CHECK report for biotmle on malbec2
This page was generated on 2019-10-16 12:11:04 -0400 (Wed, 16 Oct 2019).
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
Command output
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### Running command:
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### /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
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