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This page was generated on 2022-01-14 13:07:21 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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 tokay2


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? 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 2022/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tximeta 1.12.4  (landing page)
Michael Love
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 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 -0500 (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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tximeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tximeta_1.12.4.tar.gz
StartedAt: 2022-01-14 03:55:36 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 04:06:24 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 648.7 seconds
RetCode: 0
Status:   OK  
CheckDir: tximeta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tximeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tximeta_1.12.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/tximeta.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
addIds          25.11   2.14   27.73
retrieveCDNA    21.25   0.37   27.96
summarizeToGene  5.89   0.13    5.99
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
addIds          22.37   0.86   23.14
retrieveCDNA    17.97   0.42   24.26
summarizeToGene  7.85   0.18    8.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/tximeta_1.12.4.tar.gz && rm -rf tximeta.buildbin-libdir && mkdir tximeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tximeta.buildbin-libdir tximeta_1.12.4.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL tximeta_1.12.4.zip && rm tximeta_1.12.4.tar.gz tximeta_1.12.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 44  379k   44  167k    0     0  1061k      0 --:--:-- --:--:-- --:--:-- 1059k
100  379k  100  379k    0     0  1810k      0 --:--:-- --:--:-- --:--:-- 1808k

install for i386

* installing *source* package 'tximeta' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'tximeta'
    finding HTML links ... done
    addCDS                                  html  
    addExons                                html  
    addIds                                  html  
    getTximetaBFC                           html  
    linkedTxome                             html  
    makeDGEList                             html  
    retrieveCDNA                            html  
    retrieveDb                              html  
    splitSE                                 html  
    summarizeToGene                         html  
    tximeta-package                         html  
    finding level-2 HTML links ... done

    tximeta                                 html  
** 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

install for x64

* installing *source* package 'tximeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tximeta' as tximeta_1.12.4.zip
* DONE (tximeta)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'tximeta' successfully unpacked and MD5 sums checked

Tests output

tximeta.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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'
 length 17378397 bytes (16.6 MB)
==================================================
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
trying URL 'ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.22.ncrna.fa.gz'
Content length 956972 bytes (934 KB)
==================================================
== Skipped tests ===============================================================
* empty test (4)

[ FAIL 0 | WARN 3 | SKIP 4 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
  82.42    6.29   91.89 

tximeta.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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("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'
 length 17378397 bytes (16.6 MB)
==================================================
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Error in x$.self$finalize() : attempt to apply non-function
trying URL 'ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.22.ncrna.fa.gz'
Content length 956972 bytes (934 KB)
==================================================
== Skipped tests ===============================================================
* empty test (4)

[ FAIL 0 | WARN 3 | SKIP 4 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
  74.03    3.43   87.32 

Example timings

tximeta.Rcheck/examples_i386/tximeta-Ex.timings

nameusersystemelapsed
addIds25.11 2.1427.73
getTximetaBFC000
linkedTxome0.610.000.64
retrieveCDNA21.25 0.3727.96
retrieveDb3.480.223.46
splitSE0.140.000.14
summarizeToGene5.890.135.99
tximeta2.970.152.98

tximeta.Rcheck/examples_x64/tximeta-Ex.timings

nameusersystemelapsed
addIds22.37 0.8623.14
getTximetaBFC000
linkedTxome0.570.020.60
retrieveCDNA17.97 0.4224.26
retrieveDb4.830.164.89
splitSE0.200.000.22
summarizeToGene7.850.188.03
tximeta3.900.134.00