Marta R. Hidalgo
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/hipathia |
| Branch: RELEASE_3_7 |
| Last Commit: f841646 |
| Last Changed Date: 2018-04-30 10:35:50 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 09:00:00 -0400 (Wed, 17 Oct 2018).
| Package 689/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hipathia 1.0.0 Marta R. Hidalgo
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: hipathia |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2018-10-16 21:59:12 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 22:08:34 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 561.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hipathia.Rcheck |
| Warnings: 0 |
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###
### Running 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/hipathia.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 ‘hipathia/DESCRIPTION’ ... OK
* this is package ‘hipathia’ 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 ‘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 ... 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 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 17.332 0.583 18.215
hipathia 14.706 0.129 14.946
pathway_comparison_plot 13.631 0.076 13.838
get_pathways_summary 13.411 0.070 13.614
node_color_per_de 13.344 0.130 13.582
quantify_terms 13.135 0.090 13.333
load_pathways 13.076 0.102 13.308
normalize_paths 13.034 0.100 13.227
get_pathways_list 12.869 0.081 13.087
visualize_report 12.782 0.104 12.964
get_path_names 12.710 0.125 12.936
get_pathways_annotations 12.606 0.107 12.797
save_results 12.285 0.077 12.425
normalize_data 8.955 0.111 9.114
translate_data 7.516 0.114 7.684
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/hipathia.Rcheck/00check.log’
for details.
hipathia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hipathia ### ############################################################################## ############################################################################## * 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)
hipathia.Rcheck/tests/testthat.Rout
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.
> 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
164.108 2.098 169.344
hipathia.Rcheck/hipathia-Ex.timings
| name | user | system | elapsed | |
| create_report | 17.332 | 0.583 | 18.215 | |
| do_pca | 0.009 | 0.004 | 0.013 | |
| do_wilcoxon | 0.105 | 0.018 | 0.124 | |
| get_path_names | 12.710 | 0.125 | 12.936 | |
| get_paths_data | 0.013 | 0.001 | 0.015 | |
| get_pathways_annotations | 12.606 | 0.107 | 12.797 | |
| get_pathways_list | 12.869 | 0.081 | 13.087 | |
| get_pathways_summary | 13.411 | 0.070 | 13.614 | |
| heatmap_plot | 0.238 | 0.005 | 0.247 | |
| hhead | 0.003 | 0.001 | 0.005 | |
| hipathia | 14.706 | 0.129 | 14.946 | |
| load_pathways | 13.076 | 0.102 | 13.308 | |
| multiple_pca_plot | 0.018 | 0.003 | 0.020 | |
| node_color_per_de | 13.344 | 0.130 | 13.582 | |
| normalize_data | 8.955 | 0.111 | 9.114 | |
| normalize_paths | 13.034 | 0.100 | 13.227 | |
| paths_to_go_ancestor | 0.278 | 0.007 | 0.287 | |
| pathway_comparison_plot | 13.631 | 0.076 | 13.838 | |
| pca_plot | 0.012 | 0.002 | 0.014 | |
| quantify_terms | 13.135 | 0.090 | 13.333 | |
| save_results | 12.285 | 0.077 | 12.425 | |
| translate_data | 7.516 | 0.114 | 7.684 | |
| visualize_report | 12.782 | 0.104 | 12.964 | |