Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:02 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for deco on nebbiolo2


To the developers/maintainers of the deco package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deco.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 488/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deco 1.14.0  (landing page)
Francisco Jose Campos Laborie
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/deco
git_branch: RELEASE_3_16
git_last_commit: f841d97
git_last_commit_date: 2022-11-01 11:19:01 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deco
Version: 1.14.0
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
StartedAt: 2023-04-10 20:09:01 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:13:07 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 246.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: deco.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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")

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ENSG00000004399 ENSG00000088992 ENSG00000178977 ENSG00000116132 ENSG00000152284 
          FALSE           FALSE           FALSE           FALSE           FALSE 
ENSG00000198846 ENSG00000156535 ENSG00000173905 ENSG00000117215 ENSG00000137101 
          FALSE            TRUE            TRUE           FALSE           FALSE 
ENSG00000177990 ENSG00000171848 ENSG00000165566 ENSG00000132274 ENSG00000100100 
           TRUE            TRUE            TRUE           FALSE           FALSE 
ENSG00000196878 ENSG00000144481 ENSG00000171608 ENSG00000198626 ENSG00000136636 
           TRUE            TRUE           FALSE            TRUE            TRUE 
ENSG00000184557 ENSG00000167767 ENSG00000232040 ENSG00000163219 ENSG00000135047 
           TRUE            TRUE            TRUE           FALSE            TRUE 
ENSG00000104687 ENSG00000134668 ENSG00000135185 ENSG00000059769 ENSG00000100097 
          FALSE            TRUE           FALSE            TRUE            TRUE 
ENSG00000182866 ENSG00000066336 ENSG00000137338 ENSG00000180787 ENSG00000129038 
          FALSE           FALSE            TRUE           FALSE           FALSE 
ENSG00000135127 ENSG00000154065 ENSG00000164930 ENSG00000157557 ENSG00000130635 
          FALSE           FALSE            TRUE            TRUE            TRUE 
ENSG00000164761 ENSG00000206560 ENSG00000064393 ENSG00000111796 ENSG00000136235 
          FALSE            TRUE            TRUE           FALSE           FALSE 
ENSG00000140450 ENSG00000146070 ENSG00000133110 ENSG00000175592 ENSG00000084636 
          FALSE           FALSE            TRUE            TRUE            TRUE 
ENSG00000151617 ENSG00000157214 ENSG00000204262 ENSG00000100985 ENSG00000100196 
           TRUE            TRUE            TRUE           FALSE            TRUE 
ENSG00000168542 ENSG00000175711 ENSG00000104894 ENSG00000198513 ENSG00000196639 
           TRUE            TRUE           FALSE            TRUE            TRUE 
ENSG00000131797 ENSG00000154511 ENSG00000166387 ENSG00000152229 ENSG00000170365 
          FALSE           FALSE           FALSE           FALSE           FALSE 
ENSG00000107679 ENSG00000175183 ENSG00000155465 ENSG00000157107 ENSG00000136867 
          FALSE           FALSE           FALSE           FALSE           FALSE 
ENSG00000007237 ENSG00000020426 ENSG00000136869 ENSG00000103876 ENSG00000118292 
          FALSE            TRUE           FALSE            TRUE           FALSE 
ENSG00000177556 ENSG00000060558 ENSG00000166278 ENSG00000197746 ENSG00000143344 
          FALSE            TRUE           FALSE           FALSE           FALSE 
ENSG00000146374 ENSG00000135842 ENSG00000120158 ENSG00000112367 ENSG00000066294 
          FALSE            TRUE            TRUE           FALSE           FALSE 
ENSG00000162065 ENSG00000110446 ENSG00000091972 ENSG00000204472 ENSG00000025039 
           TRUE           FALSE           FALSE           FALSE           FALSE 
ENSG00000214194 ENSG00000113088 ENSG00000169855 ENSG00000175294 ENSG00000107443 
           TRUE           FALSE           FALSE            TRUE            TRUE 
ENSG00000080819 ENSG00000196611 ENSG00000140287 ENSG00000197993 ENSG00000164509 
          FALSE            TRUE            TRUE           FALSE            TRUE 
ENSG00000116701 ENSG00000061918 ENSG00000109323 ENSG00000198521 ENSG00000197121 
          FALSE           FALSE           FALSE           FALSE            TRUE 
ENSG00000010932 ENSG00000148180 ENSG00000146278 ENSG00000140284 ENSG00000078081 
           TRUE           FALSE           FALSE            TRUE           FALSE 
ENSG00000240024 ENSG00000043462 ENSG00000019549 ENSG00000151692 ENSG00000122025 
           TRUE           FALSE            TRUE            TRUE           FALSE 
ENSG00000060138 ENSG00000158234 ENSG00000151726 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
}
<bytecode: 0x562edc2e27c8>
<environment: namespace:base>
 --- 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.


Installation output

deco.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL deco
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘deco’ ...
** using staged installation
** R
** data
** inst
** 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 (deco)

Tests output


Example timings

deco.Rcheck/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.2380.0230.262
AnnotateDECO0.1350.0030.140
NSCAcluster0.6410.2520.894
deco-class0.0020.0000.002
deco-package0.9200.0881.007
decoNSCA0.8290.0010.829
decoRDA0.1550.0040.159
decoReport0.1530.0070.161
featureTable0.1580.0010.158
plotAssociationH2.7970.1112.909
plotDECOProfile0.1280.0120.140
plotGainingH1.3210.0511.373
plotHeatmapH0.1480.0000.148