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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings bigmelon_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/bigmelon.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bigmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bigmelon’ version ‘1.33.0’
* 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 ‘bigmelon’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
  Note: possible error in 'readPepo(barcodes = sets[!is.na(sets)], ': unused argument (barcodes = sets[!is.na(sets)]) 
See ‘/home/biocbuild/bbs-3.21-bioc/meat/bigmelon.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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’
A package should be listed in only one of these fields.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
Warning: program compiled against libxml 212 using older 211
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... WARNING
Warning: program compiled against libxml 212 using older 211
Missing or unexported object: ‘GEOquery::gunzip’
Unexported objects imported by ':::' calls:
  ‘bumphunter:::greaterOrEqual’ ‘minfi:::pickCompProbes’
  ‘minfi:::projectCellType’ ‘wateRmelon:::.impose’
  ‘wateRmelon:::.normalizeQuantiles2’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
bigpepo: possible error in readPepo(barcodes = sets[!is.na(sets)],
  manifest = manifest, n = TRUE, oob = FALSE, idatdir = path, ): unused
  argument (barcodes = sets[!is.na(sets)])
bumphunterEngine.gdsn: no visible binding for global variable
  ‘locfitByCluster’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParRegistered’
bumphunterEngine.gdsn: no visible global function definition for
  ‘registerDoSEQ’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParWorkers’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParName’
bumphunterEngine.gdsn: no visible global function definition for
  ‘getDoParVersion’
bumphunterEngine.gdsn: no visible global function definition for
  ‘smoother’
bumphunterEngine.gdsn: no visible global function definition for
  ‘regionFinder’
bumphunterEngine.gdsn: no visible global function definition for
  ‘%dorng%’
bumphunterEngine.gdsn: no visible global function definition for
  ‘foreach’
bumphunterEngine.gdsn: no visible global function definition for ‘iter’
bumphunterEngine.gdsn: no visible binding for global variable
  ‘regionFinder’
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for ‘%dorng%’
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for ‘foreach’
bumphunterEngine.gdsn : computation.tots: no visible global function
  definition for ‘iter’
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for ‘%dorng%’
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for ‘foreach’
bumphunterEngine.gdsn : computation.tots2: no visible global function
  definition for ‘iter’
es2gds: no visible global function definition for ‘colData’
estimateCellCounts.gds: no visible global function definition for
  ‘colData’
idats2gds: no visible binding for global variable ‘ChipType’
Undefined global functions or variables:
  %dorng% ChipType colData foreach getDoParName getDoParRegistered
  getDoParVersion getDoParWorkers iter locfitByCluster regionFinder
  registerDoSEQ smoother
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bigmelon-normalization.Rd: wateRmelon
  bigmelon-package.Rd: dasen, wateRmelon, gdsfmt
  ecc.Rd: convertArray
  getquantilesandranks.Rd: get.attr.gdsn
  wm-port.Rd: wateRmelon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ...

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL bigmelon
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘bigmelon’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Creating a new generic function for ‘fot’ in package ‘bigmelon’
Note: possible error in 'readPepo(barcodes = sets[!is.na(sets)], ': unused argument (barcodes = sets[!is.na(sets)]) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (bigmelon)