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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DRIMSeq_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DRIMSeq.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 ‘DRIMSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DRIMSeq’ version ‘1.34.0’
* 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 ‘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 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 ... 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 ... WARNING
Documented arguments not in \usage in Rd file 'dmSQTLtest-class.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 72.317  0.798  73.411
dmDStest-class    5.653  0.055   5.735
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/DRIMSeq.Rcheck/00check.log’
for details.