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CHECK report for transcriptogramer on celaya2

This page was generated on 2019-10-16 13:01:24 -0400 (Wed, 16 Oct 2019).

Package 1665/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptogramer 1.6.0
Diego Morais
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/transcriptogramer
Branch: RELEASE_3_9
Last Commit: 179681c
Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: transcriptogramer
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transcriptogramer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transcriptogramer_1.6.0.tar.gz
StartedAt: 2019-10-16 07:28:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:33:36 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 318.0 seconds
RetCode: 0
Status:  OK 
CheckDir: transcriptogramer.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transcriptogramer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transcriptogramer_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/transcriptogramer.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
association 4.358  1.149   5.508
* 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-3.9-bioc/meat/transcriptogramer.Rcheck/00check.log’
for details.



Installation output

transcriptogramer.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL transcriptogramer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Wed Oct 16 07:33:26 2019 
*********************************************** 
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 
 14.051   2.250 106.912 

Example timings

transcriptogramer.Rcheck/transcriptogramer-Ex.timings

nameusersystemelapsed
DE-method1.4070.1411.548
DEsymbols0.6850.2640.949
GPL5702.6810.8443.585
GSE99882.1551.0083.163
Hs7000.4800.2080.687
Hs8000.4230.2010.624
Hs9000.3390.1610.500
HsBPTerms3.3301.1004.464
Mm7000.4440.1850.629
Mm8000.3980.1920.590
Mm9000.3250.1450.470
Rn7000.5560.2610.818
Rn8000.4090.2020.611
Rn9000.3440.1790.522
Sc7000.1210.0810.202
Sc8000.1230.0780.201
Sc9000.1130.0740.189
Terms-method0.1510.0510.202
association4.3581.1495.508
clusterEnrichment-method0.0640.0230.088
clusterVisualization-method0.1070.0070.113
connectivityProperties-method0.0520.0240.075
differentiallyExpressed-method0.0690.0010.070
enrichmentPlot-method0.0350.0000.035
orderingProperties-method0.0640.0010.064
radius-method0.0380.0010.038
transcriptogramPreprocess0.0720.0010.073
transcriptogramStep1-method0.0380.0000.038
transcriptogramStep2-method0.0680.0000.069