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CHECK report for hipathia on tokay2

This page was generated on 2018-10-17 08:45:44 -0400 (Wed, 17 Oct 2018).

Package 689/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hipathia 1.0.0
Marta R. Hidalgo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/hipathia
Branch: RELEASE_3_7
Last Commit: f841646
Last Changed Date: 2018-04-30 10:35:50 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hipathia
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings hipathia_1.0.0.tar.gz
StartedAt: 2018-10-17 02:41:32 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:56:46 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 914.7 seconds
RetCode: 0
Status:  OK  
CheckDir: hipathia.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings hipathia_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/hipathia.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.0.0'
* 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 whether package 'hipathia' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
create_report            19.85   2.68   26.46
quantify_terms           14.81   0.24   15.06
save_results             13.89   0.17   14.88
normalize_paths          13.28   0.64   13.93
hipathia                 13.14   0.25   13.39
visualize_report         12.41   0.92   13.35
get_path_names           12.67   0.22   12.89
load_pathways            12.36   0.09   12.45
pathway_comparison_plot  11.89   0.09   11.98
get_pathways_summary     11.86   0.09   11.97
node_color_per_de        11.61   0.15   11.77
get_pathways_list        11.48   0.13   11.61
get_pathways_annotations 11.19   0.15   11.35
translate_data            7.95   0.30    8.29
normalize_data            7.00   0.11    7.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
create_report            18.92   0.55   20.05
node_color_per_de        14.20   0.17   14.39
hipathia                 13.77   0.12   13.89
get_pathways_annotations 13.47   0.18   13.65
get_pathways_list        12.16   0.09   12.25
pathway_comparison_plot  11.97   0.12   12.10
get_pathways_summary     11.38   0.17   11.54
quantify_terms           11.03   0.23   11.27
normalize_paths          10.98   0.13   11.11
load_pathways            11.00   0.11   11.11
normalize_data            9.97   0.14   10.11
visualize_report          9.92   0.17   10.10
save_results              9.61   0.11    9.72
get_path_names            9.42   0.12    9.54
translate_data            6.81   0.08    6.89
* 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-3.7-bioc/meat/hipathia.Rcheck/00check.log'
for details.

Installation output

hipathia.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/hipathia_1.0.0.tar.gz && rm -rf hipathia.buildbin-libdir && mkdir hipathia.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hipathia.buildbin-libdir hipathia_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL hipathia_1.0.0.zip && rm hipathia_1.0.0.tar.gz hipathia_1.0.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 82 5074k   82 4192k    0     0  44.7M      0 --:--:-- --:--:-- --:--:-- 47.6M
100 5074k  100 5074k    0     0  49.9M      0 --:--:-- --:--:-- --:--:-- 52.7M

install for i386

* installing *source* package 'hipathia' ...
** 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_highest_sig_ancestor                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  
    multiple_pca_plot                       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  
    translate_data                          html  
    translate_matrix                        html  
    visualize_report                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'hipathia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hipathia' as hipathia_1.0.0.zip
* DONE (hipathia)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'hipathia' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

hipathia.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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

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: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

> 
> 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: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 137.90    4.45  142.68

hipathia.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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

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: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

> 
> 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: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 154.17    2.50  157.01

Example timings

hipathia.Rcheck/examples_i386/hipathia-Ex.timings

nameusersystemelapsed
create_report19.85 2.6826.46
do_pca0.000.020.02
do_wilcoxon0.070.000.06
get_path_names12.67 0.2212.89
get_paths_data0.010.000.01
get_pathways_annotations11.19 0.1511.35
get_pathways_list11.48 0.1311.61
get_pathways_summary11.86 0.0911.97
heatmap_plot0.160.020.17
hhead000
hipathia13.14 0.2513.39
load_pathways12.36 0.0912.45
multiple_pca_plot0.020.020.03
node_color_per_de11.61 0.1511.77
normalize_data7.000.117.11
normalize_paths13.28 0.6413.93
paths_to_go_ancestor0.220.020.23
pathway_comparison_plot11.89 0.0911.98
pca_plot0.020.000.02
quantify_terms14.81 0.2415.06
save_results13.89 0.1714.88
translate_data7.950.308.29
visualize_report12.41 0.9213.35

hipathia.Rcheck/examples_x64/hipathia-Ex.timings

nameusersystemelapsed
create_report18.92 0.5520.05
do_pca0.000.010.02
do_wilcoxon0.130.020.14
get_path_names9.420.129.54
get_paths_data000
get_pathways_annotations13.47 0.1813.65
get_pathways_list12.16 0.0912.25
get_pathways_summary11.38 0.1711.54
heatmap_plot0.200.020.22
hhead000
hipathia13.77 0.1213.89
load_pathways11.00 0.1111.11
multiple_pca_plot0.000.030.03
node_color_per_de14.20 0.1714.39
normalize_data 9.97 0.1410.11
normalize_paths10.98 0.1311.11
paths_to_go_ancestor0.380.000.37
pathway_comparison_plot11.97 0.1212.10
pca_plot0.010.000.01
quantify_terms11.03 0.2311.27
save_results9.610.119.72
translate_data6.810.086.89
visualize_report 9.92 0.1710.10