############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:deco.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings deco_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/deco.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘deco/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘deco’ version ‘1.14.0’ * 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 ‘deco’ 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 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.analysisType’ ‘.heatplot.2’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotAssociationH: no visible binding for global variable ‘Subclasses’ plotAssociationH: no visible binding for global variable ‘h.statistic’ plotAssociationH: no visible binding for global variable ‘input.info’ plotAssociationH: no visible binding for global variable ‘DECO.subclasses’ plotAssociationH: no visible binding for global variable ‘Samples’ plotAssociationH: no visible binding for global variable ‘Features’ plotGainingH: no visible binding for global variable ‘omic.data’ plotGainingH: no visible binding for global variable ‘h.statistic’ plotGainingH: no visible binding for global variable ‘ranking’ Undefined global functions or variables: DECO.subclasses Features Samples Subclasses h.statistic input.info omic.data ranking * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘DECO.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘DECO.Rmd’ using rmarkdown ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- deco --- call from context --- which(rowSums(UP[, seq_len(n1)]) > 0 && rowSums(UP[, (n1 + 1):(n1 + n2)]) > 0) --- call from argument --- rowSums(UP[, seq_len(n1)]) > 0 && rowSums(UP[, (n1 + 1):(n1 + n2)]) > 0 --- R stacktrace --- where 1: which(rowSums(UP[, seq_len(n1)]) > 0 && rowSums(UP[, (n1 + 1):(n1 + n2)]) > 0) where 2: .freqMatrix(limmaRes, data, n1, ifelse(unsup, 0, n2), r, multi, unsup) where 3: decoRDA(data = assay(ALCL), classes = classes.ALCL, q.val = 0.01, iterations = 1000, rm.xy = FALSE, r = NULL, control = "pos", annot = FALSE, bpparam = bpparam, id.type = "ENSEMBL", pack.db = "Homo.sapiens") where 4: eval(expr, envir, enclos) where 5: eval(expr, envir, enclos) where 6: eval_with_user_handlers(expr, envir, enclos, user_handlers) where 7: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) where 8: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) where 9: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) where 12: evaluate::evaluate(...) where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) where 14: in_dir(input_dir(), expr) where 15: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) where 16: eng_r(options) where 17: block_exec(params) where 18: call_block(x) where 19: process_group.block(group) where 20: process_group(group) where 21: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) where 22: process_file(text, output) where 23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) where 24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) where 25: vweave_rmarkdown(...) where 26: engine$weave(file, quiet = quiet, encoding = enc) where 27: doTryCatch(return(expr), name, parentenv, handler) where 28: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 29: tryCatchList(expr, classes, parentenv, handlers) where 30: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output) }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) }) where 31: tools::buildVignettes(dir = "/home/biocbuild/bbs-3.16-bioc/meat/deco.Rcheck/vign_test/deco", ser_elibs = "/tmp/Rtmpd9j55m/file1d41667b8b113c.rds") --- value of length: 700 type: logical --- ENSG00000118971 ENSG00000171094 ENSG00000111536 ENSG00000137090 ENSG00000180644 FALSE TRUE TRUE TRUE TRUE ENSG00000196083 