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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:uncoverappLib.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings uncoverappLib_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/uncoverappLib.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 ‘uncoverappLib/DESCRIPTION’ ... OK
* this is package ‘uncoverappLib’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘uncoverappLib’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/uncoverappLib.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* 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
buildInput : riarrange.df: no visible binding for global variable
  'nucleotide'
buildInput : riarrange.df: no visible binding for global variable
  'count'
buildInput: no visible binding for global variable 'seqnames.1'
buildInput: no visible binding for global variable 'start.1'
buildInput: no visible binding for global variable 'end.1'
buildInput: no visible binding for global variable 'width.1'
buildInput: no visible binding for global variable 'strand.1'
buildInput : statistical_operation: no visible binding for global
  variable 'SYMBOL'
buildInput : statistical_operation: no visible binding for global
  variable 'value'
buildInput : statistical_operation: no visible global function
  definition for 'median'
buildInput : statistical_operation: no visible binding for global
  variable '.'
Undefined global functions or variables:
  . SYMBOL count end.1 median nucleotide seqnames.1 start.1 strand.1
  value width.1
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
buildInput 7.975  0.231   8.321
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/uncoverappLib.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL uncoverappLib
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘uncoverappLib’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** 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
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (uncoverappLib)