Content of mogene10sttranscriptcluster.db appears to be missing or not installed properly
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fidlay • 0
@fidlay-10894
Last seen 6.4 years ago

Hi,

I am trying to install the annotation mogene10sttranscriptcluster.db from the recent release as followed:

biocLite("mogene10sttranscriptcluster")

It seems to install properly because I didn't get any error message. But when I loaded the annotation package, I couldn't find any of the annotation content (ie ACCNUM, CHR, ALIAS2PROBE, GENENAME etc):

> head(ls("package:mogene10sttranscriptcluster.db"))

[1] "mogene10sttranscriptcluster"          "mogene10sttranscriptcluster_dbconn"  

[3] "mogene10sttranscriptcluster_dbfile"   "mogene10sttranscriptcluster_dbInfo"  

[5] "mogene10sttranscriptcluster_dbschema" "mogene10sttranscriptcluster.db"      

I tried to reinstall from the source package, but I had the same problem. Would appreciate any suggestion. 

Below is my session:

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] mogene10sttranscriptcluster.db_8.7.0 org.Mm.eg.db_3.5.0                  
 [3] AnnotationDbi_1.40.0                 ggplot2_2.2.1                       
 [5] RColorBrewer_1.1-2                   gplots_3.0.1                        
 [7] BiocInstaller_1.28.0                 pd.mta.1.0_3.12.0                   
 [9] DBI_0.7                              RSQLite_2.0                         
[11] oligo_1.42.0                         Biostrings_2.46.0                   
[13] XVector_0.18.0                       IRanges_2.12.0                      
[15] S4Vectors_0.16.0                     Biobase_2.38.0                      
[17] oligoClasses_1.40.0                  BiocGenerics_0.24.0                 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.8.0 gtools_3.5.0               splines_3.4.3             
 [4] lattice_0.20-35            colorspace_1.3-2           blob_1.1.0                
 [7] rlang_0.1.4                bit64_0.9-7                affyio_1.48.0             
[10] matrixStats_0.52.2         GenomeInfoDbData_1.0.0     foreach_1.4.4             
[13] plyr_1.8.4                 zlibbioc_1.24.0            munsell_0.4.3             
[16] gtable_0.2.0               caTools_1.17.1             codetools_0.2-15          
[19] memoise_1.1.0              labeling_0.3               ff_2.2-13                 
[22] GenomeInfoDb_1.14.0        preprocessCore_1.40.0      Rcpp_0.12.14              
[25] KernSmooth_2.23-15         scales_0.5.0               gdata_2.18.0              
[28] DelayedArray_0.4.1         affxparser_1.50.0          bit_1.1-12                
[31] digest_0.6.13              GenomicRanges_1.30.0       grid_3.4.3                
[34] tools_3.4.3                bitops_1.0-6               RCurl_1.95-4.8            
[37] lazyeval_0.2.1             tibble_1.3.4               pkgconfig_2.0.1           
[40] Matrix_1.2-12              iterators_1.0.9            compiler_3.4.3  

 

Thank you!

mogene10sttranscriptcluster • 672 views
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@james-w-macdonald-5106
Last seen 6 hours ago
United States

If you ask for the head of something, you just get the first 6 things.

> library(mogene10sttranscriptcluster.db)
> head(ls(2))
[1] "mogene10sttranscriptcluster"         
[2] "mogene10sttranscriptcluster.db"      
[3] "mogene10sttranscriptcluster_dbconn"  
[4] "mogene10sttranscriptcluster_dbfile"  
[5] "mogene10sttranscriptcluster_dbInfo"  
[6] "mogene10sttranscriptcluster_dbschema"
>

>  ls(2)
[1] "mogene10sttranscriptcluster"             
 [2] "mogene10sttranscriptcluster.db"          
 [3] "mogene10sttranscriptcluster_dbconn"      
 [4] "mogene10sttranscriptcluster_dbfile"      
 [5] "mogene10sttranscriptcluster_dbInfo"      
 [6] "mogene10sttranscriptcluster_dbschema"    
 [7] "mogene10sttranscriptclusterACCNUM"       
 [8] "mogene10sttranscriptclusterALIAS2PROBE"  
 [9] "mogene10sttranscriptclusterCHR"          
[10] "mogene10sttranscriptclusterCHRLENGTHS"   
[11] "mogene10sttranscriptclusterCHRLOC"       
[12] "mogene10sttranscriptclusterCHRLOCEND"    
[13] "mogene10sttranscriptclusterENSEMBL"      
[14] "mogene10sttranscriptclusterENSEMBL2PROBE"
[15] "mogene10sttranscriptclusterENTREZID"     
[16] "mogene10sttranscriptclusterENZYME"       
[17] "mogene10sttranscriptclusterENZYME2PROBE"
[18] "mogene10sttranscriptclusterGENENAME"     
[19] "mogene10sttranscriptclusterGO"           
[20] "mogene10sttranscriptclusterGO2ALLPROBES"
[21] "mogene10sttranscriptclusterGO2PROBE"     
[22] "mogene10sttranscriptclusterMAPCOUNTS"    
[23] "mogene10sttranscriptclusterMGI"          
[24] "mogene10sttranscriptclusterMGI2PROBE"    
[25] "mogene10sttranscriptclusterORGANISM"     
[26] "mogene10sttranscriptclusterORGPKG"       
[27] "mogene10sttranscriptclusterPATH"         
[28] "mogene10sttranscriptclusterPATH2PROBE"   
[29] "mogene10sttranscriptclusterPFAM"         
[30] "mogene10sttranscriptclusterPMID"         
[31] "mogene10sttranscriptclusterPMID2PROBE"   
[32] "mogene10sttranscriptclusterPROSITE"      
[33] "mogene10sttranscriptclusterREFSEQ"       
[34] "mogene10sttranscriptclusterSYMBOL"       
[35] "mogene10sttranscriptclusterUNIGENE"      
[36] "mogene10sttranscriptclusterUNIPROT"    
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And to be clear:

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] mogene10sttranscriptcluster.db_8.7.0 org.Mm.eg.db_3.5.0                  
[3] AnnotationDbi_1.40.0                 IRanges_2.12.0                      
[5] S4Vectors_0.16.0                     Biobase_2.38.0                      
[7] BiocGenerics_0.24.0                 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14    digest_0.6.13   DBI_0.7         RSQLite_2.0    
 [5] rlang_0.1.4     blob_1.1.0      tools_3.4.3     bit64_0.9-7    
 [9] bit_1.1-12      compiler_3.4.3  pkgconfig_2.0.1 memoise_1.1.0  
[13] tibble_1.3.4   
>
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