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CHECK report for hipathia on tokay2

This page was generated on 2019-04-09 12:38:29 -0400 (Tue, 09 Apr 2019).

Package 749/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hipathia 1.5.0
Marta R. Hidalgo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/hipathia
Branch: master
Last Commit: 4f9d7ff
Last Changed Date: 2019-01-30 12:18:19 -0400 (Wed, 30 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: hipathia
Version: 1.5.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hipathia_1.5.0.tar.gz
StartedAt: 2019-04-09 03:29:21 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:48:33 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 1151.8 seconds
RetCode: 0
Status:  OK  
CheckDir: hipathia.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hipathia_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/hipathia.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.5.0'
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'load_entrez_hgnc'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmap_plot: no visible binding for global variable 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
* 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            23.98   3.14  103.31
visualize_report         21.00   0.56   22.19
hipathia                 16.03   0.20   16.55
quantify_terms           13.78   0.49   14.89
save_results             13.63   0.62   14.37
node_color_per_de        12.82   0.30   13.34
load_pathways            12.90   0.10   13.17
normalize_paths          12.23   0.23   12.69
pathway_comparison_plot  11.85   0.48   12.48
get_path_names           11.61   0.12   11.91
get_pathways_list        11.45   0.08   11.69
get_pathways_summary     10.83   0.13   11.23
get_pathways_annotations 10.66   0.28   11.41
translate_data            8.65   0.16    9.01
normalize_data            8.57   0.19    8.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
create_report            24.48   1.73   27.21
visualize_report         18.42   0.59   19.86
quantify_terms           15.53   0.34   17.50
hipathia                 14.15   0.10   14.45
get_pathways_list        13.27   0.14   13.54
normalize_paths          12.15   0.09   12.42
get_pathways_annotations 11.97   0.22   12.61
load_pathways            12.00   0.09   12.31
pathway_comparison_plot  11.35   0.25   11.81
save_results             11.20   0.17   11.50
node_color_per_de        11.04   0.14   11.39
get_pathways_summary     10.47   0.12   10.75
get_path_names           10.26   0.21   10.63
translate_data           10.30   0.16   10.62
normalize_data            8.80   0.13    9.14
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/hipathia.Rcheck/00check.log'
for details.



Installation output

hipathia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/hipathia_1.5.0.tar.gz && rm -rf hipathia.buildbin-libdir && mkdir hipathia.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hipathia.buildbin-libdir hipathia_1.5.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL hipathia_1.5.0.zip && rm hipathia_1.5.0.tar.gz hipathia_1.5.0.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
100 5076k  100 5076k    0     0  11.6M      0 --:--:-- --:--:-- --:--:-- 11.8M

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  
    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_1.5.0.zip
* DONE (hipathia)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'hipathia' successfully unpacked and MD5 sums checked

Tests output

hipathia.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, 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: 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

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, 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: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 158.42    7.65  213.17 

hipathia.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, 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: 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

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, 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: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 148.84    4.26  156.35 

Example timings

hipathia.Rcheck/examples_i386/hipathia-Ex.timings

nameusersystemelapsed
create_report 23.98 3.14103.31
do_pca0.020.020.04
do_wilcoxon0.130.020.14
get_path_names11.61 0.1211.91
get_paths_data0.010.000.01
get_pathways_annotations10.66 0.2811.41
get_pathways_list11.45 0.0811.69
get_pathways_summary10.83 0.1311.23
heatmap_plot0.270.010.53
hhead000
hipathia16.03 0.2016.55
load_pathways12.90 0.1013.17
multiple_pca_plot0.040.010.05
node_color_per_de12.82 0.3013.34
normalize_data8.570.198.97
normalize_paths12.23 0.2312.69
paths_to_go_ancestor0.200.020.22
pathway_comparison_plot11.85 0.4812.48
pca_plot000
quantify_terms13.78 0.4914.89
save_results13.63 0.6214.37
top_pathways0.020.000.02
translate_data8.650.169.01
visualize_report21.00 0.5622.19

hipathia.Rcheck/examples_x64/hipathia-Ex.timings

nameusersystemelapsed
create_report24.48 1.7327.21
do_pca0.020.000.01
do_wilcoxon0.080.000.08
get_path_names10.26 0.2110.63
get_paths_data0.010.000.02
get_pathways_annotations11.97 0.2212.61
get_pathways_list13.27 0.1413.54
get_pathways_summary10.47 0.1210.75
heatmap_plot0.260.030.41
hhead000
hipathia14.15 0.1014.45
load_pathways12.00 0.0912.31
multiple_pca_plot0.040.000.03
node_color_per_de11.04 0.1411.39
normalize_data8.800.139.14
normalize_paths12.15 0.0912.42
paths_to_go_ancestor0.200.030.24
pathway_comparison_plot11.35 0.2511.81
pca_plot0.000.020.01
quantify_terms15.53 0.3417.50
save_results11.20 0.1711.50
top_pathways0.020.000.02
translate_data10.30 0.1610.62
visualize_report18.42 0.5919.86