Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:05 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tximeta on nebbiolo2


To the developers/maintainers of the tximeta package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tximeta.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 2022/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tximeta 1.12.4  (landing page)
Michael Love
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/tximeta
git_branch: RELEASE_3_14
git_last_commit: 78d1a79
git_last_commit_date: 2021-12-20 13:21:54 -0400 (Mon, 20 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: tximeta
Version: 1.12.4
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:tximeta.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings tximeta_1.12.4.tar.gz
StartedAt: 2022-04-12 09:47:32 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:53:15 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 343.2 seconds
RetCode: 0
Status:   OK  
CheckDir: tximeta.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:tximeta.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings tximeta_1.12.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/tximeta.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tximeta/DESCRIPTION’ ... OK
* this is package ‘tximeta’ version ‘1.12.4’
* 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 ‘tximeta’ 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
addIds          17.150  1.157  18.296
retrieveCDNA    13.244  0.680  19.213
summarizeToGene  5.385  0.250   5.545
* 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: OK


Installation output

tximeta.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL tximeta
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘tximeta’ ...
** 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 (tximeta)

Tests output

tximeta.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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.

> library("testthat")
> library("tximeta")
> test_check("tximeta")
trying URL 'ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.22.cdna.all.fa.gz'
Content type 'unknown' length 17378397 bytes (16.6 MB)
==================================================
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
trying URL 'ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.22.ncrna.fa.gz'
Content type 'unknown' length 956972 bytes (934 KB)
==================================================
[ FAIL 0 | WARN 3 | SKIP 4 | PASS 37 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (4)

[ FAIL 0 | WARN 3 | SKIP 4 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
 62.106   3.689  73.887 

Example timings

tximeta.Rcheck/tximeta-Ex.timings

nameusersystemelapsed
addIds17.150 1.15718.296
getTximetaBFC0.0000.0000.001
linkedTxome0.5800.0080.588
retrieveCDNA13.244 0.68019.213
retrieveDb3.3310.1703.416
splitSE0.1060.0120.119
summarizeToGene5.3850.2505.545
tximeta2.8460.0892.854