| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:13 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1227/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylInheritance 1.26.0 (landing page) Astrid Deschênes
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the methylInheritance package: - 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. |
| Package: methylInheritance |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylInheritance_1.26.0.tar.gz |
| StartedAt: 2024-04-17 19:03:58 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 19:13:15 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 557.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylInheritance.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylInheritance_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/methylInheritance.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.26.0’
* 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 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runPermutation 96.928 1.775 99.120
runObservation 48.064 0.884 49.055
samplesForTransgenerationalAnalysis 34.486 0.889 35.476
runOnePermutationOnAllGenerations 11.402 0.233 11.709
demoForTransgenerationalAnalysis 6.028 0.120 6.165
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
methylInheritance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylInheritance ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)
methylInheritance.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, 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, sort, 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
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 -- Wed Apr 17 19:13:04 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
37.542 0.801 38.406
methylInheritance.Rcheck/methylInheritance-Ex.timings
| name | user | system | elapsed | |
| calculateSignificantLevel | 0.018 | 0.003 | 0.020 | |
| createDataStructure | 0.076 | 0.006 | 0.083 | |
| createOutputDir | 0.001 | 0.001 | 0.002 | |
| demoForTransgenerationalAnalysis | 6.028 | 0.120 | 6.165 | |
| extractInfo | 0.176 | 0.005 | 0.186 | |
| formatInputMethylData | 0.318 | 0.028 | 0.346 | |
| getGRangesFromMethylDiff | 0.121 | 0.003 | 0.123 | |
| interGeneration | 0.956 | 0.007 | 0.964 | |
| isInterGenerationResults | 0.002 | 0.000 | 0.002 | |
| loadAllRDSResults | 0.158 | 0.002 | 0.162 | |
| loadConvergenceData | 0.232 | 0.004 | 0.238 | |
| mergePermutationAndObservation | 0.003 | 0.001 | 0.003 | |
| methylInheritanceAllResults | 0.004 | 0.002 | 0.006 | |
| methylInheritanceResults | 0.011 | 0.003 | 0.013 | |
| plotConvergenceGraph | 0.526 | 0.011 | 0.536 | |
| plotGraph | 0.389 | 0.007 | 0.397 | |
| readInterGenerationResults | 0.034 | 0.002 | 0.036 | |
| runObservation | 48.064 | 0.884 | 49.055 | |
| runOnePermutationOnAllGenerations | 11.402 | 0.233 | 11.709 | |
| runPermutation | 96.928 | 1.775 | 99.120 | |
| samplesForTransgenerationalAnalysis | 34.486 | 0.889 | 35.476 | |
| saveInterGenerationResults | 0.960 | 0.006 | 0.966 | |
| validateExtractInfo | 0.002 | 0.002 | 0.004 | |
| validateLoadConvergenceData | 0.001 | 0.000 | 0.002 | |
| validateMergePermutationAndObservation | 0.001 | 0.000 | 0.001 | |
| validateRunObservation | 0.191 | 0.010 | 0.200 | |
| validateRunPermutation | 0.192 | 0.009 | 0.202 | |