Package: transcriptogramer

Version: 1.2.1

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_1.2.1.tar.gz

StartedAt: 2018-10-17 00:28:26 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:32:01 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 215.1 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptogramer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/transcriptogramer.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.1’
* 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 ... 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 ... NOTE
differentiallyExpressed,Transcriptogram: no visible binding for global
  variable ‘x’
differentiallyExpressed,Transcriptogram: no visible binding for global
  variable ‘y’
differentiallyExpressed,Transcriptogram : <anonymous>: no visible
  binding for global variable ‘x’
differentiallyExpressed,Transcriptogram : <anonymous>: no visible
  binding for global variable ‘y’
Undefined global functions or variables:
  x y
* 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
* 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-3.7-bioc/meat/transcriptogramer.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘transcriptogramer’ ...
** 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
* DONE (transcriptogramer)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 the 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
calculating average 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 17 00:31:51 2018 
*********************************************** 
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 
 11.090   1.132  75.003 

name	user	system	elapsed
DE-method	1.072	0.053	1.135
DEsymbols	0.061	0.014	0.074
GPL570	1.612	0.312	1.943
GSE9988	1.531	0.412	1.952
Hs700	0.249	0.069	0.320
Hs800	0.207	0.049	0.258
Hs900	0.205	0.061	0.267
HsBPTerms	3.392	0.526	3.965
Mm700	0.326	0.092	0.423
Mm800	0.262	0.077	0.344
Mm900	0.226	0.068	0.301
Rn700	0.329	0.099	0.431
Rn800	0.301	0.090	0.394
Rn900	0.228	0.071	0.300
Sc700	0.081	0.031	0.113
Sc800	0.060	0.022	0.082
Sc900	0.061	0.022	0.083
association	0.020	0.002	0.022
clusterEnrichment-method	0.091	0.016	0.107
clusterVisualization-method	0.134	0.001	0.137
connectivityProperties-method	0.393	0.006	0.401
differentiallyExpressed-method	0.042	0.005	0.048
orderingProperties-method	0.078	0.018	0.096
radius-method	0.046	0.003	0.048
transcriptogramPreprocess	0.050	0.008	0.058
transcriptogramStep1-method	0.041	0.000	0.041
transcriptogramStep2-method	0.049	0.004	0.052