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This page was generated on 2022-01-21 13:05:15 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for hipathia on nebbiolo2


To the developers/maintainers of the hipathia package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hipathia.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 875/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hipathia 2.10.0  (landing page)
Marta R. Hidalgo
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/hipathia
git_branch: RELEASE_3_14
git_last_commit: bc0e4d8
git_last_commit_date: 2021-10-26 12:44:06 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hipathia
Version: 2.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hipathia_2.10.0.tar.gz
StartedAt: 2022-01-20 07:57:16 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 08:09:41 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 745.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: hipathia.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hipathia_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/hipathia.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hipathia/DESCRIPTION’ ... OK
* this is package ‘hipathia’ version ‘2.10.0’
* 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   4.4Mb
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘hipathia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: normalize_paths
> ### Title: Normalize the pathway matrix by rows
> ### Aliases: normalize_paths
> 
> ### ** Examples
> 
> data(path_vals)
> pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
+ "hsa04012"))
snapshotDate(): 2021-10-20
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'query': error reading from connection
Calls: load_pathways ... .db_create_index -> readRDS -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error in `readRDS(.db_index_file(x))`: error reading from connection
  Backtrace:
      █
   1. └─hipathia::load_pathways("hsa") test-translate-matrix.R:9:0
   2.   └─hipathia:::load_mgi(species)
   3.     └─hipathia:::hub()
   4.       ├─AnnotationHub::query(AnnotationHub(), "hpAnnot")
   5.       └─AnnotationHub::query(AnnotationHub(), "hpAnnot")
   6.         └─AnnotationHub:::.local(x, pattern, ...)
   7.           └─AnnotationHub:::.db_index_load(x)
   8.             └─base::readRDS(.db_index_file(x))
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 80 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/hipathia.Rcheck/00check.log’
for details.


Installation output

hipathia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL hipathia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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)

Tests output

hipathia.Rcheck/tests/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

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

    cache

> 
> test_check("hipathia")
translated ids = 3184 (1) 
untranslated ids = 3 (0.00094) 
multihit ids = 0 (0) 
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-hipathia.R:8:1): (code run outside of `test_that()`) ────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'query': error reading from connection
Backtrace:
     █
  1. ├─hipathia::load_pathways(...) test-hipathia.R:8:0
  2. │ └─hipathia:::load_mgi(species)
  3. │   └─hipathia:::hub()
  4. │     ├─AnnotationHub::query(AnnotationHub(), "hpAnnot")
  5. │     └─AnnotationHub::AnnotationHub()
  6. │       └─AnnotationHub::.Hub(...)
  7. │         └─AnnotationHub:::.db_create_index(hub)
  8. │           └─base::readRDS(index_path)
  9. └─base::.handleSimpleError(...)
 10.   └─base:::h(simpleError(msg, call))
── Error (test-path-annots.R:10:1): (code run outside of `test_that()`) ────────
Error in `readRDS(.db_index_file(x))`: error reading from connection
Backtrace:
    █
 1. └─hipathia::get_pathways_annotations(...) test-path-annots.R:10:0
 2.   └─hipathia:::load_annofuns(dbannot, metaginfo$species)
 3.     └─hipathia:::hub()
 4.       ├─AnnotationHub::query(AnnotationHub(), "hpAnnot")
 5.       └─AnnotationHub::query(AnnotationHub(), "hpAnnot")
 6.         └─AnnotationHub:::.local(x, pattern, ...)
 7.           └─AnnotationHub:::.db_index_load(x)
 8.             └─base::readRDS(.db_index_file(x))
── Error (test-quantify.R:10:1): (code run outside of `test_that()`) ───────────
Error in `readRDS(.db_index_file(x))`: error reading from connection
Backtrace:
    █
 1. └─hipathia::quantify_terms(results, pathways, "GO") test-quantify.R:10:0
 2.   └─hipathia:::load_annofuns(dbannot, species)
 3.     └─hipathia:::hub()
 4.       ├─AnnotationHub::query(AnnotationHub(), "hpAnnot")
 5.       └─AnnotationHub::query(AnnotationHub(), "hpAnnot")
 6.         └─AnnotationHub:::.local(x, pattern, ...)
 7.           └─AnnotationHub:::.db_index_load(x)
 8.             └─base::readRDS(.db_index_file(x))
── Error (test-translate-matrix.R:9:1): (code run outside of `test_that()`) ────
Error in `readRDS(.db_index_file(x))`: error reading from connection
Backtrace:
    █
 1. └─hipathia::load_pathways("hsa") test-translate-matrix.R:9:0
 2.   └─hipathia:::load_mgi(species)
 3.     └─hipathia:::hub()
 4.       ├─AnnotationHub::query(AnnotationHub(), "hpAnnot")
 5.       └─AnnotationHub::query(AnnotationHub(), "hpAnnot")
 6.         └─AnnotationHub:::.local(x, pattern, ...)
 7.           └─AnnotationHub:::.db_index_load(x)
 8.             └─base::readRDS(.db_index_file(x))

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 80 ]
Error: Test failures
Execution halted

Example timings

hipathia.Rcheck/hipathia-Ex.timings

nameusersystemelapsed
create_report27.304 0.39228.719
do_pca0.0590.0120.071
do_wilcoxon0.1350.0040.140
get_go_names7.6450.2608.560
get_node_names19.225 0.38120.469
get_nodes_data0.0080.0000.008
get_path_names17.954 0.48319.377
get_paths_data0.0110.0000.011
get_pathways_annotations31.686 0.50834.516
get_pathways_list19.070 0.20420.081
get_pathways_summary19.550 0.20820.224
heatmap_plot0.1550.0040.159
hhead0.0010.0000.001
hipathia28.092 0.32028.783
load_pathways18.039 0.14818.505
multiple_pca_plot0.0510.0000.051
node_color25.620 0.74026.803
node_color_per_de18.536 0.42019.310
normalize_data19.003 0.48820.005