Marta R. Hidalgo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/hipathia |
| Branch: RELEASE_3_9 |
| Last Commit: 98a7f3d |
| Last Changed Date: 2019-05-02 11:54:11 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:02:22 -0400 (Wed, 16 Oct 2019).
| Package 761/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hipathia 2.0.0 Marta R. Hidalgo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: hipathia |
| Version: 2.0.0 |
| 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_2.0.0.tar.gz |
| StartedAt: 2019-10-16 03:39:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:57:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1083.4 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_2.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/hipathia.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 ‘hipathia/DESCRIPTION’ ... OK
* this is package ‘hipathia’ version ‘2.0.0’
* 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 9.5Mb
sub-directories of 1Mb or more:
data 4.9Mb
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 34.685 1.711 38.040
get_pathways_annotations 28.504 0.246 29.126
hipathia 28.251 0.227 28.651
quantify_terms 27.805 0.400 28.787
get_node_names 27.472 0.321 27.868
get_path_names 26.960 0.233 27.389
get_pathways_summary 26.722 0.280 27.182
get_pathways_list 26.654 0.327 27.062
visualize_report 26.658 0.208 27.036
load_pathways 25.421 0.189 25.844
pathway_comparison_plot 24.304 0.327 24.824
node_color_per_de 24.299 0.219 24.676
node_color 23.980 0.195 24.347
normalize_paths 23.607 0.221 23.984
save_results 23.110 0.291 23.476
normalize_data 12.535 0.324 13.100
translate_data 11.601 0.300 12.067
* 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘hipathia’ ... ** 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 (hipathia)
hipathia.Rcheck/tests/testthat.Rout
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.
> 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
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, rowsum
>
> 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: 119 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
318.461 5.862 327.855
hipathia.Rcheck/hipathia-Ex.timings
| name | user | system | elapsed | |
| create_report | 34.685 | 1.711 | 38.040 | |
| do_pca | 0.092 | 0.016 | 0.108 | |
| do_wilcoxon | 0.169 | 0.036 | 0.204 | |
| get_go_names | 2.416 | 0.344 | 2.963 | |
| get_node_names | 27.472 | 0.321 | 27.868 | |
| get_nodes_data | 0.012 | 0.005 | 0.016 | |
| get_path_names | 26.960 | 0.233 | 27.389 | |
| get_paths_data | 0.011 | 0.004 | 0.015 | |
| get_pathways_annotations | 28.504 | 0.246 | 29.126 | |
| get_pathways_list | 26.654 | 0.327 | 27.062 | |
| get_pathways_summary | 26.722 | 0.280 | 27.182 | |
| heatmap_plot | 0.379 | 0.011 | 0.391 | |
| hhead | 0.003 | 0.002 | 0.005 | |
| hipathia | 28.251 | 0.227 | 28.651 | |
| load_pathways | 25.421 | 0.189 | 25.844 | |
| multiple_pca_plot | 0.026 | 0.004 | 0.030 | |
| node_color | 23.980 | 0.195 | 24.347 | |
| node_color_per_de | 24.299 | 0.219 | 24.676 | |
| normalize_data | 12.535 | 0.324 | 13.100 | |
| normalize_paths | 23.607 | 0.221 | 23.984 | |
| paths_to_go_ancestor | 0.420 | 0.017 | 0.437 | |
| pathway_comparison_plot | 24.304 | 0.327 | 24.824 | |
| pca_plot | 0.050 | 0.005 | 0.056 | |
| quantify_terms | 27.805 | 0.400 | 28.787 | |
| save_results | 23.110 | 0.291 | 23.476 | |
| top_pathways | 0.011 | 0.003 | 0.013 | |
| translate_data | 11.601 | 0.300 | 12.067 | |
| visualize_report | 26.658 | 0.208 | 27.036 | |