Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
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@laurent-gatto-5645
Last seen 15 days ago
Belgium

Any advice regarding the following installation error? biocLite() does not prompt for any additional updates.

> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.17.3), R version 3.2.0.
Installing package(s) ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0.tar.gz'
Content type 'application/x-gzip' length 18661634 bytes (17.8 MB)
opened URL
==================================================
downloaded 17.8 MB

* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
  call: dbGetQuery(conn, SQL)
  error: error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'dbConn' not found
Calls: ::: -> get

Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/TxDb.Hsapiens.UCSC.hg19.knownGene’

The downloaded source packages are in
    ‘/tmp/Rtmpg6vrx3/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status

For the session info below, I have also loaded AnnotationDbi, GenomicFeatures, DBI and RSQLite, as I thought these might be relevant. 

> sessionInfo()
R Under development (unstable) (2014-11-01 r66923)
Platform: x86_64-unknown-linux-gnu (64-bit)

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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] GenomicFeatures_1.19.10 AnnotationDbi_1.29.14   Biobase_2.27.1         
 [4] GenomicRanges_1.19.33   GenomeInfoDb_1.3.12     IRanges_2.1.35         
 [7] S4Vectors_0.5.16        BiocGenerics_0.13.4     RSQLite_1.0.0          
[10] DBI_0.3.1               BiocInstaller_1.17.3   

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2          BatchJobs_1.5            BBmisc_1.8              
 [4] BiocParallel_1.1.11      biomaRt_2.23.5           Biostrings_2.35.7       
 [7] bitops_1.0-6             brew_1.0-6               checkmate_1.5.1         
[10] codetools_0.2-10         compiler_3.2.0           digest_0.6.8            
[13] fail_1.2                 foreach_1.4.2            GenomicAlignments_1.3.25
[16] iterators_1.0.7          RCurl_1.95-4.5           Rsamtools_1.19.26       
[19] rtracklayer_1.27.7       sendmailR_1.2-1          stringr_0.6.2           
[22] tools_3.2.0              XML_3.98-1.1             XVector_0.7.3           
[25] zlibbioc_1.13.0        
biocinstaller installation TxDb • 3.9k views
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Entering edit mode

Just in case it sheds some additional light or additional darkness to this, I got today the same problem with TxDb.Hsapiens.UCSC.hg38.knownGene when trying to install it in R-devel. However, it installs fine from release. Here is my error and sessionInfo() in devel:

Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg38.knownGene', details:
  call: dbGetQuery(conn, SQL)
  error: error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'dbConn' not found
Calls: ::: -> get

R Under development (unstable) (2014-10-14 r66765)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C              LC_TIME=en_US.UTF8       
 [4] LC_COLLATE=en_US.UTF8     LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8   
 [7] LC_PAPER=en_US.UTF8       LC_NAME=C                 LC_ADDRESS=C             
[10] LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C      

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

other attached packages:
[1] BiocInstaller_1.17.3 vimcom_1.0-0         setwidth_1.0-3       colorout_1.0-3      

loaded via a namespace (and not attached):
[1] tools_3.2.0

 

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Entering edit mode
Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.9 years ago
United States

Yes this is only affecting the devel branch.

This is because of some changes that I made to AnnotationDbi and GenomicFeatures.  If you are using devel you need those changes in order for this package to work.  Unfortunately, GenomicFeatures is currently not yet updated to biocLite because of a separate issue that is causing the package to not build, I will work to get that resolved ASAP.  But in the meantime, if you INSTALL GenomicFeatures from svn you should be able to get the latest version (1.19.14).

 

  Marc

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Entering edit mode

Thanks, Marc. Works as expected.

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