Back to Build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2022-06-27 11:10:05 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 recountmethylation on nebbiolo1


To the developers/maintainers of the recountmethylation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recountmethylation.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1611/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recountmethylation 1.6.1  (landing page)
Sean K Maden
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/recountmethylation
git_branch: RELEASE_3_15
git_last_commit: 6b0db13
git_last_commit_date: 2022-05-28 14:44:29 -0400 (Sat, 28 May 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: recountmethylation
Version: 1.6.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings recountmethylation_1.6.1.tar.gz
StartedAt: 2022-06-26 21:30:36 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 21:31:56 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 79.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: recountmethylation.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings recountmethylation_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/recountmethylation.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recountmethylation/DESCRIPTION’ ... OK
* this is package ‘recountmethylation’ version ‘1.6.1’
* 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 ‘recountmethylation’ 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘DelayedMatrixStats’ ‘basilisk’ ‘reticulate’
Namespace in Imports field not imported from: ‘IlluminaHumanMethylation450kmanifest’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘ba.background’ ‘ba.biotinstaining.grn’ ‘ba.biotinstaining.red’
  ‘ba.bisulfiteconv1.grn’ ‘ba.bisulfiteconv1.red’ ‘ba.bisulfiteconv2’
  ‘ba.extension.grn’ ‘ba.extension.red’ ‘ba.hybridization.hi.vs.med’
  ‘ba.hybridization.med.vs.low’ ‘ba.nonpolymorphic.grn’
  ‘ba.nonpolymorphic.red’ ‘ba.restoration’ ‘ba.specificity1.grn’
  ‘ba.specificity1.red’ ‘ba.specificity2’ ‘ba.targetremoval1’
  ‘ba.targetremoval2’ ‘setup_sienv’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_fh : <anonymous>: no visible global function definition for
  ‘make_fhmatrix_autolabel’
make_si : <anonymous>: no visible global function definition for
  ‘make_hnsw_si’
query_si: no visible binding for global variable ‘v’
query_si : <anonymous>: no visible global function definition for
  ‘make_dfk_sampleid’
Undefined global functions or variables:
  make_dfk_sampleid make_fhmatrix_autolabel make_hnsw_si v
* checking Rd files ... NOTE
prepare_Rd: query_si.Rd:33-35: Dropping empty section \value
* 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 ... WARNING
'library' or 'require' call not declared from: ‘minfiData’
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
bactrl      13.621  1.040  14.663
gds_idat2rg  6.919  0.629  11.206
get_rmdl     0.260  0.033   5.763
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-servermatrix.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: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/recountmethylation.Rcheck/00check.log’
for details.



Installation output

recountmethylation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL recountmethylation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘recountmethylation’ ...
** using staged installation
** R
** 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 (recountmethylation)

Tests output

recountmethylation.Rcheck/tests/test-servermatrix.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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.

> testthat::context("Test the server matrix properties")
> 
> testthat::test_that("Properties of server matrix returned from get_rmdl 
+     and servermatrix", {
+     sm <- recountmethylation::get_servermatrix()
+     testthat::expect_true(is(sm, "matrix"))
+     testthat::expect_equal(ncol(sm), 4)
+     testthat::expect_true(is(sm[,1], "character"))
+ })
Test passed 😀
> 
> proc.time()
   user  system elapsed 
  1.307   0.067   5.770 

Example timings

recountmethylation.Rcheck/recountmethylation-Ex.timings

nameusersystemelapsed
bactrl13.621 1.04014.663
bathresh0.0010.0000.001
data_mdpost0.0170.0000.018
gds_idat2rg 6.919 0.62911.206
gds_idatquery1.6970.4134.664
get_crossreactive_cpgs0.1210.0120.137
get_fh000
get_qcsignal2.4950.3352.831
get_rmdl0.2600.0335.763
get_servermatrix0.0070.0000.007
getdb0.0000.0000.001
getrg0.3400.0320.372
hread0.0090.0000.009
make_si000
matchds_1to20.0020.0000.002
query_si0.0000.0010.001
rgse0.0800.0180.098
servermatrix0.0220.0000.336
smfilt0.0020.0000.002