Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:08 -0400 (Fri, 15 Oct 2021).

CHECK results for hipathia on tokay2

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 865/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hipathia 2.8.0  (landing page)
Marta R. Hidalgo
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/hipathia
git_branch: RELEASE_3_13
git_last_commit: c46391b
git_last_commit_date: 2021-05-19 12:35:11 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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: 2.8.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hipathia_2.8.0.tar.gz
StartedAt: 2021-10-15 00:26:35 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:56:12 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 1776.7 seconds
RetCode: 0
Status:   OK  
CheckDir: hipathia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hipathia_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/hipathia.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hipathia/DESCRIPTION' ... OK
* this is package 'hipathia' version '2.8.0'
* 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 whether package 'hipathia' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.9Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
quantify_terms           42.81   2.07   47.97
get_pathways_annotations 32.43   1.01   35.00
create_report            27.44   2.63   34.00
get_node_names           24.01   1.40   25.99
hipathia                 23.06   0.86   24.59
load_pathways            23.37   0.34   25.83
get_pathways_summary     22.82   0.53   24.10
get_path_names           21.94   0.75   23.38
get_pathways_list        21.79   0.44   22.75
node_color               20.14   0.55   21.34
visualize_report         19.42   0.48   20.56
node_color_per_de        19.19   0.48   20.31
save_results             19.08   0.41   26.42
normalize_paths          18.87   0.48   20.01
pathway_comparison_plot  18.91   0.36   19.93
normalize_data           15.30   0.46   18.71
translate_data           12.81   1.35   14.89
get_go_names              8.47   0.60    9.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
quantify_terms           43.73   1.77   48.00
get_pathways_annotations 27.76   0.87   29.94
create_report            23.83   0.81   25.81
hipathia                 21.73   0.54   22.97
load_pathways            20.53   0.53   21.78
get_pathways_list        20.33   0.56   21.42
save_results             20.28   0.56   26.54
get_path_names           20.18   0.54   21.39
normalize_paths          20.18   0.50   21.37
pathway_comparison_plot  20.14   0.37   21.12
get_pathways_summary     19.89   0.52   21.08
get_node_names           19.72   0.52   20.73
node_color               19.14   0.57   20.37
visualize_report         18.39   0.40   19.69
node_color_per_de        18.11   0.40   19.19
normalize_data           14.06   0.52   15.38
translate_data           12.86   0.44   13.97
get_go_names              7.99   0.65    9.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/hipathia.Rcheck/00check.log'
for details.

Installation output

hipathia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/hipathia_2.8.0.tar.gz && rm -rf hipathia.buildbin-libdir && mkdir hipathia.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hipathia.buildbin-libdir hipathia_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL hipathia_2.8.0.zip && rm hipathia_2.8.0.tar.gz hipathia_2.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 60 5163k   60 3144k    0     0  3193k      0  0:00:01 --:--:--  0:00:01 3192k
100 5163k  100 5163k    0     0  3656k      0  0:00:01  0:00:01 --:--:-- 3659k

install for i386

* 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
  converting help for package 'hipathia'
    finding HTML links ... done
    annotate_paths                          html  
    brca                                    html  
    brca_data                               html  
    brca_design                             html  
    comp                                    html  
    create_report                           html  
    do_pca                                  html  
    do_wilcoxon                             html  
    exp_data                                html  
    get_go_names                            html  
    get_highest_sig_ancestor                html  
    get_node_names                          html  
    get_nodes_data                          html  
    get_path_names                          html  
    get_paths_data                          html  
    get_pathway_functions                   html  
    get_pathways_annotations                html  
    get_pathways_list                       html  
    get_pathways_summary                    html  
    go_vals                                 html  
    heatmap_plot                            html  
    hhead                                   html  
    hipathia                                html  
    igraphs_upgrade                         html  
    is_accepted_species                     html  
    load_annofuns                           html  
    load_annots                             html  
    load_entrez_hgnc                        html  
    load_gobp_frame                         html  
    load_gobp_net                           html  
    load_mgi                                html  
    load_pathways                           html  
    load_pseudo_mgi                         html  
    load_xref                               html  
    mgi_from_sif                            html  
    multiple_pca_plot                       html  
    node_color                              html  
    node_color_per_de                       html  
    normalize_data                          html  
    normalize_paths                         html  
    path_vals                               html  
    paths_to_go_ancestor                    html  
    pathway_comparison_plot                 html  
    pca_plot                                html  
    quantify_terms                          html  
    results                                 html  
    save_results                            html  
    top_pathways                            html  
    translate_data                          html  
    translate_matrix                        html  
    visualize_report                        html  
** 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

install for x64

* installing *source* package 'hipathia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hipathia' as hipathia_2.8.0.zip
* DONE (hipathia)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'hipathia' successfully unpacked and MD5 sums checked

Tests output

hipathia.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.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

Attaching package: 'IRanges'

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

    windows

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")
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) 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 119 ]
> 
> proc.time()
   user  system elapsed 
 294.03   12.82  318.73

hipathia.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.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

Attaching package: 'IRanges'

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

    windows

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")
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) 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 119 ]
> 
> proc.time()
   user  system elapsed 
 264.84    8.53  290.65

Example timings

hipathia.Rcheck/examples_i386/hipathia-Ex.timings

nameusersystemelapsed
create_report27.44 2.6334.00
do_pca0.090.010.11
do_wilcoxon0.110.000.11
get_go_names8.470.609.97
get_node_names24.01 1.4025.99
get_nodes_data0.000.020.01
get_path_names21.94 0.7523.38
get_paths_data0.020.000.01
get_pathways_annotations32.43 1.0135.00
get_pathways_list21.79 0.4422.75
get_pathways_summary22.82 0.5324.10
heatmap_plot0.210.020.22
hhead000
hipathia23.06 0.8624.59
load_pathways23.37 0.3425.83
multiple_pca_plot0.080.000.08
node_color20.14 0.5521.34
node_color_per_de19.19 0.4820.31
normalize_data15.30 0.4618.71
normalize_paths18.87 0.4820.01
paths_to_go_ancestor0.190.020.20
pathway_comparison_plot18.91 0.3619.93
pca_plot0.030.000.03
quantify_terms42.81 2.0747.97
save_results19.08 0.4126.42
top_pathways0.000.030.03
translate_data12.81 1.3514.89
visualize_report19.42 0.4820.56

hipathia.Rcheck/examples_x64/hipathia-Ex.timings

nameusersystemelapsed
create_report23.83 0.8125.81
do_pca0.100.020.11
do_wilcoxon0.150.000.16
get_go_names7.990.659.36
get_node_names19.72 0.5220.73
get_nodes_data0.000.010.02
get_path_names20.18 0.5421.39
get_paths_data0.020.000.01
get_pathways_annotations27.76 0.8729.94
get_pathways_list20.33 0.5621.42
get_pathways_summary19.89 0.5221.08
heatmap_plot0.350.050.39
hhead000
hipathia21.73 0.5422.97
load_pathways20.53 0.5321.78
multiple_pca_plot0.060.000.06
node_color19.14 0.5720.37
node_color_per_de18.11 0.4019.19
normalize_data14.06 0.5215.38
normalize_paths20.18 0.5021.37
paths_to_go_ancestor0.260.000.27
pathway_comparison_plot20.14 0.3721.12
pca_plot0.050.000.05
quantify_terms43.73 1.7748.00
save_results20.28 0.5626.54
top_pathways0.020.000.02
translate_data12.86 0.4413.97
visualize_report18.39 0.4019.69