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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:magpie.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings magpie_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/magpie.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘magpie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘magpie’ version ‘1.9.0’
* 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 ‘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-3.22-bioc/meat/magpie.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL magpie
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘magpie’ ...
** this is package ‘magpie’ version ‘1.9.0’
** 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)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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 -- Thu Oct 23 01:30:58 2025 
*********************************************** 
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 
 11.235   0.490  11.714