- Remove the generated subdir in the ftp_url when creating the PXDataset object <2023-09-26 Tue> (see issue #25).
- New Github devel version.
- Delete entries in default cache before running the unit tests. This assures that the instances matche any updates in the class definition.
- New
px_file_types()andfile_types()functions to infer mass spectrometry and proteomics file types based on their extensions. - New
pxSubmissionDate()andpxPublicationDate()accessor functions.
- Deprecation warning: PXDataset class/methods and PXDataset1() constructor.
- 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.
- Address failing unit test since PRIDE URL has changed back.
- New bioconductor devel version
- New bioconductor release version
- Don't run caching example as it replies on PRIDE which is failing too often for the tests to pass on all systems.
- 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.
- Use
BiocFileCache::bfcrpathto get correct rpath, irrespective of absolute or relative.
- New bioconductor devel branch
- Annotate additional experiments as returning errors (see issues for full list) <2021-10-07 Thu>
- Annotate PXD012095 as returning an error (see #12) <2021-10-04 Mon>
- Caching PRIDE sitemap with all PXD projects.
- New
pxinstruments(),pxptms()andpxprotocols()accessors.
- Internal function to tally local project vs full PX.
-
New
PXDataset2class with richer interface and more stable data downloading functions.PXDatasetandPXDataset2work transparently andPXDataset2is now default. -
Add deprecation notice in
PXDataset()constructor.
- Improve object creating printout.
- Improve
pxCachedProjects()output.
- 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.
-
Improve documentation.
-
Check for cached PXDataset object validity.
-
Fix bug in PXDdataset internal data storage.
-
New
pxCachedProjects()function that return the cached projects. -
Fixes and improvements in the documentation.
-
PXDatasets are also cached upon creation and retrieved from cache next time they are generated.
-
cache is now returned by
rpxCache().
- 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).
pxannouced()paused (see #7).
- Remove
rappdirsfrom Suggests.
- Add
markdownto Suggests.
- Switching to
tools::R_user_dir()fromrappdirs::user_cache_dir()to set package cache directory, following changes inBiocFileCache(see for details).
- User can pass an own cache when downloading files <2021-04-03 Sat>
- Automatically detect/fix correct url <2021-03-22 Mon>
- Use
MS:1002852to get URL whenPRIDE:0000411returns empty string.
- Don't ask for cache location in non-interactive mode. This forces the usage of the default cache location (rather than usage of a Rtmp directory) and enables reusage of a persistent cache over different build/check cycles.
- Using BiocFileCache to cache PXD files that are downloaded.
- New devel version
- Define modifiable
rpx_fix_issue_5<2019-11-26 Tue>
- New devel version
- Update NEWS titles
- Temporary fix for issue #5 (wrong URL from PRIDE server) <2019-10-02 Wed>
- Don't set old class <2019-08-09 Fri>
- Delete plain NEWS now that R supports NEWS.md
- Fix NEWS
- Mention setting
methodon Windows <2019-04-16 Tue>
- Add ImmunoOncology biocView
- New release for Bioc 3.9
- New release for Bioc 3.8
- Update NEWS and pkgdown site
- replace BiocInstaller biocLite mentions with BiocManager
- New version for Bioconductor devel
- New version for Bioconductor release
- Nothing yet
- Restore reference unit test
- No commit
- 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>
- Using xml2 <2017-06-13 Tue>
- Use functions instead of methods <2017-06-13 Tue>
- Bioc devel 3.6
- Using xml2 (backported from devel) <2017-06-13 Tue>
- Use functions instead of methods (backported from devel) <2017-06-13 Tue>
- Bioc release 3.5
- Bioc devel 3.4
- Update unit test to reflect upstream changes <2017-02-26 Sun>
pxgetgains adestdirargument to specify the destination to which files should be downloaded <2017-01-27 Fri>
- Update unit test to reflect upstream changes <2017-01-25 Wed>
- Migrate vignette to BiocStyle::html_document2 <2016-12-22 Thu>
- Use NEWS.md <2016-12-28 Wed>
- Bioconductor devel 3.5
- Bioconductor release 3.4
- Updating unit tests <2016-10-04 Tue>
- Update vignette to use readMzTabData v0.9 <2016-07-24 Sun>
- unit tests <2015-06-30 Tue>
- export and document pxnodes <2015-06-30 Tue>
- Bioc version 3.2 (devel)
- Bioc version 3.1 (release)
- update vignette to reflect new files in px example, and avoid downloaded the raw data [2015-03-31 Tue]
- In pxref, dealing with cases without any-r pending publications [2014-04-01 Tue]
- fix leftover issues from renaming package (d.tenenbaum) [2014-03-30 Sun]
- renamed to rpx due to CRAN name clash [2014-03-28]
- more typos in vignette [2014-03-12 Wed]
- 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]
- Update reference in man and vignette [2014-03-11 Tue]
- Typos in vignette [2014-03-11 Tue]
- reverting pxannounced to empty signature to fix warning [2014-03-05 Wed]
- replacing download.file by getURL to download annoucement rss-ver https <2014-03-05 Wed>
- fixing pxfiles ending by \r-n Windows [2014-03-05 Wed]
- added a vignette [2014-03-05 Wed]
- handle invalid identifiers [2014-03-05 Wed]