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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASpli.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings ASpli_2.19.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/ASpli.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ASpli/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASpli' version '2.19.0'
* 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 whether package 'ASpli' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'ASpli'
See 'F:/biocbuild/bbs-3.22-bioc/meat/ASpli.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 ... 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'txdbmaker'
  All declared Imports should be used.
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DUreport.Rd: edgeR
  DUreport.norm.Rd: edgeR
  DUreport.offset.Rd: edgeR
  DUreportBinSplice-method.Rd: edgeR
  gbDUreport-method.Rd: edgeR
  jDUreport.Rd: edgeR
  junctionDUreport.Rd: edgeR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
ASpli-package           156.38   0.52  157.03
integrateSignals         85.31   0.14   85.48
jDUreport                84.91   0.10   85.07
jCounts-methods          84.03   0.03   84.07
exportIntegratedSignals  82.52   0.28   85.11
splicingReport           80.56   0.15   80.75
exportSplicingReports    80.39   0.20   83.03
gbDUreport-method        71.34   0.19   71.53
gbCounts                 71.13   0.11   71.60
* 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: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/ASpli.Rcheck/00check.log'
for details.

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###
### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL ASpli
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'ASpli' ...
** this is package 'ASpli' version '2.19.0'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'ASpli'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'ASpli'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'ASpli'
** testing if installed package keeps a record of temporary installation path
* DONE (ASpli)