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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DRIMSeq_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DRIMSeq.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 ‘DRIMSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DRIMSeq’ version ‘1.29.0’
* 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 ‘DRIMSeq’ 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:
    v0.99.0: - Bioconductor submission.
  Cannot process chunk/lines:
    v1.1.2: - Bioconductor accepted devel version.
  Cannot process chunk/lines:
    v1.1.3: - New features: 
    	i) The level of moderation is calculated automatically. 
    	ii) Permutation approach to adjust p-values in sQTL analyses.
  Cannot process chunk/lines:
    v1.1.4: - Use data frames with counts and genotypes when creating the dmDSdata and dmSQTLdata objects.
  Cannot process chunk/lines:
    v1.3.1: - Equals to v1.1.4.
  Cannot process chunk/lines:
    v1.3.2: - Implementation of the two-stage test dmTwoStageTest().
  Cannot process chunk/lines:
    Additionally:
    	i) Removing max_features argument from dmFilter.
    	ii) Keeping only the grid approach for estimating tagwise dispersion. 
    	iii) Allow to use only a subset of genes (disp_subset parameter) in common dispersion estimation to speed up the calculations; if disp_subset < 1, use set.seed() to make the analysis reproducible.
    	iv) Always use tagwise dispersion for fitting full and null models.
    	v) In one group fitting, return NA for tags having the last feature with zero counts in all samples. We always use the q-th feature as a denominator in logit calculation. In such a case all the logits are anyways Inf.
    	vi) Use plotPValues instead of plotTest
    	vii) Use 'prop' instead of 'pi' and 'disp' instead of 'gamma0'.
    	viii) Use only 'constrOptim' (old 'constrOptimG') to estimate proportions and 'optim' to estimate coefficients in the regression model. 
    	ix) Use plotProportions instead of plotFit.
    	x) No 'out_dir' parameter in plotting functions. All plotting functions return a ggplot object.
    	xi) Use term "precision" instead of "dispersion" as in DRIMSeq we directly estimate the precision parameter. Dispersion can be calculated with formula: dispersion = 1 / (1 + precision).
* 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 ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DRIMSeq.Rnw’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘DRIMSeq.Rnw’
  ...
> proc.time()
   user  system elapsed 
  0.183   0.017   0.195 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL DRIMSeq
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘DRIMSeq’ ...
** using staged installation
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘proportions’ in package ‘DRIMSeq’
** 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 (DRIMSeq)