[Bioc-devel] Annotation packages maintained by Francesco Ferrari

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Wed Mar 22 20:22:18 CET 2017


We have 24 annotation packages in the repo maintained by Francesco
Ferrari, the majority of which are broken (output below). The last time
these were updated was for Bioconductor 2.8 (3 years ago). We've tried a
number of times to contact Francesco but did not get a response.

The plan is to remove these 24 from the Bioconductor 3.5 release:

> pkgs
 [1] "gahgu133acdf"       "gahgu133a.db"       "gahgu133aprobe"   
 [4] "gahgu133bcdf"       "gahgu133b.db"       "gahgu133bprobe"   
 [7] "gahgu133plus2cdf"   "gahgu133plus2.db"   "gahgu133plus2probe"
[10] "gahgu95av2cdf"      "gahgu95av2.db"      "gahgu95av2probe"  
[13] "gahgu95bcdf"        "gahgu95b.db"        "gahgu95bprobe"    
[16] "gahgu95ccdf"        "gahgu95c.db"        "gahgu95cprobe"    
[19] "gahgu95dcdf"        "gahgu95d.db"        "gahgu95dprobe"    
[22] "gahgu95ecdf"        "gahgu95e.db"        "gahgu95eprobe" 

If anyone is interested in taking over as maintainer please let me know.


Sample R CMD check error:

   * checking examples ... ERROR
   Running examples in ‘gahgu95av2.db-Ex.R’ failed
   The error most likely occurred in:

   > ### Name: gahgu95av2_dbconn
   > ### Title: Collect information about the package annotation DB
   > ### Aliases: gahgu95av2_dbconn gahgu95av2_dbfile gahgu95av2_dbschema
   > ###   gahgu95av2_dbInfo
   > ### Keywords: utilities datasets
   > ### ** Examples
   >   ## Count the number of rows in the "probes" table:
   >   dbGetQuery(gahgu95av2_dbconn(), "SELECT COUNT(*) FROM probes")
   Error: could not find function "dbGetQuery"
   Execution halted
   * checking PDF version of manual ... OK
   * DONE

   Status: 1 ERROR, 4 NOTEs
   for details.

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