by Nate Hayden [2014-03-12 Wed]
- added Runit test [2014-03-12 Wed]
- use ae fonts in vignette [2014-03-12 Wed]
Changes in version 0.99.4
- Update reference in man and vignette [2014-03-11 Tue]
- Typos in vignette [2014-03-11 Tue]