##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:magpie.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings magpie_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/magpie.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘magpie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘magpie’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.21-bioc/meat/magpie.Rcheck/00check.log’
for details.