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 2.7.5

• New Github devel version.

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() and file_types() functions to infer mass spectrometry and proteomics file types based on their extensions.
• New pxSubmissionDate() and pxPublicationDate() accessor functions.

rpx 2.7.2

• Deprecation warning: PXDataset class/methods and PXDataset1() constructor.

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 2.5

rpx 2.5.1

• Address failing unit test since PRIDE URL has changed back.

rpx 2.5.0

• New bioconductor devel version

rpx 2.4

rpx 2.4.0

• New bioconductor release version

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::bfcrpath to get correct rpath, irrespective of absolute or relative.

rpx 2.3.0

• New bioconductor devel branch

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() and pxprotocols() accessors.

rpx 2.1.9

• Internal function to tally local project vs full PX.

rpx 2.1.8

• New PXDataset2 class with richer interface and more stable data downloading functions. PXDataset and PXDataset2 work transparently and PXDataset2 is 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 PXDataset object.
• New pxCacheInfo() function and use it to show caching info in show,PXDataset.

rpx 2.1.5

• Improve documentation.

• Check for cached PXDataset object validity.

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 1.99.8

• Remove rappdirs from Suggests.

rpx 1.99.7

• Add markdown to Suggests.

rpx 1.99.6

• Switching to tools::R_user_dir() from rappdirs::user_cache_dir() to set package cache directory, following changes in BiocFileCache (see for details).

rpx 1.99.5

• User can pass an own cache when downloading files <2021-04-03 Sat>

rpx 1.99.4

• Automatically detect/fix correct url <2021-03-22 Mon>

rpx 1.99.3

• Use MS:1002852 to get URL when PRIDE:0000411 returns empty string.

rpx 1.99.2

• 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.

rpx 1.99.1

• Using BiocFileCache to cache PXD files that are downloaded.

Changes in version 1.27.0

• New devel version

rpx 1.23

Changes in version 1.23.1

• Define modifiable rpx_fix_issue_5 <2019-11-26 Tue>

Changes in version 1.23.0

• New devel version

rpx 1.21

Changes in version 1.21.3

• Update NEWS titles

Changes in version 1.21.2

• Temporary fix for issue #5 (wrong URL from PRIDE server) <2019-10-02 Wed>

Changes in version 1.21.1

• Don’t set old class <2019-08-09 Fri>

rpx 1.19

Changes in version 1.19.4

• Delete plain NEWS now that R supports NEWS.md

Changes in version 1.19.3

• Fix NEWS

Changes in version 1.19.2

• Mention setting method on Windows <2019-04-16 Tue>

Changes in version 1.19.1

• Add ImmunoOncology biocView

Changes in version 1.19.0

• New release for Bioc 3.9

rpx 1.18

Changes in version 1.18.0

• New release for Bioc 3.8

rpx 1.17

Changes in version 1.17.2

• Update NEWS and pkgdown site

Changes in version 1.17.1

• replace BiocInstaller biocLite mentions with BiocManager

Changes in version 1.17.0

• New version for Bioconductor devel

rpx 1.16

Changes in version 1.16.0

• New version for Bioconductor release

rpx 1.13

Changes in version 1.13.5

• Nothing yet

Changes in version 1.13.4

• Restore reference unit test

Changes in version 1.13.3

• No commit

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>

Changes in version 1.13.1

• Using xml2 <2017-06-13 Tue>
• Use functions instead of methods <2017-06-13 Tue>

Changes in version 1.13.0

• Bioc devel 3.6

rpx 1.12

Changes in version 1.12.1

• Using xml2 (backported from devel) <2017-06-13 Tue>
• Use functions instead of methods (backported from devel) <2017-06-13 Tue>

Changes in version 1.12.0

• Bioc release 3.5

rpx 1.11

Changes in version 1.11.0

• Bioc devel 3.4

Changes in version 1.11.4

• Update unit test to reflect upstream changes <2017-02-26 Sun>

Changes in version 1.11.3

• pxget gains a destdir argument to specify the destination to which files should be downloaded <2017-01-27 Fri>

Changes in version 1.11.2

• Update unit test to reflect upstream changes <2017-01-25 Wed>

Changes in version 1.11.1

• Migrate vignette to BiocStyle::html_document2 <2016-12-22 Thu>
• Use NEWS.md <2016-12-28 Wed>

Changes in version 1.11.0

• Bioconductor devel 3.5

rpx 1.10

Changes in version 1.10.0

• Bioconductor release 3.4

rpx 1.9

Changes in version 1.9.4

• Updating unit tests <2016-10-04 Tue>

Changes in version 1.9.3

• Update vignette to use readMzTabData v0.9 <2016-07-24 Sun>

rpx 1.5

Changes in version 1.5.1

• unit tests <2015-06-30 Tue>
• export and document pxnodes <2015-06-30 Tue>

Changes in version 1.5.0

• Bioc version 3.2 (devel)

rpx 1.4

Changes in version 1.4.0

• Bioc version 3.1 (release)

rpx 1.3

Changes in version 1.3.1

• update vignette to reflect new files in px example, and avoid downloaded the raw data [2015-03-31 Tue]

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 0.99.8

• fix leftover issues from renaming package (d.tenenbaum) [2014-03-30 Sun]

Changes in version 0.99.7

• renamed to rpx due to CRAN name clash [2014-03-28]

Changes in version 0.99.6

• more typos in vignette [2014-03-12 Wed]

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]

Changes in version 0.99.3

• reverting pxannounced to empty signature to fix warning [2014-03-05 Wed]

Changes in version 0.99.2

• replacing download.file by getURL to download annoucement rss-ver https <2014-03-05 Wed>

Changes in version 0.99.1

• fixing pxfiles ending by n Windows [2014-03-05 Wed]

Changes in version 0.99.0

• added a vignette [2014-03-05 Wed]
• handle invalid identifiers [2014-03-05 Wed]