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

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### Running command:
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###   /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.

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### Running command:
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###   /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)

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 
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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 

name	user	system	elapsed
DE-method	1.407	0.141	1.548
DEsymbols	0.685	0.264	0.949
GPL570	2.681	0.844	3.585
GSE9988	2.155	1.008	3.163
Hs700	0.480	0.208	0.687
Hs800	0.423	0.201	0.624
Hs900	0.339	0.161	0.500
HsBPTerms	3.330	1.100	4.464
Mm700	0.444	0.185	0.629
Mm800	0.398	0.192	0.590
Mm900	0.325	0.145	0.470
Rn700	0.556	0.261	0.818
Rn800	0.409	0.202	0.611
Rn900	0.344	0.179	0.522
Sc700	0.121	0.081	0.202
Sc800	0.123	0.078	0.201
Sc900	0.113	0.074	0.189
Terms-method	0.151	0.051	0.202
association	4.358	1.149	5.508
clusterEnrichment-method	0.064	0.023	0.088
clusterVisualization-method	0.107	0.007	0.113
connectivityProperties-method	0.052	0.024	0.075
differentiallyExpressed-method	0.069	0.001	0.070
enrichmentPlot-method	0.035	0.000	0.035
orderingProperties-method	0.064	0.001	0.064
radius-method	0.038	0.001	0.038
transcriptogramPreprocess	0.072	0.001	0.073
transcriptogramStep1-method	0.038	0.000	0.038
transcriptogramStep2-method	0.068	0.000	0.069