ENSG00000135744 ENSG00000170627 ENSG00000137558 ENSG00000172348 TRUE TRUE FALSE TRUE TRUE ENSG00000127252 ENSG00000170525 ENSG00000120949 ENSG00000226979 ENSG00000189292 TRUE TRUE TRUE FALSE TRUE ENSG00000151468 ENSG00000163053 ENSG00000181617 ENSG00000172724 ENSG00000107317 TRUE TRUE FALSE FALSE FALSE ENSG00000123685 ENSG00000131203 ENSG00000134028 ENSG00000085265 ENSG00000111728 TRUE FALSE FALSE FALSE FALSE ENSG00000117322 ENSG00000000938 ENSG00000152518 ENSG00000025434 ENSG00000139194 FALSE FALSE FALSE FALSE FALSE ENSG00000150782 ENSG00000144837 ENSG00000121577 ENSG00000070269 ENSG00000111275 FALSE FALSE FALSE TRUE FALSE ENSG00000185245 ENSG00000128578 ENSG00000181894 ENSG00000145824 ENSG00000152952 FALSE TRUE FALSE FALSE TRUE ENSG00000184613 ENSG00000176485 ENSG00000196754 ENSG00000100767 ENSG00000100368 FALSE TRUE TRUE FALSE FALSE ENSG00000172243 ENSG00000163131 ENSG00000183323 ENSG00000137726 ENSG00000197208 FALSE FALSE TRUE FALSE TRUE ENSG00000132429 ENSG00000112378 ENSG00000234883 ENSG00000090382 ENSG00000148803 TRUE TRUE FALSE FALSE FALSE ENSG00000139970 ENSG00000169116 ENSG00000182118 ENSG00000177807 ENSG00000101017 FALSE FALSE TRUE FALSE FALSE ENSG00000100504 ENSG00000110777 ENSG00000155792 ENSG00000102760 ENSG00000160856 TRUE FALSE FALSE FALSE FALSE ENSG00000178764 ENSG00000121413 ENSG00000136379 ENSG00000227039 ENSG00000075426 FALSE FALSE TRUE FALSE TRUE ENSG00000169403 ENSG00000005884 ENSG00000109255 ENSG00000162391 ENSG00000181631 FALSE TRUE TRUE FALSE FALSE ENSG00000171729 ENSG00000156475 ENSG00000182326 ENSG00000165152 ENSG00000185989 FALSE TRUE FALSE TRUE FALSE ENSG00000163710 ENSG00000187474 ENSG00000164604 ENSG00000178573 ENSG00000136630 TRUE FALSE TRUE FALSE TRUE ENSG00000115590 ENSG00000104613 ENSG00000186074 ENSG00000119408 ENSG00000140563 TRUE TRUE FALSE FALSE TRUE ENSG00000204482 ENSG00000101460 ENSG00000188906 ENSG00000048462 ENSG00000139193 FALSE FALSE FALSE FALSE FALSE ENSG00000138755 ENSG00000100079 ENSG00000196730 ENSG00000183160 ENSG00000162739 FALSE FALSE FALSE FALSE FALSE ENSG00000147454 ENSG00000092140 ENSG00000103187 ENSG00000104611 ENSG00000075643 TRUE TRUE FALSE TRUE TRUE ENSG00000110448 ENSG00000121297 ENSG00000137936 ENSG00000140968 ENSG00000198121 FALSE TRUE FALSE FALSE FALSE ENSG00000165895 ENSG00000175352 ENSG00000137077 ENSG00000005100 ENSG00000135709 FALSE TRUE FALSE TRUE FALSE ENSG00000134463 ENSG00000178104 ENSG00000125730 ENSG00000117479 ENSG00000169946 FALSE TRUE FALSE TRUE FALSE ENSG00000160255 ENSG00000157873 ENSG00000105499 ENSG00000163624 ENSG00000179715 FALSE FALSE FALSE TRUE FALSE ENSG00000140945 ENSG00000127951 ENSG00000171236 ENSG00000118308 ENSG00000162692 TRUE FALSE TRUE FALSE FALSE ENSG00000105967 ENSG00000005513 ENSG00000029153 ENSG00000135052 ENSG00000107242 FALSE FALSE TRUE TRUE FALSE ENSG00000178562 ENSG00000121552 ENSG00000197249 ENSG00000164574 ENSG00000186283 FALSE FALSE TRUE TRUE FALSE ENSG00000168077 ENSG00000104774 ENSG00000143641 ENSG00000136830 ENSG00000160326 FALSE FALSE TRUE TRUE FALSE ENSG00000156234 ENSG00000138772 ENSG00000110324 ENSG00000137509 ENSG00000148344 FALSE TRUE FALSE FALSE FALSE ENSG00000170522 ENSG00000141576 ENSG00000025423 ENSG00000100307 ENSG00000185420 TRUE TRUE TRUE FALSE TRUE ENSG00000047457 ENSG00000185101 ENSG00000120549 ENSG00000158714 ENSG00000176171 FALSE FALSE TRUE FALSE TRUE ENSG00000152454 ENSG00000127990 ENSG00000224137 ENSG00000243444 ENSG00000148737 FALSE FALSE FALSE TRUE FALSE ENSG00000130402 ENSG00000134152 ENSG00000087085 ENSG00000115956 ENSG00000167930 TRUE TRUE FALSE FALSE TRUE ENSG00000140511 ENSG00000164983 ENSG00000071967 ENSG00000023608 ENSG00000162627 FALSE TRUE FALSE TRUE TRUE ENSG00000156171 ENSG00000166770 ENSG00000132970 ENSG00000174600 ENSG00000122986 