Commits · 93ba17c64b149a87a47360fd81760e8a7a6cc549 · Environmental Cheminformatics / RMassBank_by_MaliRemorker

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Jul 27, 2018
- added fix to keep the properties of child-spectra valid and a minor fix to... · 93ba17c6
  Treutler authored 6 years ago
  
  added fix to keep the properties of child-spectra valid and a minor fix to aggregate spectra without error
  93ba17c6
- minor changes · 55215a0f
  Treutler authored 6 years ago
  
  55215a0f
Jun 28, 2018

add pNH4 to step 7 · b027f652

Emma Schymanski authored 6 years ago

Attempt to fix error I just encountered in https://github.com/MassBank/RMassBank/issues/112

Unverified

b027f652

Jun 27, 2018
- Update formulaCalculator.R to account for As, Hg · 6cada572
  Emma Schymanski authored 6 years ago
  
  Attempting a fix at the RDB error messages caused by presence of As, Hg in SMILES
  Unverified
  
  6cada572
Mar 19, 2018
- Cleanup after disabling code depending on ontoCAT · fa5dcbf1
  Steffen Neumann authored 7 years ago
  
  fa5dcbf1
- Remove code depending on ontoCAT. Closes #115 · a15c9365
  Steffen Neumann authored 7 years ago
  
  a15c9365
Mar 06, 2018
- fixed merge issue · 6009dca1
  meowcat authored 7 years ago
  
  6009dca1
Jan 10, 2018
- fixed line endings #2 · f9ef3ef9
  Treutler authored 7 years ago
  
  f9ef3ef9
- fixed line endings · 7f36ba82
  Treutler authored 7 years ago
  
  7f36ba82
- minor change · dab3e18f
  Treutler authored 7 years ago
  
  dab3e18f
- minor changes · 785c29a0
  Treutler authored 7 years ago
  
  785c29a0
Nov 30, 2017

Added optional parameter RMassBank.env$verbose.output which prints information... · 52ed7116

Treutler authored 7 years ago

Added optional parameter RMassBank.env$verbose.output which prints information about absent/filtered peaks during the msmsWorkflow

52ed7116

Nov 29, 2017
- fixed the pubchem-url for curl queries: http --> https · 08d02be8
  Treutler authored 7 years ago
  
  08d02be8
- Added option 'msp' to parameter 'readMethod' in function 'msmsRead' and... · 7eaad6e2
  Treutler authored 7 years ago
  
  Added option 'msp' to parameter 'readMethod' in function 'msmsRead' and implemented the corresponding functionality in file 'leMsmsRaw.R'.
  7eaad6e2
Oct 09, 2017
- Fix an issue arising from new columns in mzR header() · 8a334988
  Michele Stravs authored 7 years ago
  
  8a334988
Jul 26, 2017
- Fix an argument misassignment that's probably been there for two years · 1fa6ed3c
  meowcat authored 7 years ago
  
  1fa6ed3c
Dec 09, 2016

Pubchem switch to https · 3e7289ed

Emma Schymanski authored 8 years ago

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RMassBank@124938 bc3139a8-67e5-0310-9ffc-ced21a209358

3e7289ed

Nov 29, 2016

fix in xcms workflow (the "standard" case 1 file for each cpdID was incorrect) · 1d861383
Michele Stravs authored 8 years ago

1d861383
fixed empty molfile issue (#165), was stray line in createMolfile · 80c90026
Michele Stravs authored 8 years ago

80c90026

Update webAccess.R - PubChem has moved to https · eb10244c

schymane authored 8 years ago

"<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\">\n<html><head>\n<title>301 Moved Permanently</title>\n</head><body>\n<h1>Moved Permanently</h1>\n<p>The document has moved <a href=\"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MXWJVTOOROXGIU-UHFFFAOYSA-N/description/json\">here</a>.</p>\n</body></html>\n"
I only tried getPcID, but fixed all http to https. This probably needs to filter through to all BioC versions.

eb10244c

May 10, 2016
- Copied code from splashR-0.0.3 · e3640fa3
  Steffen Neumann authored 8 years ago
  
  e3640fa3
Apr 11, 2016

Push current fixed version · 3271f25f

Emma Schymanski authored 8 years ago

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RMassBank@116140 bc3139a8-67e5-0310-9ffc-ced21a209358

3271f25f

Apr 02, 2016
- Cactus changed their interface to https-only · 431cced1
  ermueller authored 8 years ago
  
  431cced1
Mar 08, 2016
- Reworked isotopic annotation · 7a11f9ac
  ermueller authored 9 years ago
  
  7a11f9ac
Mar 02, 2016
- Fixed SPLASH appearing in PK · 4142038a
  ermueller authored 9 years ago
  
  4142038a
Feb 20, 2016
- Isotopic annotation a bit better · a366bd84
  ermueller authored 9 years ago
  
  a366bd84
Feb 18, 2016
- Removed global variable and modularized isotopic annotation further · 94502bd3
  ermueller authored 9 years ago
  
  94502bd3
Feb 12, 2016
- Fixed bug in Recalibration if more than 1 MS1-peak falls withing the specified m/z ppm boundaries · 95bc68b6
  ermueller authored 9 years ago
  
  95bc68b6
Feb 08, 2016
- fixes #157 · f27bce01
  Michele Stravs authored 9 years ago
  
  f27bce01
Feb 05, 2016
- Fixed bug that occurs under special conditions in workflow step 2 · b5498537
  ermueller authored 9 years ago
  
  b5498537
- Fixed some minor bugs · 3998a43f
  ermueller authored 9 years ago
  
  3998a43f
Feb 03, 2016
- Now steps 4:8 will be skipped when processing only unknowns · 81b4c0a7
  ermueller authored 9 years ago
  
  81b4c0a7
- Fix for unknowns - work faster but skipping steps 4:8 not possible yet · 6e0d9476
  ermueller authored 9 years ago
  
  6e0d9476
Jan 22, 2016
- Fix in findMz.formula so it works correctly for "special" cases like findMz.formula("", "mH") · d05725f5
  Michele Stravs authored 9 years ago
  
  d05725f5
Jan 21, 2016
- fix: the ID read from the compiled record is not numeric · 94380d9d
  Michele Stravs authored 9 years ago
  
  94380d9d
Jan 20, 2016
- Changed it so that molfiles don't get generated when tentative or unknown,... · ea9850ed
  ermueller authored 9 years ago
  
  Changed it so that molfiles don't get generated when tentative or unknown, also no mention in list.tsv
  ea9850ed
- Added new tentative and unknown functionality to RMassbank · c6377202
  ermueller authored 9 years ago
  
  c6377202
Jan 19, 2016
- Fixed minor bug related to double slashes in records with the parser · 1dda9652
  ermueller authored 9 years ago
  
  1dda9652
Jan 18, 2016
- PK integrated · a11bab46
  ermueller authored 9 years ago
  
  a11bab46
Jan 06, 2016
- Changed docs because of that bug · d2a8695e
  ermueller authored 9 years ago
  
  d2a8695e