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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings methylInheritance_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/methylInheritance.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.33.0’
* package encoding: UTF-8
* 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 ‘methylInheritance’ can be installed ... OK
* checking installed package size ... OK
* 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 code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 ... NOTE
checkRd: (-1) demoForTransgenerationalAnalysis.Rd:59-61: Lost braces
    59 |     \item \code{\link{runPermutation}} {for running a
       |                                        ^
checkRd: (-1) demoForTransgenerationalAnalysis.Rd:62-63: Lost braces
    62 |     \item \code{\link{runObservation}} {for running an
       |                                        ^
checkRd: (-1) isInterGenerationResults.Rd:21: Lost braces; missing escapes or markup?
    21 | "_permutation_{permutationID}.RDS" extension.}
       |               ^
checkRd: (-1) methylInheritance-package.Rd:19-21: Lost braces
    19 |     \item \code{\link{runPermutation}} {for running a
       |                                        ^
checkRd: (-1) methylInheritance-package.Rd:22-23: Lost braces
    22 |     \item \code{\link{runObservation}} {for running an
       |                                        ^
checkRd: (-1) methylInheritanceResults.Rd:293-294: Lost braces
   293 |     \item \code{\link{extractInfo}} {for extracting the
       |                                     ^
checkRd: (-1) readInterGenerationResults.Rd:25: Lost braces; missing escapes or markup?
    25 | "_permutation_{permutationID}.RDS" extension.}
       |               ^
checkRd: (-1) runOnePermutationOnAllGenerations.Rd:144-173: Lost braces
   144 | itemize{
       |        ^
checkRd: (-1) samplesForTransgenerationalAnalysis.Rd:48-50: Lost braces
    48 |     \item \code{\link{runPermutation}} {for running a
       |                                        ^
checkRd: (-1) saveInterGenerationResults.Rd:27: Lost braces; missing escapes or markup?
    27 | "_permutation_{permutationID}.RDS" extension.}
       |               ^
* 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 ‘methylInheritance-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: demoForTransgenerationalAnalysis
> ### Title: The methylation information from samples over three generations.
> ###   Information for each generation is stored in a 'methylRawList' format
> ###   (for demo purpose).
> ### Aliases: demoForTransgenerationalAnalysis
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> ## Loading dataset
> data(demoForTransgenerationalAnalysis)
> 
> ## Run a permutation analysis
> runObservation(methylKitData = demoForTransgenerationalAnalysis,
+     outputDir = "test_demo", type = "tiles", vSeed = 2001)
Error in sortSeqlevels(regions) : could not find function "sortSeqlevels"
Calls: runObservation ... lapply -> FUN -> FUN -> regionCounts -> regionCounts
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/methylInheritance.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL methylInheritance
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘methylInheritance’ ...
** this is package ‘methylInheritance’ version ‘1.33.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘GenomeInfoDb’ for request: ‘seqlengths’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘seqlevels’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘seqnames’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘sortSeqlevels’ when loading ‘methylKit’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘GenomeInfoDb’ for request: ‘seqlengths’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘seqlevels’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘seqnames’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘sortSeqlevels’ when loading ‘methylKit’
** testing if installed package can be loaded from final location
No methods found in package ‘GenomeInfoDb’ for request: ‘seqlengths’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘seqlevels’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘seqnames’ when loading ‘methylKit’
No methods found in package ‘GenomeInfoDb’ for request: ‘sortSeqlevels’ when loading ‘methylKit’
** testing if installed package keeps a record of temporary installation path
* DONE (methylInheritance)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("methylInheritance")
No methods found in package 'GenomeInfoDb' for request: 'seqlengths' when loading 'methylKit'
No methods found in package 'GenomeInfoDb' for request: 'seqlevels' when loading 'methylKit'
No methods found in package 'GenomeInfoDb' for request: 'seqnames' when loading 'methylKit'
No methods found in package 'GenomeInfoDb' for request: 'sortSeqlevels' when loading 'methylKit'
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
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Permutation Analysis

Number of Generations:  3 
Number of Permutations:  20 

Observation Results: 
        SOURCE ELEMENT ANALYSIS   TYPE RESULT
1  OBSERVATION   SITES       i2 HYPER1      4
2  OBSERVATION   SITES       i2 HYPER2      1
3  OBSERVATION   SITES       i2  HYPO1      2
4  OBSERVATION   SITES       i2  HYPO2      2
5  OBSERVATION   SITES     iAll  HYPER      0
6  OBSERVATION   SITES     iAll   HYPO      0
7  OBSERVATION   TILES       i2 HYPER1   1000
8  OBSERVATION   TILES       i2 HYPER2      0
9  OBSERVATION   TILES       i2  HYPO1      0
10 OBSERVATION   TILES       i2  HYPO2      0
11 OBSERVATION   TILES     iAll  HYPER      0
12 OBSERVATION   TILES     iAll   HYPO      0


RUNIT TEST PROTOCOL -- Fri Jun 27 23:59:41 2025 
*********************************************** 
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
methylInheritance RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: Use of `formatForGraphDataFrame$RESULT` is discouraged.
ℹ Use `RESULT` instead. 
2: In max(i) : no non-missing arguments to max; returning -Inf
3: In max(i) : no non-missing arguments to max; returning -Inf
> 
> proc.time()
   user  system elapsed 
 36.291   1.009  37.292