Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:08:33 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 transcriptogramer on machv2


To the developers/maintainers of the transcriptogramer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/transcriptogramer.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 1983/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptogramer 1.16.0  (landing page)
Diego Morais
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/transcriptogramer
git_branch: RELEASE_3_14
git_last_commit: 2bd1dc6
git_last_commit_date: 2021-10-26 12:39:59 -0500 (Tue, 26 Oct 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: transcriptogramer
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:transcriptogramer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings transcriptogramer_1.16.0.tar.gz
StartedAt: 2022-01-16 19:08:04 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 19:13:51 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 347.6 seconds
RetCode: 0
Status:   OK  
CheckDir: transcriptogramer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:transcriptogramer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings transcriptogramer_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/transcriptogramer.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘transcriptogramer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘transcriptogramer’ version ‘1.16.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘transcriptogramer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/transcriptogramer.Rcheck/00check.log’
for details.



Installation output

transcriptogramer.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘transcriptogramer’ ...
** using staged installation
** 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 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 (transcriptogramer)

Tests output

transcriptogramer.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("transcriptogramer")

preprocessing input data... step 1 of 1
calculating node properties... step 1 of 2
** this may take some time...
applying sliding window and mounting resulting data... step 2 of 2
** this may take some time...
done!
mapping identifiers to ENSEMBL Peptide ID... step 1 of 2
averaging over all identifiers related to the same protein... step 2 of 2
done!
applying sliding window and mounting resulting data... step 1 of 1
done!


RUNIT TEST PROTOCOL -- Sun Jan 16 19:13:40 2022 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
transcriptogramer RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 16.107   1.290 109.553 

Example timings

transcriptogramer.Rcheck/transcriptogramer-Ex.timings

nameusersystemelapsed
DE-method1.5760.0561.632
DEsymbols0.2640.3070.572
GPL5700.8870.7571.694
GSE99880.8741.0421.935
Hs7000.1790.2530.462
Hs8000.1450.1970.343
Hs9000.1010.1390.239
HsBPTerms1.1871.0732.307
Mm7000.1990.2880.487
Mm8000.1590.2300.388
Mm9000.1250.1900.335
Rn7000.1860.2530.439
Rn8000.1440.1950.339
Rn9000.1260.1700.295
Sc7000.0480.0830.131
Sc8000.0390.0720.139
Sc9000.0400.0670.107
Terms-method0.1020.0050.108
association1.4631.2862.775
clusterEnrichment-method0.0520.0060.058
clusterVisualization-method0.0800.0070.087
connectivityProperties-method0.0480.0030.051
differentiallyExpressed-method0.0720.0090.082
enrichmentPlot-method0.0470.0000.047
orderingProperties-method0.0690.0030.071
radius-method0.0540.0020.056
transcriptogramPreprocess0.5740.0120.588
transcriptogramStep1-method0.0520.0030.056
transcriptogramStep2-method0.0350.0010.036