Question: Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
1
gravatar for knishida
4.4 years ago by
knishida20
United States
knishida20 wrote:

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

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by knishida20
1

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

 

ADD REPLYlink written 4.4 years ago by James W. MacDonald51k

Thanks James.

I review ath1121501.db schema and AnnotationDbi spec.

ADD REPLYlink written 4.4 years ago by knishida20
Answer: Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
2
gravatar for Marc Carlson
4.4 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:

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

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Marc Carlson7.2k
Answer: Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
2
gravatar for Marc Carlson
4.4 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:

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

ADD COMMENTlink written 4.4 years ago by Marc Carlson7.2k
Answer: Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
0
gravatar for knishida
4.4 years ago by
knishida20
United States
knishida20 wrote:

Hi Marc,

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

Thanks a lot.

 

Kozo

ADD COMMENTlink written 4.4 years ago by knishida20
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