##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Cogito.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Cogito_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Cogito.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Cogito/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Cogito' version '1.14.0'
* 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 whether package 'Cogito' 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.md':
No news entries found.
* 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 ... 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 ... ERROR
Running examples in 'Cogito-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summarizeRanges
> ### Title: Summarize Aggregated GRanges
> ### Aliases: summarizeRanges
> 
> ### ** Examples
> 
> mm9 <- TxDb.Mmusculus.UCSC.mm9.knownGene::TxDb.Mmusculus.UCSC.mm9.knownGene
> 
> ### small artificial example ###
> ranges.RNA.control <-
+     GRanges(seq = "chr10",
+             IRanges(c(41023369, 41211825, 41528287, 41994926, 42301673,
+                         43256520, 43618919, 49503584, 51349066, 52099001),
+                     c(41023544, 41212385, 41528663, 41995357, 42302290,
+                         43257075, 43619492, 49504033, 51349425, 52099521)),
+             seqinfo = GenomeInfoDb::seqinfo(mm9),
+             expr = runif(5, 0, 1))
> ranges.RNA.condition <-
+     GRanges(seq = "chr10",
+             IRanges(c(41013942, 41208731, 41535166, 41999999, 42292275, 
+                         43256194, 43615562, 49497888, 51347046, 52092180),
+                     c(41014274, 41209664, 41536039, 42000182, 42292965, 
+                         43256430, 43615866, 49498362, 51347969, 52092733)),
+             seqinfo = GenomeInfoDb::seqinfo(mm9),
+             expr = runif(5, 0, 1))
> ranges.ChIP.control <-
+     GRanges(seq = "chr10",
+             IRanges(c(41022835, 41307587, 42197924, 42302387, 42893825,
+                         43259749, 43620352, 43721891, 44248812, 45207572,
+                         49508713, 51309978, 51348779, 52101900, 52265513),
+                     c(41022954, 41307745, 42198201, 42302555, 42893974,
+                         43259889, 43620604, 43722051, 44248920, 45207704,
+                         49508859, 51310187, 51348921, 52102030, 52265689)),
+             seqinfo = GenomeInfoDb::seqinfo(mm9),
+             score = round(runif(15, 5, 90)))
> 
> example.dataset <- list(RNA = GRangesList(control = ranges.RNA.control,
+                                             condition = ranges.RNA.condition),
+                         ChIP = ranges.ChIP.control)
> 
> aggregated.ranges <- aggregateRanges(ranges = example.dataset,
+                                         organism = mm9,
+                                         name = "art.example",
+                                         verbose = TRUE)
start function Cogito::aggregateRanges
  84 genes were dropped because they have exons located on both strands of the
  same reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
- annotating with RNA
0%---------------------25%---------------------50%----------------------75%---------------------100%
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
- annotating with ChIP
> 
> # adding information about conditions
> aggregated.ranges$config$conditions <- list(condition = c("RNA.condition.expr"),
+                                             control = c("RNA.control.expr",
+                                                         "ChIP.score"))
> summarizeRanges(aggregated.ranges = aggregated.ranges,
+                 outputFormat = "pdf",
+                 verbose = TRUE)
start function Cogito::summarizeRanges
summary of attached values 
0%---------------------25%---------------------50%----------------------75%---------------------100%
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
summary of attached values of tracks with the same technology 
0%---------------------25%---------------------50%----------------------75%---------------------100%
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
pairwise comparisons of attached values from different tracks 
0%---------------------25%---------------------50%----------------------75%---------------------100%
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
save data
write report


processing file: 2025-04-29_art.example_custom.rmd
pdftex: major issue: So far, you have not checked for updates as a MiKTeX user.
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.

Sorry, but pdfcrop.exe did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\biocbuild\AppData\Local\MiKTeX\miktex\log\pdfcrop.log

Sorry, but pdfcrop.exe did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

  C:\Users\biocbuild\AppData\Local\MiKTeX\miktex\log\pdfcrop.log
output file: 2025-04-29_art.example_custom.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS 2025-04-29_art.example_custom.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc196b045de5c58.tex --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "E:\biocbuild\bbs-3.21-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --highlight-style tango --pdf-engine pdflatex --variable graphics --variable "geometry:margin=1in" 
Error: LaTeX failed to compile E:/biocbuild/bbs-3.21-bioc/meat/Cogito.Rcheck/2025-04-29_art.example_report.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
Execution halted
* 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, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/Cogito.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Cogito
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'Cogito' ...
** this is package 'Cogito' version '1.14.0'
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (Cogito)

R version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(Cogito)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: jsonlite
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: entropy
> 
> test_check("Cogito")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
  14.39    0.76   20.62