Error in makeAnnotationHubMetadataFunction

[lgatto]

Yesterday, building and checking was successful. I must have updated a package a dependency, as I don't remember having changed anything, but now I get

 -> % R-3.2 CMD build ProteomicsAnnotationHubData
* checking for file ‘ProteomicsAnnotationHubData/DESCRIPTION’ ... OK
* preparing ‘ProteomicsAnnotationHubData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘ProteomicsAnnotationHubData’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
erwinia_carotovora.fasta
F063721.dat-mztab.txt
PXD000001
TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
INFO [2015-08-22 01:18:57] Preparer Class: PXD000001FastaToAAStringSetPreparer
Error in makeAnnotationHubMetadataFunction(currentMetadata, justRunUnitTest = justRunUnitTest,  : 
  unused argument (BiocVersion)
Error : unable to load R code in package ‘ProteomicsAnnotationHubData’
ERROR: lazy loading failed for package ‘ProteomicsAnnotationHubData’
* removing ‘/tmp/RtmpA1tuwQ/Rinst57b42a4453e3/ProteomicsAnnotationHubData’
      -----------------------------------
ERROR: package installation failed

Session info:

R version 3.2.1 Patched (2015-07-01 r68620)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

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

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

other attached packages:
[1] AnnotationHubData_0.0.239 futile.logger_1.4.1      
[3] GenomicRanges_1.21.18     GenomeInfoDb_1.5.13      
[5] IRanges_2.3.18            S4Vectors_0.7.13         
[7] BiocGenerics_0.15.6       AnnotationHub_2.1.39     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.0                  plyr_1.8.3                  
 [3] BiocInstaller_1.19.11        XVector_0.9.2               
 [5] GenomicFeatures_1.21.18      bitops_1.0-6                
 [7] futile.options_1.0.0         tools_3.2.1                 
 [9] zlibbioc_1.15.0              biomaRt_2.25.1              
[11] digest_0.6.8                 jsonlite_0.9.16             
[13] RSQLite_1.0.0                graph_1.47.2                
[15] OrganismDbi_1.11.42          GEOquery_2.35.5             
[17] shiny_0.12.2                 DBI_0.3.1                   
[19] rBiopaxParser_2.7.0          rtracklayer_1.29.18         
[21] httr_1.0.0                   stringr_1.0.0               
[23] Biostrings_2.37.6            data.table_1.9.4            
[25] Biobase_2.29.1               R6_2.1.1                    
[27] AnnotationDbi_1.31.17        RBGL_1.45.1                 
[29] XML_3.98-1.3                 BiocParallel_1.3.50         
[31] reshape2_1.4.1               lambda.r_1.1.7              
[33] magrittr_1.5                 Rsamtools_1.21.15           
[35] htmltools_0.2.6              GenomicAlignments_1.5.12    
[37] SummarizedExperiment_0.3.3   AnnotationForge_1.11.17     
[39] mime_0.3                     interactiveDisplayBase_1.7.1
[41] xtable_1.7-4                 httpuv_1.3.3                
[43] stringi_0.5-5                RCurl_1.95-4.7              
[45] chron_2.3-47                

Note that AnnotationHub and AnnotationHubData are build from svn, at revision 107679.

@sonali-bioc any idea?

[sonali-bioc]

Hi Laurent,

Val added a new argument makeAnnotationHubResource

BiocVersion=biocVersion()

For example -

if one passes a function called make2bit to makeAnnotationHubResource like this

makeAnnotationHubResource("UCSC2BitPreparer", make2bit)

then make2bit should have a signature like

make2bit <- function(currentMetadata, justRunUnitTest=FALSE,
                     BiocVersion=biocVersion()){
# code.. 
}

You can look at the latest AnnotationHubData for more examples.

Best, Sonali.

[lgatto]

Thanks!