Hello!

After JSONIO package installation I can't install interactiveDisplay package because of some problem with class specification. What should do to fix that?

Thank you!

> biocLite("interactiveDisplay")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.0.
Installing package(s) ‘interactiveDisplay’
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/interactiveDisplay_1.6.0.tar.gz'
Content type 'application/x-gzip' length 4789174 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

* installing *source* package ‘interactiveDisplay’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  object 'vI' not found
ERROR: lazy loading failed for package ‘interactiveDisplay’
* removing ‘/home/vyacheslav/R/x86_64-pc-linux-gnu-library/3.1/interactiveDisplay’

The downloaded source packages are in
    ‘/tmp/Rtmp7eXK1X/downloaded_packages’
Old packages: 'graph', 'GSEABase', 'interactiveDisplayBase', 'RBGL', 'shiny',
  'biomaRt', 'BitSeq', 'DESeq', 'edgeR', 'HilbertVis', 'limma', 'pcaMethods',
  'pkgKitten', 'plotrix', 'prettyR', 'qvalue', 'sp', 'testthat', 'zlibbioc',
  'survival'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘interactiveDisplay’ had non-zero exit status

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

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

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

other attached packages:
[1] interactiveDisplayBase_1.6.0 metagenomeSeq_1.10.0        
[3] RColorBrewer_1.1-2           limma_3.24.10               
[5] Biobase_2.28.0               BiocGenerics_0.14.0         
[7] BiocInstaller_1.18.3        

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6        matrixStats_0.14.0 codetools_0.2-11   gtools_3.5.0      
 [5] digest_0.6.8       mime_0.3           bitops_1.0-6       R6_2.0.1          
 [9] xtable_1.7-4       KernSmooth_2.23-14 gplots_2.17.0      gdata_2.16.1      
[13] mzR_2.2.1          xcms_1.44.0        tools_3.2.0        ProtGenerics_1.0.0
[17] shiny_0.12.1       httpuv_1.3.2       caTools_1.17.1     htmltools_0.2.6   

Hi,

Hmm, I reinstalled RJSONIO and BiocGenerics myself and cannot reproduce your error.

Searching this:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : object 'vI' not found

Gives a lot of results suggesting an update of your packages.  I seem to recall RJSONIO harmlessly throwing messages in the past, it may be the case that your error is falsely attributed to it.  Still, RJSONIO doesn't complain on my system at the moment.

I notice you selected not to update.

###########

Old packages: 'graph', 'GSEABase', 'interactiveDisplayBase', 'RBGL', 'shiny',
  'biomaRt', 'BitSeq', 'DESeq', 'edgeR', 'HilbertVis', 'limma', 'pcaMethods',
  'pkgKitten', 'plotrix', 'prettyR', 'qvalue', 'sp', 'testthat', 'zlibbioc',
  'survival'
Update all/some/none? [a/s/n]: n

###########

How about trying the following and then try installing interactiveDisplay:

biocLite(c('RJSONIO', 'BiocGenerics', 'graph', 'GSEABase', 'interactiveDisplayBase', 'RBGL', 'shiny', 'biomaRt', 'BitSeq', 'DESeq', 'edgeR', 'HilbertVis', 'limma', 'pcaMethods', 'pkgKitten', 'plotrix', 'prettyR', 'qvalue', 'sp', 'testthat', 'zlibbioc', 'survival'))

biocLite("interactiveDisplay")

-Shawn

Hi again,

I tried to use your recommendations, unfortunately it does not work. Nevertheless, the problem was solved after reinstallation of libxml2 and libcurl4 libraries.

Thank you for your help!