Marta R. Hidalgo
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/hipathia |
| Branch: master |
| Last Commit: 724be73 |
| Last Changed Date: 2019-12-02 13:06:23 -0500 (Mon, 02 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:51:04 -0500 (Thu, 16 Jan 2020).
| Package 790/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hipathia 2.3.0 Marta R. Hidalgo
| malbec2 | Linux (Ubuntu 18.04.3 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: 2.3.0 |
| 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_2.3.0.tar.gz |
| StartedAt: 2020-01-16 05:24:47 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 05:47:25 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 1358.1 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_2.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/hipathia.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.3.0’
* 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 9.6Mb
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 (user + system) or elapsed time > 5s
user system elapsed
quantify_terms 51.187 2.824 54.859
get_pathways_annotations 37.760 1.601 40.024
create_report 36.693 1.814 40.240
hipathia 33.996 1.042 35.354
save_results 32.710 1.016 33.861
get_pathways_list 32.184 0.840 33.255
visualize_report 32.187 0.757 33.135
normalize_paths 31.986 0.853 33.021
pathway_comparison_plot 31.832 0.831 32.868
get_node_names 31.330 0.963 32.408
get_path_names 31.168 0.754 32.185
load_pathways 30.530 1.026 31.899
node_color_per_de 29.849 0.685 30.863
node_color 28.925 0.817 29.958
get_pathways_summary 28.626 0.736 29.662
normalize_data 18.706 0.849 20.146
translate_data 16.698 0.767 17.776
get_go_names 7.649 1.277 9.266
* 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-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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
401.147 15.963 421.355
hipathia.Rcheck/hipathia-Ex.timings
| name | user | system | elapsed | |
| create_report | 36.693 | 1.814 | 40.240 | |
| do_pca | 0.099 | 0.015 | 0.114 | |
| do_wilcoxon | 0.208 | 0.048 | 0.256 | |
| get_go_names | 7.649 | 1.277 | 9.266 | |
| get_node_names | 31.330 | 0.963 | 32.408 | |
| get_nodes_data | 0.012 | 0.004 | 0.016 | |
| get_path_names | 31.168 | 0.754 | 32.185 | |
| get_paths_data | 0.012 | 0.004 | 0.016 | |
| get_pathways_annotations | 37.760 | 1.601 | 40.024 | |
| get_pathways_list | 32.184 | 0.840 | 33.255 | |
| get_pathways_summary | 28.626 | 0.736 | 29.662 | |
| heatmap_plot | 0.325 | 0.020 | 0.400 | |
| hhead | 0.002 | 0.001 | 0.002 | |
| hipathia | 33.996 | 1.042 | 35.354 | |
| load_pathways | 30.530 | 1.026 | 31.899 | |
| multiple_pca_plot | 0.096 | 0.004 | 0.101 | |
| node_color | 28.925 | 0.817 | 29.958 | |
| node_color_per_de | 29.849 | 0.685 | 30.863 | |
| normalize_data | 18.706 | 0.849 | 20.146 | |
| normalize_paths | 31.986 | 0.853 | 33.021 | |
| paths_to_go_ancestor | 0.428 | 0.016 | 0.444 | |
| pathway_comparison_plot | 31.832 | 0.831 | 32.868 | |
| pca_plot | 0.061 | 0.006 | 0.067 | |
| quantify_terms | 51.187 | 2.824 | 54.859 | |
| save_results | 32.710 | 1.016 | 33.861 | |
| top_pathways | 0.010 | 0.003 | 0.013 | |
| translate_data | 16.698 | 0.767 | 17.776 | |
| visualize_report | 32.187 | 0.757 | 33.135 | |