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Question: error in creating custom "org.MeSH.XXX.db" package with MeSHDbi
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gravatar for Ceca Bojic
2.7 years ago by
Ceca Bojic10
Serbia And Montenegro
Ceca Bojic10 wrote:

Hi everyone,

I have problem in reproducing vignette example from MeSHDbi package.

That is, when I run:

> example("makeGeneMeSHPackage")

It should use  preformatted data frames "PAO1" and "metaPAO1" to construct custom org.MeSH.XXX.db package that can subsequently be loaded via library() and queried with Annotation.dbi or RSQLite, or at least that is how other org.MeSH.XXX.db packages behave (org.MeSH.Hsa.db, for instance).

but

> example("makeGeneMeSHPackage")

mGMSHP> ## makeGeneMeSHPackage enable users to construct
mGMSHP> ## user's own custom MeSH package
mGMSHP> 
mGMSHP> ## this is test data which means the relationship between
mGMSHP> ## Entrez gene IDs of Pseudomonas aeruginosa PAO1
mGMSHP> ## and its MeSH IDs.
mGMSHP> data(PAO1)

mGMSHP> head(PAO1)
  GENEID  MESHID MESHCATEGORY SOURCEID
1 877657 D000265            D   937805
2 877657 D000265            D   937805
3 877657 D001412            B   937805
4 877657 D001412            B   937805
5 877657 D001426            D   937805
6 877657 D001483            G   937805
                                      SOURCEDB
1 Bacillus subtilis subsp. spizizenii str. 168
2 Bacillus subtilis subsp. spizizenii str. 168
3 Bacillus subtilis subsp. spizizenii str. 168
4 Bacillus subtilis subsp. spizizenii str. 168
5 Bacillus subtilis subsp. spizizenii str. 168
6 Bacillus subtilis subsp. spizizenii str. 168

mGMSHP> # We are also needed to prepare meta data as follows.
mGMSHP> data(metaPAO1)

mGMSHP> metaPAO1
             NAME
1      SOURCEDATE
2      SOURCENAME
3       SOURCEURL
4        DBSCHEMA
5 DBSCHEMAVERSION
6        ORGANISM
7         SPECIES
8         package
9         Db type
                                  VALUE
1                          31-July-2013
2                                BLASTP
3 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
4                  org.Pae.PAO1.MeSH.db
5                                   1.0
6           Pseudomonas aeruginosa PAO1
7                                      
8                         AnnotationDbi
9                               BLASTDb

mGMSHP> ## sets up a temporary directory for this example
mGMSHP> ## (users won't need to do this step)
mGMSHP> destination <- tempfile()

mGMSHP> dir.create(destination)

mGMSHP> ## makes an Organism package for human called Homo.sapiens
mGMSHP> makeGeneMeSHPackage(pkgname = "org.MeSH.Pae.db",
mGMSHP+                     data = PAO1,
mGMSHP+           metadata = metaPAO1,
mGMSHP+                     organism = "Pseudomonas aeruginosa PAO1",
mGMSHP+                     version = "1.0.0",
mGMSHP+                     maintainer = "Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>",
mGMSHP+                     author = "Koki Tsuyuzaki",
mGMSHP+                     destDir = destination,
mGMSHP+                     license="Artistic-2.0")
Creating package in /var/folders/19/6n33ytjd6nd1m9rtrt6plcfm0000gn/T//RtmpFLPUeT/filef4160c94d3/org.MeSH.Pae.db 
[1] TRUE
Warning messages:
1: 'dbBeginTransaction' is deprecated.
Use 'dbBegin' instead.
See help("Deprecated") 
2: 'dbBeginTransaction' is deprecated.
Use 'dbBegin' instead.
See help("Deprecated") 

so when I try to load it, it says:

> library("org.MeSH.Pae.db")
Error in library("org.MeSH.Pae.db") : 
  ‘org.MeSH.Pae.db’ is not a valid installed package

could someone give me a clue what went wrong? Should there be another sequence of commands that should "install" this package properly? 

I would really appreciate any help with this.

Best,

Svetlana Bojic, MD

session info output is below:

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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] grid      parallel  stats     graphics 
[5] grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] meshr_1.0.4              
 [2] org.MeSH.Syn.db_1.0.0    
 [3] org.MeSH.Bsu.168.db_1.0.0
 [4] org.MeSH.Atu.K84.db_1.0.0
 [5] org.MeSH.Aca.db_1.0.0    
 [6] org.MeSH.Hsa.db_1.0.0    
 [7] org.Hs.eg.db_2.14.0      
 [8] cummeRbund_2.6.1         
 [9] Gviz_1.8.4               
[10] rtracklayer_1.24.2       
[11] GenomicRanges_1.16.4     
[12] IRanges_1.22.10          
[13] fastcluster_1.1.16       
[14] reshape2_1.4.1           
[15] ggplot2_1.0.0            
[16] Category_2.30.0          
[17] GO.db_2.14.0             
[18] RSQLite_1.0.0            
[19] Matrix_1.1-5             
[20] fdrtool_1.2.13           
[21] MeSH.PCR.db_1.0.0        
[22] MeSH.db_1.0.1            
[23] MeSH.AOR.db_1.0.0        
[24] MeSHDbi_1.0.2            
[25] GSEABase_1.26.0          
[26] graph_1.42.0             
[27] annotate_1.42.1          
[28] AnnotationDbi_1.26.1     
[29] GenomeInfoDb_1.0.2       
[30] Biobase_2.24.0           
[31] BiocGenerics_0.10.0      
[32] limma_3.20.9             
[33] phyloseq_1.8.2           
[34] RMySQL_0.10.2            
[35] DBI_0.3.1                
[36] viz14_0.0.10             

