[Debian-med-packaging] Bug#735547: Should we package some BioConductor databases (Was: Bug#735547: autopkgtest fails on missing runit, stderr, and non-packaged "reactome.db" and "hom.Hs.inp.db")

Sun Jan 19 21:42:23 UTC 2014

Hi,

I tried to track down this issue and created packaging stuff for all
missing databases in

       svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-reactome.db/trunk/
       svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-hgu95av2.db/trunk/
       svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-hom.hs.inp.db/trunk/
       svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.tguttatatestingsubset.eg.db/trunk/
       svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.at.tair.db/trunk/
       svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-org.sc.sgd.db/trunk/
       svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-go.db/trunk/

to verify whether we would be able to fix the failed test reported
below.

On Thu, Jan 16, 2014 at 12:29:32PM +0100, Martin Pitt wrote:
> Package: r-bioc-annotationdbi
> Version: 1.24.0-1
> 
> Hello,
> 
> r-bioc-annotationdbi's autopkgtest currently fails [1]:
> 
>   Error in BiocGenerics:::testPackage("AnnotationDbi") : 
>     RUnit package not found
> 
> After adding it (r-cran-runit), it fails because the test produces a
> lot of stderror.
> 
> Attached debdiff fixes these, but the autopkgtest then fails with:
> 
>   Error in library("org.TguttataTestingSubset.eg.db") : 
>     there is no package called 'org.TguttataTestingSubset.eg.db'
>   Loading required package: hom.Hs.inp.db
>   Error in eval(expr, envir, enclos) : object 'hom.Hs.inp.db' not found
> ...
>   In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>     there is no package called 'reactome.db'
> 
> It seems these aren't packaged yet?

So in principle these databases could be packaged (modulo verifying all
the sources for the sake of beeing able license wise) but if you look at
the attached output of the unit-test you will notice that even with the
databases installed it will not succeed.

Before I now go on really uploading all the databases I would like to
ask the Debian Med community whether these quite large packages (the
largest one is reactome.db:

$ ls -l reactome.db_1.46.1.tar.gz r-bioc-reactome.db_1.46.1-1_all.deb 
-rw-r--r-- 1 tillea admin 119618936 Jan 19 13:17 r-bioc-reactome.db_1.46.1-1_all.deb
-rw-rw-r-- 1 tillea admin 260264440 Jan 16 14:33 reactome.db_1.46.1.tar.gz

the others are about one order of magnitude smaller but still large
just to test a leaf package).

So if there is no really good reason that these packages serve some
better purpose than testing r-bioc-annotationdbi I would rather disable
this test.  Instead we could add a paragraph in README.test how to build
the packages and run the test.

What do you think?

Kind regards

       Andreas.

-- 
http://fam-tille.de
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> require("AnnotationDbi")
Loading required package: AnnotationDbi
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
    get, intersect, is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following objects are masked from 'package:BiocGenerics':

    conditions, conditions<-, counts, counts<-, design, design<-,
    dispTable, dispTable<-, estimateDispersions, estimateSizeFactors,
    sizeFactors, sizeFactors<-

There were 12 warnings (use warnings() to see them)
> AnnotationDbi:::.test()
Loading required package: org.Hs.eg.db
Loading required package: DBI

Timing stopped at: 0.004 0 0.004 
Error in checkEquals(c("1", "10", "100"), head(res, n = 3)) : 
  2 string mismatches
In addition: Warning messages:
1: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
2: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
3: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
4: In .local(x, ...) : returned vector has duplicated names
5: In .local(x, ...) : returned vector has duplicated names
Loading required package: org.At.tair.db

Loading required package: org.Sc.sgd.db

Loading required package: GO.db

Loading required package: hgu95av2.db

Warning: You have selected the following columns that can have a many to one
  relationship with the primary key: PFAM, IPI, PROSITE, ACCNUM, ALIAS,
  CHR, CHRLOC, CHRLOCEND, ENZYME, MAP, PATH, PMID, REFSEQ, UNIGENE,
  ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, UNIPROT, GO, EVIDENCE, ONTOLOGY,
  GOALL, EVIDENCEALL, ONTOLOGYALL, OMIM, UCSCKG . Because you have
  selected more than a few such columns there is a risk that this
  selection may balloon up into a very large result as the number of
  rows returned multiplies accordingly. To experience smaller/more
  manageable results and faster retrieval times, you might want to
  consider selecting these columns separately.

Timing stopped at: 0.032 0 0.032 
Error in checkTrue(all(res == c("100008579", "100008580"))) : 
  Test not TRUE

In addition: There were 16 warnings (use warnings() to see them)
Loading required package: hom.Hs.inp.db

Loading required package: reactome.db

RUNIT TEST PROTOCOL -- Sun Jan 19 14:40:25 2014 
*********************************************** 
Number of test functions: 62 
Number of errors: 0 
Number of failures: 2 

1 Test Suite : 
AnnotationDbi RUnit Tests - 62 test functions, 0 errors, 2 failures
FAILURE in test_ls: Error in checkEquals(c("1", "10", "100"), head(res, n = 3)) : 
  2 string mismatches
FAILURE in test_keys: Error in checkTrue(all(res == c("100008579", "100008580"))) : 
  Test not TRUE

Test files with failing tests

   test_bimap.R 
     test_ls 

   test_select_NOSCHEMA.R 
     test_keys 

Error in BiocGenerics:::testPackage("AnnotationDbi") : 
  unit tests failed for package AnnotationDbi
Calls: <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: In .generateExtraRows(tab, keys, jointype) :
  'select' resulted in 1:many mapping between keys and return rows
2: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
3: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
4: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
5: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
6: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
7: In sqliteInitDriver(max.con, fetch.default.rec, force.reload, shared.cache) :
  RS-DBI driver warning: (SQLite mismatch between compiled version 3.7.16.1 and runtime version 3.8.2)
8: In .generateExtraRows(tab, keys, jointype) :
  'select' resulted in 1:many mapping between keys and return rows
9: In .generateExtraRows(tab, keys, jointype) :
  'select' resulted in 1:many mapping between keys and return rows
10: In .generateExtraRows(tab, keys, jointype) :
  'select' resulted in 1:many mapping between keys and return rows
Execution halted