Josie Hayes
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/adductomicsR |
| Branch: RELEASE_3_9 |
| Last Commit: bc8a049 |
| Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:04:09 -0400 (Wed, 16 Oct 2019).
| Package 19/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| adductomicsR 1.0.0 Josie Hayes
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: adductomicsR |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:adductomicsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings adductomicsR_1.0.0.tar.gz |
| StartedAt: 2019-10-16 00:24:15 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:29:06 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 290.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: adductomicsR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:adductomicsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings adductomicsR_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/adductomicsR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adductomicsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘adductomicsR’ version ‘1.0.0’
* 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 ‘adductomicsR’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
rtDevModelling 18.557 1.781 72.326
outputPeakTable 6.913 0.639 7.993
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
stop("failed to load resource", "\n name: ", names(x), "\n title: ", x$title,
"\n reason: ", conditionMessage(err), call. = FALSE)
})
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: value[[3L]](cond)
18: stop("failed to load resource", "\n name: ", names(x), "\n title: ", x$title, "\n reason: ",
conditionMessage(err), call. = FALSE)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Error: (unknown) (@test_rtDevModelling.R#6)
Error: testthat unit tests failed
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/adductomicsR.Rcheck/00check.log’
for details.
adductomicsR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL adductomicsR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘adductomicsR’ ... ** using staged installation ** R ** 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 (adductomicsR)
adductomicsR.Rcheck/tests/testthat.Rout.fail
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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(adductomicsR)
Loading required package: adductData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(adductData)
> library(testthat)
>
> test_check("adductomicsR")
── 1. Error: (unknown) (@test_rtDevModelling.R#6) ─────────────────────────────
failed to load resource
name: EH1960
title: Rda for adductomics mass spec for sample ORB35022 samples from Grigoryan et al, 2016, Anal Chem
reason: Empty reply from server
1: suppressMessages(suppressWarnings(temp[["EH1960"]])) at testthat/test_rtDevModelling.R:6
2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
3: suppressWarnings(temp[["EH1960"]])
4: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
5: temp[["EH1960"]]
6: temp[["EH1960"]]
7: .local(x, i, j, ...)
8: callNextMethod(x, i, j, ..., force = force, verbose = verbose)
9: eval(call, callEnv)
10: eval(call, callEnv)
11: .nextMethod(x, i, j, ..., force = force, verbose = verbose)
12: .local(x, i, j, ...)
13: .Hub_get1(x[idx], force = force, verbose = verbose)
14: tryCatch({
fls <- cache(getHub(class), force = force, verbose = verbose)
.get1(class)
}, error = function(err) {
stop("failed to load resource", "\n name: ", names(x), "\n title: ", x$title,
"\n reason: ", conditionMessage(err), call. = FALSE)
})
15: tryCatchList(expr, classes, parentenv, handlers)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: value[[3L]](cond)
18: stop("failed to load resource", "\n name: ", names(x), "\n title: ", x$title, "\n reason: ",
conditionMessage(err), call. = FALSE)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Error: (unknown) (@test_rtDevModelling.R#6)
Error: testthat unit tests failed
Execution halted
adductomicsR.Rcheck/adductomicsR-Ex.timings
| name | user | system | elapsed | |
| IsotopicDistributionMod | 1.333 | 0.129 | 1.462 | |
| adductQuant | 0.000 | 0.001 | 0.001 | |
| digestMod | 0.013 | 0.001 | 0.014 | |
| filterAdductTable | 0.021 | 0.010 | 0.035 | |
| findPeaks | 0.001 | 0.000 | 0.001 | |
| generateTargTable | 0.025 | 0.002 | 0.027 | |
| loessWrapperMod | 0.364 | 0.009 | 0.375 | |
| outputPeakTable | 6.913 | 0.639 | 7.993 | |
| rtDevModelling | 18.557 | 1.781 | 72.326 | |
| specSimPepId | 0.000 | 0.000 | 0.001 | |