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          
 [2] ade4_1.6-2               
 [3] ape_3.2                  
 [4] assertthat_0.1           
 [5] base64enc_0.1-2          
 [6] BatchJobs_1.5            
 [7] BBmisc_1.9               
 [8] BiocParallel_0.6.1       
 [9] biom_0.3.12              
[10] biomaRt_2.20.0           
[11] Biostrings_2.32.1        
[12] biovizBase_1.12.3        
[13] bitops_1.0-6             
[14] brew_1.0-6               
[15] BSgenome_1.32.0          
[16] checkmate_1.5.1          
[17] cluster_2.0.1            
[18] codetools_0.2-10         
[19] colorspace_1.2-5         
[20] data.table_1.9.2         
[21] DESeq2_1.4.5             
[22] dichromat_2.0-0          
[23] digest_0.6.8             
[24] dplyr_0.4.1              
[25] fail_1.2                 
[26] foreach_1.4.2            
[27] foreign_0.8-63           
[28] Formula_1.2-0            
[29] genefilter_1.46.1        
[30] geneplotter_1.42.0       
[31] GenomicAlignments_1.0.6  
[32] GenomicFeatures_1.16.3   
[33] GenomicFiles_1.0.1       
[34] ggbio_1.12.10            
[35] ggvis_0.4                
[36] gridExtra_0.9.1          
[37] gtable_0.1.2             
[38] Heatplus_2.10.0          
[39] Hmisc_3.15-0             
[40] htmltools_0.2.6          
[41] httpuv_1.3.2             
[42] igraph_0.7.1             
[43] iterators_1.0.7          
[44] lattice_0.20-30          
[45] latticeExtra_0.6-26      
[46] locfit_1.5-9.1           
[47] magrittr_1.5             
[48] MASS_7.3-39              
[49] matrixStats_0.14.0       
[50] mgcv_1.8-5               
[51] mime_0.2                 
[52] multtest_2.20.0          
[53] munsell_0.4.2            
[54] nlme_3.1-120             
[55] nnet_7.3-9               
[56] parody_1.22.0            
[57] permute_0.8-3            
[58] plyr_1.8.1               
[59] proto_0.3-10             
[60] R6_2.0.1                 
[61] RBGL_1.40.1              
[62] RColorBrewer_1.1-2       
[63] Rcpp_0.11.4              
[64] RcppArmadillo_0.4.650.1.1
[65] RCurl_1.95-4.5           
[66] RJSONIO_1.3-0            
[67] rpart_4.1-9              
[68] Rsamtools_1.16.1         
[69] scales_0.2.4             
[70] sendmailR_1.2-1          
[71] shiny_0.11.1             
[72] SparseM_1.6              
[73] splines_3.1.0            
[74] stats4_3.1.0             
[75] stringr_0.6.2            
[76] survival_2.38-1          
[77] tcltk_3.1.0              
[78] tools_3.1.0              
[79] topGO_2.16.0             
[80] VariantAnnotation_1.10.5 
[81] vegan_2.2-1              
[82] XML_3.98-1.1             
[83] xtable_1.7-4             
[84] XVector_0.4.0            
[85] zlibbioc_1.10.0          

 

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Ceca Bojic10
0
gravatar for James W. MacDonald
2.7 years ago by
United States
James W. MacDonald45k wrote:

Did you install the package? After building, you should do

install.packages("org.MeSH.Pae.db", type = "source", repos = NULL)

Then the package should load normally.

ADD COMMENTlink written 2.7 years ago by James W. MacDonald45k
0
gravatar for Ceca Bojic
2.7 years ago by
Ceca Bojic10
Serbia And Montenegro
Ceca Bojic10 wrote:

Thank you James for really fast reply,

but no, it doesn't seem to work.

The new error message is as follows:

> install.packages("org.MeSH.Pae.db", type="source", repos=NULL)
Warning: invalid package ‘org.MeSH.Pae.db’
Error: ERROR: no packages specified
Warning in install.packages :
  installation of package ‘org.MeSH.Pae.db’ had non-zero exit status

It seems that the building itself was invalid. Maybe it is something about specifying the destination directory, which was, in the vignette example done with :

> destination <- tempfile()

> dir.create(destination)

I do try to deduce where all the other packages, made from sqlite files, went with:

> dbfile(org.MeSH.Hsa.db)

[1] "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/org.MeSH.Hsa.db/extdata/org.MeSH.Hsa.db.sqlite"

and have used the above path (truncated in various ways) as  destDir parameter in makeGeneMeSHPackage function call, but with no success so far.

Since all the packages are, in fact sqlite tables, could I simply create one with RSQLite package? I have no previous experience in creating any type of package myself, so I could really use some advice on this.

Best,

Svetlana Bojic, MD

 

 

ADD COMMENTlink written 2.7 years ago by Ceca Bojic10
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