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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LinTInd.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LinTInd_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/LinTInd.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LinTInd/DESCRIPTION’ ... OK
* this is package ‘LinTInd’ version ‘1.10.0’
* 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 ‘LinTInd’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BuildTree: no visible global function definition for ‘write.csv’
FindIndel : find_barcode: no visible global function definition for
  ‘is’
FindIndel: no visible global function definition for ‘write.table’
IndelForm: no visible global function definition for ‘write.csv’
IndelIdents: no visible global function definition for ‘write.csv’
IndelIdents : max_reads_stat: no visible global function definition for
  ‘is’
IndelPlot: no visible binding for global variable ‘Site’
IndelPlot: no visible binding for global variable ‘Freq’
PlotTree: no visible binding for global variable ‘tags’
PlotTree: no visible binding for global variable ‘celltype’
PlotTree: no visible binding for global variable ‘Freq’
PlotTree : SortTree: no visible binding for global variable
  ‘tag_number’
PlotTree: no visible binding for global variable ‘y’
PlotTree: no visible binding for global variable ‘variable’
PlotTree: no visible binding for global variable ‘value’
ReadFasta: no visible global function definition for ‘read.table’
TagProcess: no visible binding for global variable ‘i’
change_form_stat : <anonymous>: no visible binding for global variable
  ‘scarref’
change_form_stat: no visible binding for global variable ‘scarref’
Undefined global functions or variables:
  Freq Site celltype i is read.table scarref tag_number tags value
  variable write.csv write.table y
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: cellsinfo.Rd:10: Dropping empty section \source
prepare_Rd: cellsinfo.Rd:11-12: Dropping empty section \references
prepare_Rd: celltype.Rd:10: Dropping empty section \source
prepare_Rd: celltype.Rd:11-12: Dropping empty section \references
prepare_Rd: cutsite.Rd:10: Dropping empty section \source
prepare_Rd: cutsite.Rd:11-12: Dropping empty section \references
prepare_Rd: data.Rd:10: Dropping empty section \source
prepare_Rd: data.Rd:11-12: Dropping empty section \references
prepare_Rd: example_data.Rd:15-17: Dropping empty section \details
prepare_Rd: example_data.Rd:18-20: Dropping empty section \source
prepare_Rd: example_data.Rd:21-23: Dropping empty section \references
prepare_Rd: ref.Rd:10: Dropping empty section \source
prepare_Rd: ref.Rd:11-12: Dropping empty section \references
prepare_Rd: scarform.Rd:10: Dropping empty section \source
prepare_Rd: scarform.Rd:11-12: Dropping empty section \references
prepare_Rd: scarinfo.Rd:10: Dropping empty section \source
prepare_Rd: scarinfo.Rd:11-12: Dropping empty section \references
prepare_Rd: scarref.Rd:10: Dropping empty section \source
prepare_Rd: scarref.Rd:11-12: Dropping empty section \references
prepare_Rd: scarref_all.Rd:10: Dropping empty section \source
prepare_Rd: scarref_all.Rd:11-12: Dropping empty section \references
prepare_Rd: tag.Rd:10: Dropping empty section \source
prepare_Rd: tag.Rd:11-12: Dropping empty section \references
prepare_Rd: treeinfo.Rd:10: Dropping empty section \source
prepare_Rd: treeinfo.Rd:11-12: Dropping empty section \references
* 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
FindIndel 0.075  0.013   8.005
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/LinTInd.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LinTInd
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘LinTInd’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
[1] "Node$fields will be deprecated in the next release. Please use Node$attributes instead."
[1] "Node$fieldsAll will be deprecated in the next release. Please use Node$attributesAll instead."
** inst
** byte-compile and prepare package for lazy loading
** 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 (LinTInd)