Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-01-21 13:06:38 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for methylInheritance on tokay2


To the developers/maintainers of the methylInheritance package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1121/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylInheritance 1.18.0  (landing page)
Astrid DeschĂȘnes
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/methylInheritance
git_branch: RELEASE_3_14
git_last_commit: 0387c10
git_last_commit_date: 2021-10-26 12:34:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: methylInheritance
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylInheritance.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methylInheritance_1.18.0.tar.gz
StartedAt: 2022-01-20 22:47:01 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 23:01:57 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 895.9 seconds
RetCode: 0
Status:   OK  
CheckDir: methylInheritance.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylInheritance.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings methylInheritance_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/methylInheritance.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylInheritance/DESCRIPTION' ... OK
* this is package 'methylInheritance' version '1.18.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
runPermutation                      124.12   0.27  124.36
runObservation                       57.09   0.72   57.81
samplesForTransgenerationalAnalysis  43.25   0.37   43.69
runOnePermutationOnAllGenerations    14.57   0.25   14.86
demoForTransgenerationalAnalysis      7.83   0.51    8.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
runPermutation                      121.18   0.03  121.18
runObservation                       54.54   0.11   54.59
samplesForTransgenerationalAnalysis  42.19   0.09   42.28
runOnePermutationOnAllGenerations    14.25   0.06   14.32
demoForTransgenerationalAnalysis      8.31   0.12    8.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: OK


Installation output

methylInheritance.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/methylInheritance_1.18.0.tar.gz && rm -rf methylInheritance.buildbin-libdir && mkdir methylInheritance.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylInheritance.buildbin-libdir methylInheritance_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL methylInheritance_1.18.0.zip && rm methylInheritance_1.18.0.tar.gz methylInheritance_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1456k  100 1456k    0     0  3004k      0 --:--:-- --:--:-- --:--:-- 3009k

install for i386

* installing *source* package 'methylInheritance' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methylInheritance'
    finding HTML links ... done
    calculateSignificantLevel               html  
    createDataStructure                     html  
    createOutputDir                         html  
    demoForTransgenerationalAnalysis        html  
    extractInfo                             html  
    formatInputMethylData                   html  
    getGRangesFromMethylDiff                html  
    interGeneration                         html  
    isInterGenerationResults                html  
    loadAllRDSResults                       html  
    loadConvergenceData                     html  
    mergePermutationAndObservation          html  
    methylInheritance-package               html  
    methylInheritanceAllResults             html  
    methylInheritanceResults                html  
    plotConvergenceGraph                    html  
    plotGraph                               html  
    readInterGenerationResults              html  
    runObservation                          html  
    runOnePermutationOnAllGenerations       html  
    runPermutation                          html  
    samplesForTransgenerationalAnalysis     html  
    saveInterGenerationResults              html  
    validateExtractInfo                     html  
    validateLoadConvergenceData             html  
    validateMergePermutationAndObservation
                                            html  
    validateRunObservation                  html  
    validateRunPermutation                  html  
** 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

install for x64

* installing *source* package 'methylInheritance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylInheritance' as methylInheritance_1.18.0.zip
* DONE (methylInheritance)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'methylInheritance' successfully unpacked and MD5 sums checked

Tests output

methylInheritance.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
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 -- Thu Jan 20 23:01:00 2022 
*********************************************** 
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. 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 
  43.03    1.54   44.89 

methylInheritance.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
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 -- Thu Jan 20 23:01:48 2022 
*********************************************** 
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. 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 
  46.37    0.81   47.18 

Example timings

methylInheritance.Rcheck/examples_i386/methylInheritance-Ex.timings

nameusersystemelapsed
calculateSignificantLevel0.040.000.03
createDataStructure0.060.000.06
createOutputDir000
demoForTransgenerationalAnalysis7.830.518.34
extractInfo0.290.000.30
formatInputMethylData0.330.070.39
getGRangesFromMethylDiff0.190.030.25
interGeneration1.530.001.53
isInterGenerationResults0.000.010.02
loadAllRDSResults0.190.000.19
loadConvergenceData0.370.000.40
mergePermutationAndObservation000
methylInheritanceAllResults0.000.020.02
methylInheritanceResults0.030.000.03
plotConvergenceGraph0.600.000.59
plotGraph0.360.010.38
readInterGenerationResults0.060.000.06
runObservation57.09 0.7257.81
runOnePermutationOnAllGenerations14.57 0.2514.86
runPermutation124.12 0.27124.36
samplesForTransgenerationalAnalysis43.25 0.3743.69
saveInterGenerationResults1.70.01.7
validateExtractInfo000
validateLoadConvergenceData000
validateMergePermutationAndObservation0.020.000.02
validateRunObservation0.170.000.17
validateRunPermutation0.170.000.17

methylInheritance.Rcheck/examples_x64/methylInheritance-Ex.timings

nameusersystemelapsed
calculateSignificantLevel0.010.020.04
createDataStructure0.090.000.09
createOutputDir000
demoForTransgenerationalAnalysis8.310.128.44
extractInfo0.220.000.22
formatInputMethylData0.220.020.24
getGRangesFromMethylDiff0.110.000.10
interGeneration1.440.001.44
isInterGenerationResults000
loadAllRDSResults0.220.000.22
loadConvergenceData0.260.000.27
mergePermutationAndObservation000
methylInheritanceAllResults000
methylInheritanceResults0.010.000.02
plotConvergenceGraph0.740.000.73
plotGraph0.370.000.38
readInterGenerationResults0.060.000.06
runObservation54.54 0.1154.59
runOnePermutationOnAllGenerations14.25 0.0614.32
runPermutation121.18 0.03121.18
samplesForTransgenerationalAnalysis42.19 0.0942.28
saveInterGenerationResults1.280.001.29
validateExtractInfo0.020.000.01
validateLoadConvergenceData000
validateMergePermutationAndObservation000
validateRunObservation0.110.000.11
validateRunPermutation0.110.020.13