Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-01 17:17:51 -0500 (Wed, 01 Dec 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 875/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hipathia 2.10.0  (landing page)
Marta R. Hidalgo
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
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 20.04.3 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: 2.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hipathia_2.10.0.tar.gz
StartedAt: 2021-12-01 00:08:13 -0500 (Wed, 01 Dec 2021)
EndedAt: 2021-12-01 00:37:28 -0500 (Wed, 01 Dec 2021)
EllapsedTime: 1754.3 seconds
RetCode: 0
Status:   OK  
CheckDir: hipathia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings hipathia_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/hipathia.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.10.0'
* 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 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           43.69   2.38   49.45
get_pathways_annotations 30.18   1.19   32.87
create_report            24.86   2.48   30.73
get_pathways_summary     22.76   0.94   24.45
hipathia                 22.47   0.81   23.95
get_path_names           22.63   0.42   23.74
load_pathways            22.56   0.36   24.23
get_pathways_list        21.35   0.89   22.80
pathway_comparison_plot  21.63   0.47   22.78
normalize_paths          20.73   0.47   21.86
node_color_per_de        19.98   0.61   21.25
visualize_report         19.22   0.55   20.41
node_color               19.27   0.34   20.25
save_results             18.95   0.61   20.27
get_node_names           18.51   0.45   19.36
normalize_data           15.72   0.60   17.18
translate_data           12.63   0.67   14.03
get_go_names              7.82   0.83    9.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
quantify_terms           44.42   1.85   48.71
get_pathways_annotations 26.19   0.83   28.46
create_report            23.19   0.81   25.14
save_results             23.58   0.40   24.48
load_pathways            22.42   0.42   23.54
visualize_report         21.72   0.40   23.01
normalize_paths          21.39   0.46   22.53
pathway_comparison_plot  21.22   0.52   22.40
get_pathways_list        20.56   0.57   21.67
hipathia                 20.60   0.37   21.62
get_path_names           19.97   0.56   21.19
get_pathways_summary     20.08   0.38   21.19
node_color_per_de        19.54   0.44   20.62
get_node_names           19.31   0.58   20.39
node_color               19.29   0.46   20.39
translate_data           16.06   0.42   17.14
normalize_data           14.91   0.35   15.94
get_go_names              8.00   0.57    9.25
* 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-3.14-bioc/meat/hipathia.Rcheck/00check.log'
for details.



Installation output

hipathia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/hipathia_2.10.0.tar.gz && rm -rf hipathia.buildbin-libdir && mkdir hipathia.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hipathia.buildbin-libdir hipathia_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL hipathia_2.10.0.zip && rm hipathia_2.10.0.tar.gz hipathia_2.10.0.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
  3 5163k    3  167k    0     0   740k      0  0:00:06 --:--:--  0:00:06  740k
 55 5163k   55 2848k    0     0  2305k      0  0:00:02  0:00:01  0:00:01 2306k
100 5163k  100 5163k    0     0  2763k      0  0:00:01  0:00:01 --:--:-- 2764k

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_2.10.0.zip
* DONE (hipathia)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'hipathia' successfully unpacked and MD5 sums checked

Tests output

hipathia.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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

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

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 
 300.53   13.59  325.31 

hipathia.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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

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

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 
 286.92    9.07  307.82 

Example timings

hipathia.Rcheck/examples_i386/hipathia-Ex.timings

nameusersystemelapsed
create_report24.86 2.4830.73
do_pca0.100.020.11
do_wilcoxon0.140.000.14
get_go_names7.820.839.70
get_node_names18.51 0.4519.36
get_nodes_data000
get_path_names22.63 0.4223.74
get_paths_data000
get_pathways_annotations30.18 1.1932.87
get_pathways_list21.35 0.8922.80
get_pathways_summary22.76 0.9424.45
heatmap_plot0.220.010.24
hhead000
hipathia22.47 0.8123.95
load_pathways22.56 0.3624.23
multiple_pca_plot0.050.020.07
node_color19.27 0.3420.25
node_color_per_de19.98 0.6121.25
normalize_data15.72 0.6017.18
normalize_paths20.73 0.4721.86
paths_to_go_ancestor0.190.030.22
pathway_comparison_plot21.63 0.4722.78
pca_plot0.060.010.08
quantify_terms43.69 2.3849.45
save_results18.95 0.6120.27
top_pathways0.010.010.03
translate_data12.63 0.6714.03
visualize_report19.22 0.5520.41

hipathia.Rcheck/examples_x64/hipathia-Ex.timings

nameusersystemelapsed
create_report23.19 0.8125.14
do_pca0.050.000.05
do_wilcoxon0.130.020.15
get_go_names8.000.579.25
get_node_names19.31 0.5820.39
get_nodes_data0.020.000.01
get_path_names19.97 0.5621.19
get_paths_data0.010.000.01
get_pathways_annotations26.19 0.8328.46
get_pathways_list20.56 0.5721.67
get_pathways_summary20.08 0.3821.19
heatmap_plot0.170.030.21
hhead000
hipathia20.60 0.3721.62
load_pathways22.42 0.4223.54
multiple_pca_plot0.040.020.07
node_color19.29 0.4620.39
node_color_per_de19.54 0.4420.62
normalize_data14.91 0.3515.94
normalize_paths21.39 0.4622.53
paths_to_go_ancestor0.250.020.27
pathway_comparison_plot21.22 0.5222.40
pca_plot0.950.000.95
quantify_terms44.42 1.8548.71
save_results23.58 0.4024.48
top_pathways0.020.000.02
translate_data16.06 0.4217.14
visualize_report21.72 0.4023.01