Package: transcriptogramer

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptogramer_1.0.0.tar.gz

StartedAt: 2018-04-12 10:26:09 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:29:10 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 180.8 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 --no-vignettes --timings transcriptogramer_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/transcriptogramer.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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   4.5Mb
* 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 loading without being on the library search path ... 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
check_algorithm: no visible binding for global variable ‘name’
check_ontology: no visible binding for global variable ‘name’
check_statistic: no visible binding for global variable ‘name’
Undefined global functions or variables:
  name
* 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 installed files from ‘inst/doc’ ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/transcriptogramer.Rcheck/00check.log’
for details.

* installing *source* package ‘transcriptogramer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (transcriptogramer)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 -- Thu Apr 12 10:29:03 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 
  8.729   0.451  41.465 

name	user	system	elapsed
DE-method	0.684	0.046	0.737
DEsymbols	0.006	0.001	0.007
GPL570	0.034	0.004	0.037
GSE9988	1.584	0.368	1.961
Hs700	0.257	0.068	0.331
Hs800	0.204	0.054	0.269
Hs900	0.187	0.050	0.243
HsBPTerms	3.149	0.436	3.632
Mm700	0.335	0.077	0.418
Mm800	0.240	0.067	0.309
Mm900	0.263	0.073	0.345
Rn700	0.286	0.084	0.376
Rn800	0.262	0.079	0.341
Rn900	0.210	0.061	0.272
Sc700	0.070	0.025	0.100
Sc800	0.064	0.024	0.089
Sc900	0.045	0.017	0.065
association	0.193	0.018	0.214
clusterEnrichment-method	0.289	0.014	0.307
clusterVisualization-method	0.035	0.011	0.048
connectivityProperties-method	0.047	0.005	0.052
differentiallyExpressed-method	0.051	0.003	0.053
orderingProperties-method	0.048	0.011	0.059
radius-method	0.052	0.003	0.056
transcriptogramPreprocess	0.033	0.001	0.034
transcriptogramStep1-method	0.043	0.005	0.050
transcriptogramStep2-method	0.044	0.000	0.044