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This page was generated on 2024-04-17 11:36:07 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1222/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethTargetedNGS 1.34.0  (landing page)
Muhammad Ahmer Jamil
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/MethTargetedNGS
git_branch: RELEASE_3_18
git_last_commit: b3b59e3
git_last_commit_date: 2023-10-24 10:43:03 -0400 (Tue, 24 Oct 2023)
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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MethTargetedNGS on nebbiolo2


To the developers/maintainers of the MethTargetedNGS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethTargetedNGS.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: MethTargetedNGS
Version: 1.34.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MethTargetedNGS.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MethTargetedNGS_1.34.0.tar.gz
StartedAt: 2024-04-16 00:42:27 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 00:44:14 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 106.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MethTargetedNGS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MethTargetedNGS.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MethTargetedNGS_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MethTargetedNGS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MethTargetedNGS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethTargetedNGS’ version ‘1.34.0’
* 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 ‘MethTargetedNGS’ 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 ... NOTE
compare_samples: no visible global function definition for ‘par’
compare_samples: no visible global function definition for ‘lines’
fishertest_cpg: no visible global function definition for ‘fisher.test’
fishertest_cpg: no visible global function definition for ‘p.adjust’
fishertest_cpg: no visible global function definition for ‘barplot’
fishertest_cpg: no visible global function definition for ‘abline’
methAlign: no visible global function definition for ‘subject’
methAlign: no visible global function definition for ‘pattern’
nhmmer: no visible global function definition for ‘read.table’
nhmmer: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  abline barplot fisher.test lines p.adjust par pattern read.table
  setNames subject
Consider adding
  importFrom("graphics", "abline", "barplot", "lines", "par")
  importFrom("stats", "fisher.test", "p.adjust", "setNames")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MethTargetedNGS.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MethTargetedNGS.Rcheck/00check.log’
for details.



Installation output

MethTargetedNGS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MethTargetedNGS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MethTargetedNGS’ ...
** 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 (MethTargetedNGS)

Tests output


Example timings

MethTargetedNGS.Rcheck/MethTargetedNGS-Ex.timings

nameusersystemelapsed
bconv0.0000.0020.003
compare_samples3.5640.0683.633
fishertest_cpg3.4350.0363.471
hmmbuild0.0010.0000.001
methAlign1.7080.0161.725
methAvg1.7720.0231.796
methEntropy1.6480.0001.647
methHeatmap1.6940.0321.725
nhmmer0.0020.0000.001
odd_ratio3.3280.0323.359