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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1205/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylInheritance 1.29.0  (landing page)
Astrid Deschênes
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/methylInheritance
git_branch: devel
git_last_commit: 9bfdd08
git_last_commit_date: 2024-04-30 10:57:48 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for methylInheritance on palomino4

To the developers/maintainers of the methylInheritance package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylInheritance.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: methylInheritance
Version: 1.29.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylInheritance.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylInheritance_1.29.0.tar.gz
StartedAt: 2024-06-10 05:10:35 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:23:07 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 751.9 seconds
RetCode: 0
Status:   OK  
CheckDir: methylInheritance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylInheritance.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings methylInheritance_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/methylInheritance.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'methylInheritance/DESCRIPTION' ... OK
* this is package 'methylInheritance' version '1.29.0'
* 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 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
runPermutation                      113.40   1.59  115.06
runObservation                       53.57   0.91   54.52
samplesForTransgenerationalAnalysis  36.95   0.93   38.01
runOnePermutationOnAllGenerations    12.93   0.25   13.31
demoForTransgenerationalAnalysis      5.50   0.27    5.78
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/methylInheritance.Rcheck/00check.log'
for details.


Installation output

methylInheritance.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL methylInheritance
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'methylInheritance' ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methylInheritance)

Tests output

methylInheritance.Rcheck/tests/runTests.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
Loading required package: stats4
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
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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 -- Mon Jun 10 05:22:48 2024 
*********************************************** 
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 
  37.42   10.20   47.82 

Example timings

methylInheritance.Rcheck/methylInheritance-Ex.timings

nameusersystemelapsed
calculateSignificantLevel0.030.000.03
createDataStructure0.060.000.07
createOutputDir000
demoForTransgenerationalAnalysis5.500.275.78
extractInfo0.250.010.31
formatInputMethylData0.30.00.3
getGRangesFromMethylDiff0.070.000.09
interGeneration1.290.021.30
isInterGenerationResults000
loadAllRDSResults0.180.030.22
loadConvergenceData0.170.020.20
mergePermutationAndObservation000
methylInheritanceAllResults0.000.010.02
methylInheritanceResults0.020.020.03
plotConvergenceGraph0.480.010.50
plotGraph0.360.000.36
readInterGenerationResults0.040.000.03
runObservation53.57 0.9154.52
runOnePermutationOnAllGenerations12.93 0.2513.31
runPermutation113.40 1.59115.06
samplesForTransgenerationalAnalysis36.95 0.9338.01
saveInterGenerationResults0.930.030.96
validateExtractInfo000
validateLoadConvergenceData0.000.010.01
validateMergePermutationAndObservation000
validateRunObservation0.110.000.11
validateRunPermutation0.090.050.14