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CHECK report for hipathia on tokay1

This page was generated on 2019-04-13 11:29:13 -0400 (Sat, 13 Apr 2019).

Package 726/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hipathia 1.4.1
Marta R. Hidalgo
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/hipathia
Branch: RELEASE_3_8
Last Commit: 6296d69
Last Changed Date: 2019-02-06 08:32:01 -0400 (Wed, 06 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hipathia
Version: 1.4.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings hipathia_1.4.1.tar.gz
StartedAt: 2019-04-13 03:02:54 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:17:20 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 866.0 seconds
RetCode: 0
Status:  OK  
CheckDir: hipathia.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings hipathia_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/hipathia.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.4.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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            21.67   2.70   27.73
visualize_report         15.14   0.64   15.78
quantify_terms           12.80   0.25   13.04
pathway_comparison_plot  11.98   0.21   12.19
normalize_paths          11.61   0.32   11.92
hipathia                 11.61   0.23   11.84
load_pathways            10.80   0.74   11.53
save_results             11.12   0.08   11.21
node_color_per_de        10.58   0.11   10.69
get_pathways_annotations 10.53   0.08   10.61
get_pathways_list        10.10   0.10   10.19
get_path_names            9.76   0.24   10.00
get_pathways_summary      9.26   0.06    9.32
normalize_data            7.47   0.17    7.64
translate_data            6.81   0.09    6.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
create_report            20.18   1.36   21.88
visualize_report         12.51   0.36   12.87
hipathia                 10.69   0.17   10.86
get_pathways_list         9.59   0.06    9.66
get_pathways_summary      9.27   0.13    9.39
get_pathways_annotations  9.27   0.12    9.39
quantify_terms            8.97   0.26    9.23
node_color_per_de         9.14   0.06    9.21
get_path_names            8.82   0.14    8.96
pathway_comparison_plot   8.80   0.10    8.89
normalize_paths           8.50   0.10    8.59
save_results              8.37   0.17    8.55
load_pathways             8.41   0.11    8.51
normalize_data            7.61   0.09    7.70
translate_data            5.90   0.11    6.00
* 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-3.8-bioc/meat/hipathia.Rcheck/00check.log'
for details.



Installation output

hipathia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/hipathia_1.4.1.tar.gz && rm -rf hipathia.buildbin-libdir && mkdir hipathia.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hipathia.buildbin-libdir hipathia_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL hipathia_1.4.1.zip && rm hipathia_1.4.1.tar.gz hipathia_1.4.1.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  17.6M      0 --:--:-- --:--:-- --:--:-- 17.8M

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
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_1.4.1.zip
* DONE (hipathia)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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, 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 
 126.85    4.79  131.93 

hipathia.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, 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 
 132.04    2.57  134.90 

Example timings

hipathia.Rcheck/examples_i386/hipathia-Ex.timings

nameusersystemelapsed
create_report21.67 2.7027.73
do_pca0.010.000.02
do_wilcoxon0.070.010.07
get_path_names 9.76 0.2410.00
get_paths_data0.000.010.02
get_pathways_annotations10.53 0.0810.61
get_pathways_list10.10 0.1010.19
get_pathways_summary9.260.069.32
heatmap_plot0.170.000.18
hhead000
hipathia11.61 0.2311.84
load_pathways10.80 0.7411.53
multiple_pca_plot0.010.010.03
node_color_per_de10.58 0.1110.69
normalize_data7.470.177.64
normalize_paths11.61 0.3211.92
paths_to_go_ancestor1.280.121.40
pathway_comparison_plot11.98 0.2112.19
pca_plot0.000.010.02
quantify_terms12.80 0.2513.04
save_results11.12 0.0811.21
top_pathways0.020.000.01
translate_data6.810.096.91
visualize_report15.14 0.6415.78

hipathia.Rcheck/examples_x64/hipathia-Ex.timings

nameusersystemelapsed
create_report20.18 1.3621.88
do_pca000
do_wilcoxon0.040.020.06
get_path_names8.820.148.96
get_paths_data000
get_pathways_annotations9.270.129.39
get_pathways_list9.590.069.66
get_pathways_summary9.270.139.39
heatmap_plot0.180.000.19
hhead000
hipathia10.69 0.1710.86
load_pathways8.410.118.51
multiple_pca_plot0.010.020.03
node_color_per_de9.140.069.21
normalize_data7.610.097.70
normalize_paths8.500.108.59
paths_to_go_ancestor0.990.011.00
pathway_comparison_plot8.800.108.89
pca_plot0.010.000.02
quantify_terms8.970.269.23
save_results8.370.178.55
top_pathways0.000.020.02
translate_data5.900.116.00
visualize_report12.51 0.3612.87