############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Cogito.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Cogito_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Cogito.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * 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 * using option ‘--no-vignettes’ * checking for file ‘Cogito/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Cogito’ version ‘1.10.0’ * 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 ‘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 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 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: 2024-05-09_art.example_custom.rmd output file: 2024-05-09_art.example_custom.knit.md /home/biocbuild/bin/pandoc +RTS -K512m -RTS 2024-05-09_art.example_custom.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.19-bioc/meat/Cogito.Rcheck/2024-05-09_art.example_report.tex --lua-filter /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --highlight-style tango --pdf-engine pdflatex --variable graphics --variable 'geometry:margin=1in' ! LaTeX Error: File `/home/biocbuild/bbs-3.19-bioc/meat/Cogito.Rcheck/2024-05-0 9_art.example_report_files/figure-latex/Heatmap comparisons between attached va lues-1' not found. Error: LaTeX failed to compile /home/biocbuild/bbs-3.19-bioc/meat/Cogito.Rcheck/2024-05-09_art.example_report.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See 2024-05-09_art.example_report.log for more info. 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/Cogito.Rcheck/00check.log’ for details.