Back to Multiple platform build/check report for BioC 3.15
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-18 11:07:05 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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? here 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 454/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dasper 1.5.1  (landing page)
David Zhang
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/dasper
git_branch: master
git_last_commit: 0b93fe2
git_last_commit_date: 2022-01-10 17:26:37 -0500 (Mon, 10 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocParallel' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: dasper
Version: 1.5.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dasper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings dasper_1.5.1.tar.gz
StartedAt: 2022-01-17 18:44:02 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 18:56:10 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 728.3 seconds
RetCode: 0
Status:   OK  
CheckDir: dasper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dasper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings dasper_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/dasper.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dasper/DESCRIPTION' ... OK
* this is package 'dasper' version '1.5.1'
* 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 whether package 'dasper' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'D:/biocbuild/bbs-3.15-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 87.02  21.80  113.97
junction_process 52.03   3.92   59.43
plot_sashimi     29.62   1.85   32.87
ref_load          9.30   0.31   10.20
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/dasper.Rcheck/00check.log'
for details.



Installation output

dasper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL dasper
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
  converting help for package 'dasper'
    finding HTML links ... done
    coverage_process                        html  
    dasper                                  html  
    deprecated                              html  
    junction_load                           html  
    junction_process                        html  
    junctions_example                       html  
    finding level-2 HTML links ... done

    outlier_process                         html  
    plot_sashimi                            html  
    ref_load                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dasper)
Making 'packages.html' ... done

Tests output

dasper.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
== Skipped tests ===============================================================
* On CRAN (3)

[ FAIL 0 | WARN 1 | SKIP 3 | PASS 228 ]
> 
> proc.time()
   user  system elapsed 
   6.07    0.84  379.60 

Example timings

dasper.Rcheck/dasper-Ex.timings

nameusersystemelapsed
coverage_process 87.02 21.80113.97
junction_load0.130.010.14
junction_process52.03 3.9259.43
outlier_process000
plot_sashimi29.62 1.8532.87
ref_load 9.30 0.3110.20