Package: hipathia

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hipathia.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hipathia_1.4.1.tar.gz

StartedAt: 2019-04-16 00:34:05 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:43:39 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 574.1 seconds

RetCode: 0

Status:  OK

CheckDir: hipathia.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:hipathia.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hipathia_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/hipathia.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hipathia/DESCRIPTION’ ... OK
* this is package ‘hipathia’ version ‘1.4.1’
* 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 ‘hipathia’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   4.3Mb
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘load_entrez_hgnc’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmap_plot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
create_report            22.839  0.810  24.609
hipathia                 17.574  0.222  17.991
visualize_report         16.595  0.152  16.841
get_pathways_summary     13.848  0.081  14.079
save_results             13.595  0.081  13.847
quantify_terms           13.405  0.080  13.565
load_pathways            13.171  0.055  13.346
pathway_comparison_plot  13.135  0.078  13.315
get_path_names           12.845  0.119  13.045
node_color_per_de        12.890  0.071  13.051
get_pathways_list        12.846  0.063  13.013
normalize_paths          12.800  0.074  12.981
get_pathways_annotations 10.895  0.073  11.008
normalize_data           10.207  0.120  10.424
translate_data            8.595  0.068   8.735
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/hipathia.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 hipathia
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘hipathia’ ...
** 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 (hipathia)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> library(hipathia)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: AnnotationHub
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:igraph':

    normalize, path, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:AnnotationHub':

    cache

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:igraph':

    simplify

The following objects are masked from 'package:base':

    aperm, apply

> 
> test_check("hipathia")
HiPathia processing...
hsa03320 - PPAR signaling pathway 
hsa04012 - ErbB signaling pathway 
HiPathia processing...
hsa03320 - PPAR signaling pathway 
hsa04012 - ErbB signaling pathway 
translated ids = 3184 (1) 
untranslated ids = 3 (0.00094) 
multihit ids = 0 (0) 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
156.242   2.406 160.433 

name	user	system	elapsed
create_report	22.839	0.810	24.609
do_pca	0.009	0.002	0.011
do_wilcoxon	0.072	0.005	0.078
get_path_names	12.845	0.119	13.045
get_paths_data	0.013	0.002	0.015
get_pathways_annotations	10.895	0.073	11.008
get_pathways_list	12.846	0.063	13.013
get_pathways_summary	13.848	0.081	14.079
heatmap_plot	0.291	0.008	0.304
hhead	0.001	0.001	0.001
hipathia	17.574	0.222	17.991
load_pathways	13.171	0.055	13.346
multiple_pca_plot	0.023	0.003	0.026
node_color_per_de	12.890	0.071	13.051
normalize_data	10.207	0.120	10.424
normalize_paths	12.800	0.074	12.981
paths_to_go_ancestor	1.098	0.117	1.221
pathway_comparison_plot	13.135	0.078	13.315
pca_plot	0.009	0.002	0.010
quantify_terms	13.405	0.080	13.565
save_results	13.595	0.081	13.847
top_pathways	0.011	0.003	0.013
translate_data	8.595	0.068	8.735
visualize_report	16.595	0.152	16.841