Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-01-28 11:08:34 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
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

CHECK results for dasper on merida1


To the developers/maintainers of the dasper package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dasper.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 469/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dasper 1.9.0  (landing page)
David Zhang
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/dasper
git_branch: master
git_last_commit: 7fc89b3
git_last_commit_date: 2022-11-01 11:23:22 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: dasper
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dasper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dasper_1.9.0.tar.gz
StartedAt: 2023-01-28 00:20:15 -0500 (Sat, 28 Jan 2023)
EndedAt: 2023-01-28 00:51:41 -0500 (Sat, 28 Jan 2023)
EllapsedTime: 1886.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: dasper.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dasper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dasper_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/dasper.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dasper/DESCRIPTION’ ... OK
* this is package ‘dasper’ version ‘1.9.0’
* 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 ‘dasper’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/dasper.Rcheck/00install.out’ for details.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘grid:::calcControlPoints’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.classify_junc: no visible binding for global variable ‘lend’
.classify_junc: no visible binding for global variable ‘rstart’
.coverage_to_plot_get: no visible binding for global variable ‘.’
.coverage_to_plot_get: no visible binding for global variable
  ‘case_control’
.get_ref_exons_annot: no visible binding for global variable ‘.’
.plot_coverage: no visible binding for global variable ‘case_control’
.plot_junctions: no visible binding for global variable ‘size’
annotate_junc_ref: no visible global function definition for
  ‘ensemblGenome’
annotate_junc_ref: no visible global function definition for
  ‘basedir<-’
annotate_junc_ref: no visible global function definition for ‘read.gtf’
annotate_junc_ref: no visible global function definition for
  ‘getSpliceTable’
Undefined global functions or variables:
  . basedir<- case_control ensemblGenome getSpliceTable lend read.gtf
  rstart size
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
coverage_process 139.213 18.510 432.278
junction_process 100.191  3.088 142.736
plot_sashimi      49.247  1.634  83.025
ref_load          13.344  0.838  22.779
* 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:
  Error in `stringr::str_detect(seqnames(x), "chr")`: `string` must be a vector, not a <Rle> object.
  Backtrace:
      ▆
   1. ├─dasper:::.coverage_load(...) at test-utils.R:39:2
   2. │ └─dasper:::.chr_check(regions, chr_format)
   3. │   └─stringr::str_detect(seqnames(x), "chr")
   4. │     └─stringr:::check_lengths(string, pattern)
   5. │       └─vctrs::vec_size_common(...)
   6. └─vctrs:::stop_scalar_type(`<fn>`(`<Rle>`), "string", `<env>`)
   7.   └─vctrs:::stop_vctrs(...)
   8.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
  
  [ FAIL 2 | WARN 2 | SKIP 1 | PASS 186 ]
  Error: Test failures
  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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/dasper.Rcheck/00check.log’
for details.


Installation output

dasper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dasper
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘dasper’ ...
** using non-staged installation via StagedInstall field
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (dasper)

Tests output

dasper.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(testthat)
> library(dasper)
> 
> test_check("dasper")
Starting 2 test processes
[ FAIL 2 | WARN 2 | SKIP 1 | PASS 186 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (1)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot_sashimi.R:343'): (code run outside of `test_that()`) ──────
<vctrs_error_scalar_type/vctrs_error/rlang_error/error/condition>
Error in `stringr::str_detect(seqnames(x), "chr")`: `string` must be a vector, not a <Rle> object.
Backtrace:
     ▆
  1. ├─dasper:::.coverage_to_plot_get(...) at test-plot_sashimi.R:343:0
  2. │ ├─... %>% ...
  3. │ └─dasper:::.coverage_load(...)
  4. │   └─dasper:::.chr_check(regions, chr_format)
  5. │     └─stringr::str_detect(seqnames(x), "chr")
  6. │       └─stringr:::check_lengths(string, pattern)
  7. │         └─vctrs::vec_size_common(...)
  8. ├─dplyr::tibble(...)
  9. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
 10. │   └─rlang::eval_tidy(xs[[j]], mask)
 11. ├─base::unlist(.)
 12. └─vctrs:::stop_scalar_type(`<fn>`(`<Rle>`), "string", `<env>`)
 13.   └─vctrs:::stop_vctrs(...)
 14.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))
── Error ('test-utils.R:39'): (code run outside of `test_that()`) ──────────────
<vctrs_error_scalar_type/vctrs_error/rlang_error/error/condition>
Error in `stringr::str_detect(seqnames(x), "chr")`: `string` must be a vector, not a <Rle> object.
Backtrace:
    ▆
 1. ├─dasper:::.coverage_load(...) at test-utils.R:39:2
 2. │ └─dasper:::.chr_check(regions, chr_format)
 3. │   └─stringr::str_detect(seqnames(x), "chr")
 4. │     └─stringr:::check_lengths(string, pattern)
 5. │       └─vctrs::vec_size_common(...)
 6. └─vctrs:::stop_scalar_type(`<fn>`(`<Rle>`), "string", `<env>`)
 7.   └─vctrs:::stop_vctrs(...)
 8.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))

[ FAIL 2 | WARN 2 | SKIP 1 | PASS 186 ]
Error: Test failures
Execution halted

Example timings

dasper.Rcheck/dasper-Ex.timings

nameusersystemelapsed
coverage_process139.213 18.510432.278
junction_load0.3460.0060.464
junction_process100.191 3.088142.736
outlier_process0.0010.0010.000
plot_sashimi49.247 1.63483.025
ref_load13.344 0.83822.779