Content of mogene10sttranscriptcluster.db appears to be missing or not installed properly
1
0
Entering edit mode
fidlay • 0
@fidlay-10894
Last seen 6.9 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 • 754 views
ADD COMMENT
0
Entering edit mode
@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"    
ADD COMMENT
0
Entering edit mode

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   
>
ADD REPLY

Login before adding your answer.

Traffic: 529 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6