| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:27 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1189/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylInheritance 1.23.0 (landing page) Astrid Deschênes
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: methylInheritance |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings methylInheritance_1.23.0.tar.gz |
| StartedAt: 2023-04-11 21:29:09 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 21:38:35 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 565.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylInheritance.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings methylInheritance_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/methylInheritance.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.23.0’
* 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 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 ... 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 111.204 0.628 111.201
runObservation 53.198 0.740 53.601
samplesForTransgenerationalAnalysis 37.785 0.101 36.094
runOnePermutationOnAllGenerations 13.814 0.207 13.409
demoForTransgenerationalAnalysis 6.246 0.283 6.527
* 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 ...
‘methylInheritance.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
methylInheritance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL methylInheritance ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 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 -- Tue Apr 11 21:37:42 2023
***********************************************
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
43.106 1.039 44.131
methylInheritance.Rcheck/methylInheritance-Ex.timings
| name | user | system | elapsed | |
| calculateSignificantLevel | 0.016 | 0.000 | 0.016 | |
| createDataStructure | 0.053 | 0.004 | 0.058 | |
| createOutputDir | 0.000 | 0.001 | 0.001 | |
| demoForTransgenerationalAnalysis | 6.246 | 0.283 | 6.527 | |
| extractInfo | 0.177 | 0.000 | 0.178 | |
| formatInputMethylData | 0.204 | 0.040 | 0.244 | |
| getGRangesFromMethylDiff | 0.094 | 0.000 | 0.095 | |
| interGeneration | 0.954 | 0.008 | 0.963 | |
| isInterGenerationResults | 0.000 | 0.001 | 0.002 | |
| loadAllRDSResults | 0.190 | 0.001 | 0.191 | |
| loadConvergenceData | 0.189 | 0.000 | 0.189 | |
| mergePermutationAndObservation | 0.002 | 0.000 | 0.003 | |
| methylInheritanceAllResults | 0.005 | 0.000 | 0.004 | |
| methylInheritanceResults | 0.005 | 0.008 | 0.012 | |
| plotConvergenceGraph | 0.477 | 0.008 | 0.484 | |
| plotGraph | 0.417 | 0.004 | 0.421 | |
| readInterGenerationResults | 0.037 | 0.000 | 0.037 | |
| runObservation | 53.198 | 0.740 | 53.601 | |
| runOnePermutationOnAllGenerations | 13.814 | 0.207 | 13.409 | |
| runPermutation | 111.204 | 0.628 | 111.201 | |
| samplesForTransgenerationalAnalysis | 37.785 | 0.101 | 36.094 | |
| saveInterGenerationResults | 1.139 | 0.000 | 1.138 | |
| validateExtractInfo | 0.000 | 0.002 | 0.002 | |
| validateLoadConvergenceData | 0.001 | 0.001 | 0.001 | |
| validateMergePermutationAndObservation | 0.001 | 0.000 | 0.001 | |
| validateRunObservation | 0.103 | 0.020 | 0.123 | |
| validateRunPermutation | 0.106 | 0.016 | 0.122 | |