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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MoonlightR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MoonlightR_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MoonlightR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MoonlightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MoonlightR’ version ‘1.27.0’
* 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 ‘MoonlightR’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'GDCquery(project = CancerProject, ': unused argument (legacy = TRUE) 
See ‘/home/biocbuild/bbs-3.17-bioc/meat/MoonlightR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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
getDataTCGA: possible error in GDCquery(project = CancerProject,
  data.category = "Gene expression", data.type = "Gene expression
  quantification", platform = "Illumina HiSeq", file.type = "results",
  legacy = TRUE): unused argument (legacy = TRUE)
getDataTCGA: possible error in GDCquery(project = CancerProject,
  data.category = "Gene expression", data.type = "Gene expression
  quantification", platform = "Illumina HiSeq", file.type = "results",
  barcode = c(dataSmTP, dataSmNT), legacy = TRUE): unused argument
  (legacy = TRUE)
getDataTCGA: possible error in GDCquery(project = CancerProject,
  data.category = "Gene expression", data.type = "Gene expression
  quantification", platform = "Illumina HiSeq", file.type = "results",
  barcode = c(sample(dataSmTP, nSample), sample(dataSmNT, nSample)),
  legacy = TRUE): unused argument (legacy = TRUE)
getDataTCGA: possible error in GDCquery(project = CancerProject, legacy
  = TRUE, data.category = "DNA methylation", platform = "Illumina Human
  Methylation 27"): unused argument (legacy = TRUE)
getDataTCGA: possible error in GDCquery(project = CancerProject, legacy
  = TRUE, data.category = "DNA methylation", platform = "Illumina Human
  Methylation 27", barcode = sampDown): unused argument (legacy = TRUE)
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
URA     17.973  0.680  17.356
FEA     14.052  0.204  14.255
plotFEA  8.954  0.236   9.190
DPA      6.995  0.200   7.214
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Moonlight.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MoonlightR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MoonlightR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘MoonlightR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'GDCquery(project = CancerProject, ': unused argument (legacy = TRUE) 
Note: possible error in 'GDCquery(project = CancerProject, ': unused argument (legacy = TRUE) 
Note: possible error in 'GDCquery(project = CancerProject, ': unused argument (legacy = TRUE) 
Note: possible error in 'GDCquery(project = CancerProject, ': unused argument (legacy = TRUE) 
Note: possible error in 'GDCquery(project = CancerProject, ': unused argument (legacy = TRUE) 
** 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 (MoonlightR)