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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:FunciSNP.data.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings FunciSNP.data_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/FunciSNP.data.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FunciSNP.data/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FunciSNP.data’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FunciSNP.data’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'FunciSNP.data' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.12-data-experiment/meat/FunciSNP.data.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   2.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘IRanges’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘FunciSNP.data-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lincRNA.hg19.rda
> ### Title: Known long intergentic non coding RNA
> ### Aliases: lincRNA.hg19.rda lincRNA
> ### Keywords: datasets
> 
> ### ** Examples
> 
> lincRNA
An object of class "RangedData"
<S4 Type Object>
attr(,"ranges")
IRangesList object of length 41:
$`1`
IRanges object with 1192 ranges and 0 metadata columns:
                     start       end     width
                 <integer> <integer> <integer>
  TCONS_00000720 209701799 209741018     39220
  TCONS_00000721 209701885 209720925     19041
  TCONS_00001039  95392853  95433017     40165
  TCONS_00001040  95392966  95429158     36193
  TCONS_00001042  95392966  95429158     36193
             ...       ...       ...       ...
  TCONS_00001361 247537324 247538837      1514
  TCONS_00001362 247549930 247556961      7032
  TCONS_00001363 247802917 247803681       765
  TCONS_00001364 248675755 248676345       591
  TCONS_00000435 249153362 249158995      5634

...
<40 more elements>
attr(,"values")
SplitDataFrameList of length 41
$`1`
DataFrame with 1192 rows and 2 columns
                 strand     score
               <factor> <numeric>
TCONS_00000720       -1         0
TCONS_00000721       -1         0
TCONS_00001039       1          0
TCONS_00001040       1          0
TCONS_00001042       1          0
...                 ...       ...
TCONS_00001361        1         0
TCONS_00001362        1         0
TCONS_00001363        1         0
TCONS_00001364        1         0
TCONS_00000435        1         0

...
<40 more elements>
attr(,"elementType")
[1] "ANY"
attr(,"elementMetadata")
`\001NULL\001`
attr(,"metadata")
list()
> dim(lincRNA)
NULL
> head(lincRNA)
Error in x[seq_len(n)] : object of type 'S4' is not subsettable
Calls: head -> head -> head.default
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/FunciSNP.data.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL FunciSNP.data
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘FunciSNP.data’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'FunciSNP.data' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'FunciSNP.data' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (FunciSNP.data)