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CHECK report for adductomicsR on celaya2

This page was generated on 2019-10-16 13:04:09 -0400 (Wed, 16 Oct 2019).

Package 19/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adductomicsR 1.0.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

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

Command output

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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.


Installation output

adductomicsR.Rcheck/00install.out

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###
### 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)

Tests output

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

Example timings

adductomicsR.Rcheck/adductomicsR-Ex.timings

nameusersystemelapsed
IsotopicDistributionMod1.3330.1291.462
adductQuant0.0000.0010.001
digestMod0.0130.0010.014
filterAdductTable0.0210.0100.035
findPeaks0.0010.0000.001
generateTargTable0.0250.0020.027
loessWrapperMod0.3640.0090.375
outputPeakTable6.9130.6397.993
rtDevModelling18.557 1.78172.326
specSimPepId0.0000.0000.001