Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
3
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knishida ▴ 20
@knishida-8230
Last seen 20 months ago
United States

I confirmed the "Post Title" with R 3.2.1(and 3.2.0), ath1121501.db 3.1.3, AnnotationDbi 1.30.1

 

This should return "Large character (20335 elements, 1.2 Mb)"

You can reproduce the "Large character (20335 elements, 1.2 Mb)" with R 3.1.3, ath1121501.db 3.0.0, AnnotationDbi 1.28.2 

 

Thanks,

Kozo

annotation arabidopsis thaliana • 987 views
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I can confirm that this package is completely busted:

> dbGetQuery(ath1121501_dbconn(), "select * from map_counts;")
       map_name count
1        ACCNUM     0
2      GENENAME     0
3        SYMBOL     0
4           CHR     0
5          PMID     0
6    PMID2PROBE     0
7    CHRLENGTHS     7
8            GO     0
9      GO2PROBE     0
10 GO2ALLPROBES     0
11         PATH     0
12   PATH2PROBE     0
13       ENZYME     0
14 ENZYME2PROBE     0
15       CHRLOC     0
16    CHRLOCEND     0
17       ARACYC     0
18 ARACYCENZYME     0
19        TOTAL 22810

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] hgu133plus2.db_3.1.3 org.Hs.eg.db_3.1.2   ath1121501.db_3.1.3
 [4] org.At.tair.db_3.1.2 RSQLite_1.0.0        DBI_0.3.1           
 [7] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.1   IRanges_2.2.4       
[10] S4Vectors_0.6.0      Biobase_2.28.0       BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] tools_3.2.0

 

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Thanks James.

I review ath1121501.db schema and AnnotationDbi spec.

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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States

Wow.  Thanks for this bug report.  I have code that checks for these things but apparently the probes for arabidopsis have slipped past my current dragnet for missing fields.

I will find out what went wrong and fix the package.  And then I will update the dragnet so this kind of problem doesn't happen again.  Once I have repaired the package I will let you know.  But until I report back to this thread you won't be able to get much used out of the following two packages:

ag.db_3.1.2.tar.gz

ath1121501.db_3.1.2.tar.gz


The complementary arabidopsis OrgDb package (org.At.tair.db_3.1.2.tar.gz), is unaffected as the only problem seems to be the affy based probe data.

 

 Marc

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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States

OK.  I have just pushed repaired packages online for these two chip packages.  Look for version 3.1.4 to appear within the next day or so on the website.

 

 Marc

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knishida ▴ 20
@knishida-8230
Last seen 20 months ago
United States

Hi Marc,

I confirmed that mappedkeys(ath1121501ACCNUM) returns Large character (20335 elements, 1.2 Mb) in version 3.1.4.

Thanks a lot.

 

Kozo

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