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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings QSutils_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/QSutils.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘QSutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QSutils’ version ‘1.19.0’
* 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:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 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 ‘QSutils’ can be installed ... OK
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.99.8
    	Internal changes:
    		- QSutils review correction:
    			· Add exports to NAMESPACE
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.99.4,5, and 7
    	Internal changes:
    		- QSutils review correction:
    			· fn.ab function correction
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.99.3
    	Internal changes:
    	  - QSutils review correction:
    	  		· Vignette: add chunk names
    			· R Change class -> is()
    			· R hide helper functions
    			· R join more than one function in one file
    			· R vectorize some apply
    			· R Change fn.ab.1,fn.ab.2 and fn.ab.3 -> fn.ab with 3 agruments in fn
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.99.2
    	Internal changes:
    	  - Biocheck NOTEs correction:
    	  		· Change sapply()->vapply()
    			· Change 1:... -> seq_len()
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.99.1
    	Internal changes:
    	  - Correction of WARNINGS and ERRORS
    	    with Biocheck:
    		  · Collapse() example ERROR.
    		  · Change class == -> is() or !is()
    		  · Update R version dependency from 3.4.0 to 3.5.
    		  · Correct -> 'VignetteIndexEntry{VignetteTitle}' in QSUtils-Alignment.Rmd
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘QSUtils-Alignment.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘QSutils-Diversity.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘QSutils-Simulation.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘QSUtils-Alignment.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.201   0.005   0.200 

... incomplete output.  Crash?
when running code in ‘QSutils-Diversity.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.165   0.035   0.195 

... incomplete output.  Crash?
when running code in ‘QSutils-Simulation.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.189   0.016   0.200 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/QSutils.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL QSutils
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘QSutils’ ...
** using staged installation
** R
** 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 (QSutils)