| Back to Long Tests report for BioC 3.15 |
This page was generated on 2022-10-15 21:00:02 -0400 (Sat, 15 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4383 |
| 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 autonomics package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2/26 | Hostname | OS / Arch | CHECK | |||||||
| autonomics 1.4.0 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | ERROR | |||||||
| Package: autonomics |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no autonomics_1.4.0.tar.gz |
| StartedAt: 2022-10-15 08:00:26 -0400 (Sat, 15 Oct 2022) |
| EndedAt: 2022-10-15 08:02:17 -0400 (Sat, 15 Oct 2022) |
| EllapsedTime: 111.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: autonomics.Rcheck |
| Warnings: NA |
autonomics.Rcheck/tests/test_long_1_download.Rout.fail
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.
> context('download_data')
Error in context("download_data") : could not find function "context"
Execution halted
autonomics.Rcheck/tests/test_long_3_read_proteingroups_billing16.Rout.fail
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.
> context('read_proteingroups: billing16')
Error in context("read_proteingroups: billing16") :
could not find function "context"
Execution halted
autonomics.Rcheck/tests/test_long_3_read_proteingroups_billing19.Rout.fail
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.
> context('read_proteingroups: billing19')
Error in context("read_proteingroups: billing19") :
could not find function "context"
Execution halted
autonomics.Rcheck/tests/test_long_3_read_rnaseq_bams.Rout.fail
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.
> if (requireNamespace('Rsubread', quietly = TRUE)){
+ context('read_rnaseq_bams')
+ file <- download_data('billing16.bam.zip')
+ test_that('read_rnaseq_bams(file, cpm=FALSE)', {
+ object <- read_rnaseq_bams(
+ file, paired=TRUE, genome='hg38', cpm=FALSE, plot=FALSE)
+ expect_s4_class(object, 'SummarizedExperiment')
+ expect_identical(SummarizedExperiment::assayNames(object),'log2counts')
+ })
+
+ test_that('read_rnaseq_bams(file)', {
+ object <- read_rnaseq_bams(
+ file, paired=TRUE, genome='hg38', plot=FALSE)
+ expect_s4_class(object, 'SummarizedExperiment')
+ expect_identical(SummarizedExperiment::assayNames(object),'log2cpm')
+ })
+
+ test_that('read_rnaseq_bams(file, pca = TRUE)', {
+ object <- read_rnaseq_bams(
+ file, paired=TRUE, genome='hg38', pca=TRUE, plot=FALSE)
+ expect_s4_class(object, 'SummarizedExperiment')
+ expect_identical(SummarizedExperiment::assayNames(object),'log2cpm')
+ expect_true('pca1' %in% svars(object))
+ expect_true('pca1' %in% fvars(object))
+ expect_true('pca' %in% names(S4Vectors::metadata(object)))
+ })
+
+ test_that("read_rnaseq_counts(file, fit='limma')", {
+ object <- read_rnaseq_bams(
+ file, paired=TRUE, genome='hg38', fit='limma', plot=FALSE)
+ expect_s4_class(object, 'SummarizedExperiment')
+ expect_true('limma' %in% names(S4Vectors::metadata(object)))
+ })
+ }
Error in context("read_rnaseq_bams") : could not find function "context"
Execution halted
autonomics.Rcheck/tests/test_long_3_read_rnaseq_covid19.Rout.fail
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.
> context('read_rnaseq_counts: GSE161731')
Error in context("read_rnaseq_counts: GSE161731") :
could not find function "context"
Execution halted
autonomics.Rcheck/tests/test_long_8_fit.Rout.fail
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.
> sumexp_contains_fit <- function(object, fit = 'limma'){
+ is(object, 'SummarizedExperiment') &
+ is.array(S4Vectors::metadata(object)[[fit]]) &
+ (nrow(S4Vectors::metadata(object)[[fit]])==nrow(object))
+ }
>
> #==============================================================================
>
> context('fit: GSE161731')
Error in context("fit: GSE161731") : could not find function "context"
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no autonomics_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/autonomics.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘autonomics’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... SKIPPED
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'normimpute'
‘ref’ ‘pos’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘test_long_1_download.R’
Running ‘test_long_3_read_proteingroups_billing16.R’
Running ‘test_long_3_read_proteingroups_billing19.R’
Running ‘test_long_3_read_rnaseq_bams.R’
Running ‘test_long_3_read_rnaseq_covid19.R’
Running ‘test_long_8_fit.R’
ERROR
Running the tests in ‘longtests/test_long_1_download.R’ failed.
Complete output:
> context('download_data')
Error in context("download_data") : could not find function "context"
Execution halted
Running the tests in ‘longtests/test_long_3_read_proteingroups_billing16.R’ failed.
Complete output:
> context('read_proteingroups: billing16')
Error in context("read_proteingroups: billing16") :
could not find function "context"
Execution halted
Running the tests in ‘longtests/test_long_3_read_proteingroups_billing19.R’ failed.
Complete output:
> context('read_proteingroups: billing19')
Error in context("read_proteingroups: billing19") :
could not find function "context"
Execution halted
Running the tests in ‘longtests/test_long_3_read_rnaseq_bams.R’ failed.
Last 13 lines of output:
+ expect_identical(SummarizedExperiment::assayNames(object),'log2cpm')
+ expect_true('pca1' %in% svars(object))
+ expect_true('pca1' %in% fvars(object))
+ expect_true('pca' %in% names(S4Vectors::metadata(object)))
+ })
+
+ test_that("read_rnaseq_counts(file, fit='limma')", {
+ object <- read_rnaseq_bams(
+ file, paired=TRUE, genome='hg38', fit='limma', plot=FALSE)
+ expect_s4_class(object, 'SummarizedExperiment')
+ expect_true('limma' %in% names(S4Vectors::metadata(object)))
+ })
+ }
Error in context("read_rnaseq_bams") : could not find function "context"
Execution halted
Running the tests in ‘longtests/test_long_3_read_rnaseq_covid19.R’ failed.
Complete output:
> context('read_rnaseq_counts: GSE161731')
Error in context("read_rnaseq_counts: GSE161731") :
could not find function "context"
Execution halted
Running the tests in ‘longtests/test_long_8_fit.R’ failed.
Complete output:
> sumexp_contains_fit <- function(object, fit = 'limma'){
+ is(object, 'SummarizedExperiment') &
+ is.array(S4Vectors::metadata(object)[[fit]]) &
+ (nrow(S4Vectors::metadata(object)[[fit]])==nrow(object))
+ }
>
> #==============================================================================
>
> context('fit: GSE161731')
Error in context("fit: GSE161731") : could not find function "context"
Execution halted
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/autonomics.Rcheck/00check.log’
for details.
autonomics.Rcheck/00install.out
* installing *source* package ‘autonomics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '/' ** 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 (autonomics)