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CHECK report for biotmle on malbec2

This page was generated on 2019-10-16 12:11:04 -0400 (Wed, 16 Oct 2019).

Package 171/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biotmle 1.8.0
Nima Hejazi
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/biotmle
Branch: RELEASE_3_9
Last Commit: 1df3dd9
Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ ERROR ]
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: biotmle
Version: 1.8.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:biotmle.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings biotmle_1.8.0.tar.gz
StartedAt: 2019-10-16 00:08:54 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:11:33 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 158.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: biotmle.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:biotmle.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings biotmle_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/biotmle.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biotmle/DESCRIPTION’ ... OK
* this is package ‘biotmle’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ‘biotmle’ 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 ... ERROR
Running examples in ‘biotmle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biomarkertmle
> ### Title: Biomarker Evaluation with Targeted Minimum Loss-Based Estimation
> ###   of the ATE
> ### Aliases: biomarkertmle
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(biotmleData)
> data(illuminaData)
> library(SummarizedExperiment)
Loading required package: GenomicRanges
Loading required package: stats4
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:dplyr’:

    combine, intersect, setdiff, union

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: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:dplyr’:

    first, rename

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following objects are masked from ‘package:dplyr’:

    collapse, desc, slice

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

The following object is masked from ‘package:dplyr’:

    count

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

> "%ni%" <- Negate("%in%")
> 
> colData(illuminaData) <- colData(illuminaData) %>%
+   data.frame() %>%
+   dplyr::mutate(age = as.numeric(age > median(age))) %>%
+   DataFrame()
> 
> varInt_index <- which(names(colData(illuminaData)) %in% "benzene")
> 
> biomarkerTMLEout <- biomarkertmle(
+   se = illuminaData[1:2, ],
+   varInt = varInt_index,
+   parallel = FALSE,
+   family = "gaussian",
+   g_lib = c("SL.mean", "SL.glm"),
+   Q_lib = "SL.glm"
+ )
Warning in biomarkertmle(se = illuminaData[1:2, ], varInt = varInt_index,  :
  Sequential evaluation is strongly discouraged. 
 Proceed with caution.
Loading required package: globals
Loading required package: future

Attaching package: ‘future’

The following object is masked from ‘package:SummarizedExperiment’:

    values

The following object is masked from ‘package:GenomicRanges’:

    values

The following object is masked from ‘package:IRanges’:

    values

The following object is masked from ‘package:S4Vectors’:

    values

Loading required package: foreach
Loading required package: iterators
Error: BiocParallel errors
  element index: 1
  first error: task 1 failed - "group length is 0 but data length > 0"
Execution halted
* 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:
         family = "gaussian", g_lib = c("SL.mean", "SL.glm"), Q_lib = "SL.mean") at testthat/test-modtest_ic.R:19
  2: BiocParallel::bplapply(Y[, seq_along(Y)], biomarkerTMLE_exposure, W = W, A = A, a = unique(A), 
         g_lib = g_lib, Q_lib = Q_lib, family = family, subj_ids = subj_ids, ...)
  3: BiocParallel::bplapply(Y[, seq_along(Y)], biomarkerTMLE_exposure, W = W, A = A, a = unique(A), 
         g_lib = g_lib, Q_lib = Q_lib, family = family, subj_ids = subj_ids, ...)
  4: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
  5: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: (unknown) (@test-biomarkertmle.R#20) 
  2. Error: (unknown) (@test-modtest_ic.R#19) 
  
  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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/biotmle.Rcheck/00check.log’
for details.


Installation output

biotmle.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL biotmle
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘biotmle’ ...
** 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 (biotmle)

Tests output

biotmle.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-pc-linux-gnu (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(testthat)
> library(biotmle)
biotmle v1.8.0: Targeted Learning with Moderated Statistics for Biomarker Discovery
> 
> test_check("biotmle")
── 1. Error: (unknown) (@test-biomarkertmle.R#20)  ─────────────────────────────
BiocParallel errors
  element index: 1
  first error: task 1 failed - "group length is 0 but data length > 0"
1: biomarkertmle(se = illuminaData[1:2, ], varInt = varInt_index, parallel = FALSE, 
       family = "gaussian", g_lib = c("SL.mean", "SL.glm"), Q_lib = "SL.mean") at testthat/test-biomarkertmle.R:20
2: BiocParallel::bplapply(Y[, seq_along(Y)], biomarkerTMLE_exposure, W = W, A = A, a = unique(A), 
       g_lib = g_lib, Q_lib = Q_lib, family = family, subj_ids = subj_ids, ...)
3: BiocParallel::bplapply(Y[, seq_along(Y)], biomarkerTMLE_exposure, W = W, A = A, a = unique(A), 
       g_lib = g_lib, Q_lib = Q_lib, family = family, subj_ids = subj_ids, ...)
4: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
5: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)

── 2. Error: (unknown) (@test-modtest_ic.R#19)  ────────────────────────────────
BiocParallel errors
  element index: 1
  first error: task 1 failed - "group length is 0 but data length > 0"
1: biomarkertmle(se = illuminaData[1:2, ], varInt = varInt_index, parallel = FALSE, 
       family = "gaussian", g_lib = c("SL.mean", "SL.glm"), Q_lib = "SL.mean") at testthat/test-modtest_ic.R:19
2: BiocParallel::bplapply(Y[, seq_along(Y)], biomarkerTMLE_exposure, W = W, A = A, a = unique(A), 
       g_lib = g_lib, Q_lib = Q_lib, family = family, subj_ids = subj_ids, ...)
3: BiocParallel::bplapply(Y[, seq_along(Y)], biomarkerTMLE_exposure, W = W, A = A, a = unique(A), 
       g_lib = g_lib, Q_lib = Q_lib, family = family, subj_ids = subj_ids, ...)
4: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
5: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 5 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
1. Error: (unknown) (@test-biomarkertmle.R#20) 
2. Error: (unknown) (@test-modtest_ic.R#19) 

Error: testthat unit tests failed
Execution halted

Example timings

biotmle.Rcheck/biotmle-Ex.timings

nameusersystemelapsed
bioTMLE-class2.2040.1322.630