| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-03-29 11:05:02 -0400 (Wed, 29 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4482 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4278 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4306 |
| 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 | ||||
|
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. |
| Package 488/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| deco 1.14.0 (landing page) Francisco Jose Campos Laborie
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| 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: 2023-03-27 20:12:56 -0400 (Mon, 27 Mar 2023) |
| EndedAt: 2023-03-27 20:16:54 -0400 (Mon, 27 Mar 2023) |
| EllapsedTime: 237.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: deco.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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/RtmpDyBsvW/file1675616deaac23.rds")
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ENSG00000169855 ENSG00000175294 ENSG00000107443 ENSG00000080819 ENSG00000196611
FALSE TRUE TRUE FALSE TRUE
ENSG00000140287 ENSG00000197993 ENSG00000164509 ENSG00000116701 ENSG00000061918
TRUE FALSE TRUE FALSE FALSE
ENSG00000109323 ENSG00000198521 ENSG00000197121 ENSG00000010932 ENSG00000148180
FALSE FALSE TRUE TRUE FALSE
ENSG00000146278 ENSG00000140284 ENSG00000078081 ENSG00000240024 ENSG00000043462
FALSE TRUE FALSE TRUE FALSE
ENSG00000019549 ENSG00000151692 ENSG00000122025 ENSG00000060138 ENSG00000158234
TRUE TRUE FALSE TRUE TRUE
ENSG00000151726 ENSG00000188505 ENSG00000156738 ENSG00000105369 ENSG00000165272
TRUE FALSE FALSE FALSE TRUE
ENSG00000159403 ENSG00000167912 ENSG00000109089 ENSG00000130584 ENSG00000161405
FALSE FALSE TRUE TRUE FALSE
ENSG00000166501 ENSG00000170647 ENSG00000179593 ENSG00000130558 ENSG00000167600
FALSE FALSE FALSE FALSE FALSE
ENSG00000110047 ENSG00000198752 ENSG00000101096 ENSG00000166130 ENSG00000115896
FALSE TRUE FALSE TRUE FALSE
ENSG00000075213 ENSG00000129353 ENSG00000164251 ENSG00000105355 ENSG00000167232
FALSE FALSE TRUE TRUE FALSE
ENSG00000074706 ENSG00000132185 ENSG00000174123 ENSG00000135736 ENSG00000150907
FALSE FALSE FALSE FALSE FALSE
ENSG00000136573 ENSG00000174500 ENSG00000188848 ENSG00000180257 ENSG00000118513
FALSE FALSE FALSE FALSE TRUE
ENSG00000164691 ENSG00000175745 ENSG00000178175 ENSG00000123610 ENSG00000197498
FALSE FALSE FALSE TRUE TRUE
ENSG00000186818 ENSG00000154839 ENSG00000127586 ENSG00000173588 ENSG00000176845
FALSE TRUE TRUE TRUE TRUE
ENSG00000134061 ENSG00000100234 ENSG00000153485 ENSG00000112290 ENSG00000164542
FALSE FALSE FALSE TRUE TRUE
ENSG00000231057 ENSG00000167815 ENSG00000092470 ENSG00000165092 ENSG00000177706
FALSE TRUE TRUE FALSE TRUE
ENSG00000188994 ENSG00000176890 ENSG00000171444 ENSG00000167483 ENSG00000151503
TRUE TRUE FALSE FALSE TRUE
ENSG00000197711 ENSG00000184451 ENSG00000170571 ENSG00000177084 ENSG00000109906
FALSE FALSE FALSE TRUE FALSE
ENSG00000215252 ENSG00000169442 ENSG00000165312 ENSG00000152207
FALSE FALSE TRUE FALSE
--- 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: 0x55fcde7d77c8>
<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.
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)
deco.Rcheck/deco-Ex.timings
| name | user | system | elapsed | |
| ALCLdata | 0.210 | 0.012 | 0.222 | |
| AnnotateDECO | 0.136 | 0.004 | 0.140 | |
| NSCAcluster | 0.589 | 0.308 | 0.897 | |
| deco-class | 0.001 | 0.000 | 0.001 | |
| deco-package | 0.838 | 0.056 | 0.893 | |
| decoNSCA | 0.841 | 0.000 | 0.841 | |
| decoRDA | 0.164 | 0.000 | 0.164 | |
| decoReport | 0.14 | 0.00 | 0.14 | |
| featureTable | 0.134 | 0.004 | 0.137 | |
| plotAssociationH | 2.144 | 0.112 | 2.256 | |
| plotDECOProfile | 0.137 | 0.000 | 0.136 | |
| plotGainingH | 1.222 | 0.036 | 1.257 | |
| plotHeatmapH | 0.139 | 0.008 | 0.147 | |