FALSE FALSE FALSE FALSE FALSE ENSG00000104763 ENSG00000214900 ENSG00000188112 ENSG00000157150 ENSG00000156804 FALSE TRUE TRUE TRUE TRUE ENSG00000176595 ENSG00000074410 ENSG00000091129 ENSG00000120256 ENSG00000166128 TRUE TRUE TRUE TRUE FALSE ENSG00000170921 ENSG00000100351 ENSG00000107249 ENSG00000168209 ENSG00000187957 TRUE FALSE TRUE TRUE TRUE ENSG00000108984 ENSG00000142552 ENSG00000162267 ENSG00000169071 ENSG00000134460 FALSE TRUE FALSE TRUE TRUE ENSG00000038427 ENSG00000087237 ENSG00000170955 ENSG00000129993 ENSG00000172183 TRUE FALSE TRUE FALSE FALSE ENSG00000164066 ENSG00000115594 ENSG00000148848 ENSG00000242265 ENSG00000170323 TRUE TRUE TRUE FALSE FALSE ENSG00000117394 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FALSE FALSE FALSE FALSE FALSE ENSG00000146416 ENSG00000153898 ENSG00000167634 ENSG00000133636 ENSG00000115828 TRUE FALSE TRUE FALSE FALSE ENSG00000186187 ENSG00000189013 ENSG00000206538 ENSG00000133818 ENSG00000136158 TRUE TRUE TRUE FALSE FALSE ENSG00000151136 ENSG00000132514 ENSG00000153802 ENSG00000101670 ENSG00000174944 TRUE FALSE TRUE FALSE FALSE ENSG00000145287 ENSG00000011426 ENSG00000101347 ENSG00000169413 ENSG00000203995 FALSE TRUE FALSE FALSE TRUE ENSG00000198901 ENSG00000095015 ENSG00000163297 ENSG00000172005 ENSG00000110841 TRUE FALSE TRUE FALSE TRUE ENSG00000172752 ENSG00000172575 ENSG00000100453 ENSG00000102879 ENSG00000159023 FALSE FALSE TRUE FALSE FALSE ENSG00000108551 ENSG00000163625 ENSG00000152078 ENSG00000111679 ENSG00000143674 TRUE TRUE TRUE FALSE TRUE ENSG00000160593 ENSG00000215417 ENSG00000180096 ENSG00000188257 ENSG00000168961 FALSE TRUE FALSE FALSE FALSE ENSG00000064886 ENSG00000140678 ENSG00000140939 ENSG00000183044 ENSG00000175463 FALSE FALSE TRUE FALSE FALSE 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ENSG00000188505 ENSG00000156738 TRUE TRUE TRUE FALSE FALSE ENSG00000105369 ENSG00000165272 ENSG00000176907 ENSG00000159403 ENSG00000167912 FALSE TRUE FALSE FALSE FALSE ENSG00000109089 ENSG00000130584 ENSG00000161405 ENSG00000166501 ENSG00000170647 TRUE TRUE FALSE FALSE FALSE ENSG00000179593 ENSG00000130558 ENSG00000167600 ENSG00000110047 ENSG00000198752 FALSE FALSE FALSE FALSE TRUE ENSG00000101096 ENSG00000166130 ENSG00000115896 ENSG00000075213 ENSG00000129353 FALSE TRUE FALSE FALSE FALSE ENSG00000164251 ENSG00000105355 ENSG00000167232 ENSG00000074706 ENSG00000132185 TRUE TRUE FALSE FALSE FALSE ENSG00000174123 ENSG00000135736 ENSG00000150907 ENSG00000136573 ENSG00000174500 FALSE FALSE FALSE FALSE FALSE ENSG00000188848 ENSG00000180257 ENSG00000118513 ENSG00000164691 ENSG00000175745 FALSE FALSE TRUE FALSE FALSE ENSG00000178175 ENSG00000123610 ENSG00000240583 ENSG00000197498 ENSG00000182240 FALSE TRUE FALSE TRUE FALSE ENSG00000186818 ENSG00000198089 ENSG00000112796 ENSG00000173588 ENSG00000143153 FALSE FALSE FALSE TRUE FALSE ENSG00000204597 ENSG00000134061 ENSG00000100234 ENSG00000231991 ENSG00000091106 FALSE FALSE FALSE TRUE FALSE ENSG00000112290 ENSG00000111879 ENSG00000092470 ENSG00000165092 ENSG00000183808 TRUE TRUE TRUE FALSE TRUE ENSG00000119596 ENSG00000188994 ENSG00000171444 ENSG00000167483 ENSG00000139734 TRUE TRUE FALSE FALSE TRUE ENSG00000197711 ENSG00000169495 ENSG00000177084 ENSG00000109906 ENSG00000078902 FALSE FALSE TRUE FALSE FALSE ENSG00000138336 ENSG00000169442 ENSG00000179277 ENSG00000152207 ENSG00000247973 TRUE FALSE FALSE FALSE TRUE --- function from context --- function (x, arr.ind = FALSE, useNames = TRUE) { wh <- .Internal(which(x)) if (isTRUE(arr.ind) && !is.null(d <- dim(x))) arrayInd(wh, d, dimnames(x), useNames = useNames) else wh } --- function search by body --- Function which in namespace base has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/deco.Rcheck/00check.log’ for details.