##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dearseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dearseq_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/dearseq.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dearseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dearseq’ version ‘1.23.0’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘dearseq’ 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 ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) plot.dearseq.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{signif_threshold}{a value between \code{0} and {1} specifying the 
       |                                                      ^
checkRd: (-1) plot_ord_pvals.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{signif_threshold}{a value between \code{0} and {1} specifying the 
       |                                                      ^
checkRd: (-1) summary.dearseq.Rd:15: Lost braces; missing escapes or markup?
    15 | \item{signif_threshold}{a value between \code{0} and {1} specifying the 
       |                                                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'dear_seq.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’ ‘[stats]{bandwidth}’

Non-topic package-anchored link(s) in Rd file 'dgsa_seq.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’ ‘[stats]{bandwidth}’

Non-topic package-anchored link(s) in Rd file 'sp_weights.Rd':
  ‘[stats]{bandwidth}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 94045 Segmentation fault: 11  LANGUAGE=en _R_CHECK_INTERNALS2_=1 R_LIBS=/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpHz6kDP/RLIBS_15305334bbd71 R_ENVIRON_USER='' R_LIBS_USER='NULL' R_LIBS_SITE='NULL' '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'dearseq-Ex.Rout' 2>&1 < 'dearseq-Ex.R'
 ERROR
Running examples in ‘dearseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vc_score_perm
> ### Title: Computes variance component score test statistics and its
> ###   permuted distribution
> ### Aliases: vc_score_perm
> ### Keywords: internal
> 
> ### ** Examples
> 
> set.seed(123)
> 
> ##generate some fake data
> ########################
> n <- 100
> r <- 12
> t <- matrix(rep(1:3), r/3, ncol=1, nrow=r)
> sigma <- 0.4
> b0 <- 1
> 
> #under the null:
> b1 <- 0
> #under the alternative:
> b1 <- 0.7
> y.tilde <- b0 + b1*t + rnorm(r, sd = sigma)
> y <- t(matrix(rnorm(n*r, sd = sqrt(sigma*abs(y.tilde))), ncol=n, nrow=r) +
+       matrix(rep(y.tilde, n), ncol=n, nrow=r))
> x <- matrix(1, ncol=1, nrow=r)
> 
> #run test
> scoreTest <- vc_score_perm(y, x, phi=t, w=matrix(1, ncol=ncol(y),
+                                                 nrow=nrow(y)),
+                     Sigma_xi=matrix(1), indiv=rep(1:(r/3), each=3),
+                     parallel_comp = FALSE)

 *** caught segfault ***
address 0x107e00000, cause 'invalid permissions'

Traceback:
 1: FUN(X[[i]], ...)
 2: lapply(X, FUN, ...)
 3: pblapply(X = X, FUN = FUN, ..., cl = cl)
 4: pbapply::pbsapply(perm_list, compute_genewise_scores, indiv_mat = indiv_mat,     avg_xtx_inv_tx = avg_xtx_inv_tx, cl = par_clust)
 5: vc_score_perm(y, x, phi = t, w = matrix(1, ncol = ncol(y), nrow = nrow(y)),     Sigma_xi = matrix(1), indiv = rep(1:(r/3), each = 3), parallel_comp = FALSE)
An irrecoverable exception occurred. R is aborting now ...
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/dearseq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dearseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘dearseq’ ...
** this is package ‘dearseq’ version ‘1.23.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (dearseq)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(dearseq)
> 
> test_check("dearseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  1.390   0.114   1.682