Back to Multiple platform build/check report for BioC 3.8
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GeneAccord on tokay1

This page was generated on 2019-04-13 11:29:34 -0400 (Sat, 13 Apr 2019).

Package 589/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAccord 1.0.0
Ariane L. Moore
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GeneAccord
Branch: RELEASE_3_8
Last Commit: 21f4613
Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 2018)
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: GeneAccord
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAccord.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneAccord_1.0.0.tar.gz
StartedAt: 2019-04-13 02:26:31 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:30:15 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 223.7 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneAccord.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAccord.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GeneAccord_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GeneAccord.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 'GeneAccord/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAccord' version '1.0.0'
* 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 'GeneAccord' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.1Mb
* 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
** running examples for arch 'x64' ... OK
* 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-3.8-bioc/meat/GeneAccord.Rcheck/00check.log'
for details.



Installation output

GeneAccord.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GeneAccord_1.0.0.tar.gz && rm -rf GeneAccord.buildbin-libdir && mkdir GeneAccord.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAccord.buildbin-libdir GeneAccord_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GeneAccord_1.0.0.zip && rm GeneAccord_1.0.0.tar.gz GeneAccord_1.0.0.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
  0 2737k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2737k  100 2737k    0     0  38.5M      0 --:--:-- --:--:-- --:--:-- 39.9M

install for i386

* installing *source* package 'GeneAccord' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneAccord'
    finding HTML links ... done
    GeneAccord                              html  
    all_genes_tbl                           html  
    avg_rates_m                             html  
    build_null_test_statistic               html  
    clone_tbl_all_pats_all_trees            html  
    compute_rates_clon_excl                 html  
    compute_test_stat_avg_rate              html  
    convert_ensembl_to_reactome_pw_tbl      html  
    create_ensembl_gene_tbl_hg              html  
    create_tbl_ent_clones                   html  
    create_tbl_tree_collection              html  
    ecdf_list                               html  
    ecdf_lr_test_clon_excl_avg_rate         html  
    ensembl_to_hgnc                         html  
    ensembl_to_reactome                     html  
    ensg_reactome_path_map                  html  
    ensmusg_reactome_path_map               html  
    extract_num_clones_tbl                  html  
    generate_ecdf_test_stat                 html  
    generate_test_stat_hist                 html  
    get_hist_clon_excl                      html  
    get_hist_clon_excl_this_pat_this_pair   html  
    get_rate_diff_branch_ent_pair           html  
    heatmap_clones_gene_pat                 html  
    hgnc_to_ensembl                         html  
    is_diff_branch_ent_pair                 html  
    list_of_clon_excl_all_pats              html  
    list_of_num_trees_all_pats              html  
    map_pairs_to_hgnc_symbols               html  
    merge_clones_identical_ents             html  
    pairs_in_patients_hist                  html  
    plot_ecdf_test_stat                     html  
    plot_rates_clon_excl                    html  
    take_pairs_and_get_patients             html  
    vis_pval_distr_num_pat                  html  
    write_res_pairs_to_disk                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GeneAccord' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneAccord' as GeneAccord_1.0.0.zip
* DONE (GeneAccord)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GeneAccord' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GeneAccord.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("assertthat")
> 
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
> 
> test_check("GeneAccord")
== testthat results  ===========================================================
OK: 27 SKIPPED: 6 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
  16.18    0.35   16.54 

GeneAccord.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("assertthat")
> 
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
> 
> test_check("GeneAccord")
== testthat results  ===========================================================
OK: 27 SKIPPED: 6 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
  19.23    0.35   19.59 

Example timings

GeneAccord.Rcheck/examples_i386/GeneAccord-Ex.timings

nameusersystemelapsed
GeneAccord1.360.001.36
build_null_test_statistic2.410.022.42
compute_rates_clon_excl0.090.000.09
compute_test_stat_avg_rate0.060.000.06
convert_ensembl_to_reactome_pw_tbl0.240.020.25
create_ensembl_gene_tbl_hg000
create_tbl_ent_clones0.120.000.13
create_tbl_tree_collection0.290.000.28
ecdf_lr_test_clon_excl_avg_rate0.520.000.51
ensembl_to_hgnc000
ensembl_to_reactome0.030.000.03
extract_num_clones_tbl000
generate_ecdf_test_stat0.50.00.5
generate_test_stat_hist0.790.000.80
get_hist_clon_excl0.350.000.34
get_hist_clon_excl_this_pat_this_pair0.010.000.02
get_rate_diff_branch_ent_pair0.220.000.22
heatmap_clones_gene_pat0.710.010.72
hgnc_to_ensembl000
is_diff_branch_ent_pair000
map_pairs_to_hgnc_symbols000
merge_clones_identical_ents0.060.000.06
pairs_in_patients_hist0.030.000.03
plot_ecdf_test_stat0.360.000.36
plot_rates_clon_excl0.190.000.19
take_pairs_and_get_patients0.090.000.10
vis_pval_distr_num_pat0.020.010.03
write_res_pairs_to_disk000

GeneAccord.Rcheck/examples_x64/GeneAccord-Ex.timings

nameusersystemelapsed
GeneAccord2.120.042.18
build_null_test_statistic3.210.003.20
compute_rates_clon_excl0.120.000.12
compute_test_stat_avg_rate0.060.000.07
convert_ensembl_to_reactome_pw_tbl0.250.020.26
create_ensembl_gene_tbl_hg000
create_tbl_ent_clones0.140.000.14
create_tbl_tree_collection0.400.000.39
ecdf_lr_test_clon_excl_avg_rate0.750.000.75
ensembl_to_hgnc000
ensembl_to_reactome0.010.000.02
extract_num_clones_tbl0.030.000.03
generate_ecdf_test_stat0.850.000.84
generate_test_stat_hist1.140.001.14
get_hist_clon_excl0.390.000.39
get_hist_clon_excl_this_pat_this_pair0.010.000.02
get_rate_diff_branch_ent_pair0.250.000.25
heatmap_clones_gene_pat0.690.010.70
hgnc_to_ensembl000
is_diff_branch_ent_pair0.020.000.02
map_pairs_to_hgnc_symbols000
merge_clones_identical_ents0.040.000.04
pairs_in_patients_hist0.030.020.05
plot_ecdf_test_stat0.440.000.44
plot_rates_clon_excl0.220.000.22
take_pairs_and_get_patients0.130.000.12
vis_pval_distr_num_pat0.010.000.02
write_res_pairs_to_disk0.020.000.01