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This page was generated on 2024-03-28 11:36:40 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1133/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
magpie 1.3.1  (landing page)
Daoyu Duan
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/magpie
git_branch: devel
git_last_commit: 7b3602e
git_last_commit_date: 2023-12-15 13:03:45 -0400 (Fri, 15 Dec 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for magpie on nebbiolo1


To the developers/maintainers of the magpie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/magpie.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: magpie
Version: 1.3.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:magpie.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings magpie_1.3.1.tar.gz
StartedAt: 2024-03-27 23:50:50 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:55:41 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 290.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: magpie.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:magpie.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings magpie_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/magpie.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* 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 ‘magpie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘magpie’ version ‘1.3.1’
* 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 ‘magpie’ 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 code 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 ... NOTE
checkRd: (-1) QuickPower.Rd:28: Lost braces
    28 | {GSE46705: }{Human HeLa cell line: Two replicates of wild type (WT) and two replicates of knockdown (KD) of complex METTL3.}\cr
       |             ^
checkRd: (-1) QuickPower.Rd:29: Lost braces; missing escapes or markup?
    29 | {GSE55575: }{Mouse embryonic fibroblasts: Two replicates of wild type (WT) and four replicates of knockdown (KD) of WTAP.}\cr
       | ^
checkRd: (-1) QuickPower.Rd:29: Lost braces
    29 | {GSE55575: }{Mouse embryonic fibroblasts: Two replicates of wild type (WT) and four replicates of knockdown (KD) of WTAP.}\cr
       |             ^
checkRd: (-1) QuickPower.Rd:30: Lost braces; missing escapes or markup?
    30 | {GSE115105: }{Two sample types from WT and YTHDF1 KO mice. Each type has two replicates.}\cr
       | ^
checkRd: (-1) QuickPower.Rd:30: Lost braces
    30 | {GSE115105: }{Two sample types from WT and YTHDF1 KO mice. Each type has two replicates.}\cr
       |              ^
checkRd: (-1) QuickPower.Rd:31: Lost braces; missing escapes or markup?
    31 | {GSE94613: }{Human leukemia cell line: Four replicates of wild type (WT) and eight replicates of knockdown (KD) of complex METTL3.}
       | ^
checkRd: (-1) QuickPower.Rd:31: Lost braces
    31 | {GSE94613: }{Human leukemia cell line: Four replicates of wild type (WT) and eight replicates of knockdown (KD) of complex METTL3.}
       |             ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'powerEval.Rd':
powerEval
  Code: function(Input.file, IP.file, BamDir, annoDir, variable,
                 bam_factor, nsim = 10, N.reps = c(2, 3, 5),
                 depth_factor = c(1, 2, 5), thres = c(0.01, 0.05, 0.1,
                 0.2), dmrProp = NULL, Test_method = "TRESS")
  Docs: function(Input.file, IP.file, BamDir, annoDir, variable,
                 bam_factor, nsim = 10, N.reps = c(2, 3, 5),
                 depth_factor = c(1, 2, 5), thres = c(0.01, 0.05, 0.1,
                 0.2), Test_method = "TRESS")
  Argument names in code not in docs:
    dmrProp
  Mismatches in argument names:
    Position: 11 Code: dmrProp Docs: Test_method

* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/magpie.Rcheck/00check.log’
for details.


Installation output

magpie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL magpie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘magpie’ ...
** 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 (magpie)

Tests output

magpie.Rcheck/tests/runTest.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> BiocGenerics:::testPackage("magpie")


RUNIT TEST PROTOCOL -- Wed Mar 27 23:55:19 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
magpie RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 12.009   0.683  12.683 

Example timings

magpie.Rcheck/magpie-Ex.timings

nameusersystemelapsed
PlotAll0.0380.0000.038
PlotRes0.0060.0000.006
PlotStrata0.0080.0000.008
QuickPower0.0010.0000.001
WriteToxlsx0.3590.0310.391
WriteToxlsx_strata0.0320.0080.040
plotAll_Strata0.0170.0040.021
power.test0.0010.0000.001
powerEval000