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This page was generated on 2022-03-23 12:06:39 -0400 (Wed, 23 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4148
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4075
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4135
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GenomicDataCommons on tokay2


To the developers/maintainers of the GenomicDataCommons package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDataCommons.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 749/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.18.0  (landing page)
Sean Davis
Snapshot Date: 2022-03-22 01:55:07 -0400 (Tue, 22 Mar 2022)
git_url: https://git.bioconductor.org/packages/GenomicDataCommons
git_branch: RELEASE_3_14
git_last_commit: 48c12fe
git_last_commit_date: 2021-10-26 12:34:22 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: GenomicDataCommons
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDataCommons.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomicDataCommons_1.18.0.tar.gz
StartedAt: 2022-03-22 19:41:19 -0400 (Tue, 22 Mar 2022)
EndedAt: 2022-03-22 19:44:28 -0400 (Tue, 22 Mar 2022)
EllapsedTime: 188.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDataCommons.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDataCommons.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomicDataCommons_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomicDataCommons.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicDataCommons/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicDataCommons' version '1.18.0'
* 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 'GenomicDataCommons' can be installed ... OK
* checking installed package size ... OK
* 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
Namespaces in Imports field not imported from:
  'S4Vectors' 'SummarizedExperiment'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
transfer: no visible binding for global variable 'file_id'
Undefined global functions or variables:
  file_id
* 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 R/sysdata.rda ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomicDataCommons.Rcheck/00check.log'
for details.



Installation output

GenomicDataCommons.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenomicDataCommons_1.18.0.tar.gz && rm -rf GenomicDataCommons.buildbin-libdir && mkdir GenomicDataCommons.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenomicDataCommons_1.18.0.zip && rm GenomicDataCommons_1.18.0.tar.gz GenomicDataCommons_1.18.0.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     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  537k  100  537k    0     0   793k      0 --:--:-- --:--:-- --:--:--  794k

install for i386

* installing *source* package 'GenomicDataCommons' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicDataCommons'
    finding HTML links ... done
    GenomicDataCommons                      html  
    aggregations                            html  
    available_expand                        html  
    available_fields                        html  
    available_values                        html  
    constants                               html  
    count                                   html  
    default_fields                          html  
    entity_name                             html  
    expand                                  html  
    faceting                                html  
    field_description                       html  
    filtering                               html  
    gdc_cache                               html  
    gdc_client                              html  
    gdc_clinical                            html  
    gdc_token                               html  
    gdcdata                                 html  
    grep_fields                             html  
    id_field                                html  
    ids                                     html  
    make_filter                             html  
    manifest                                html  
    mapping                                 html  
    query                                   html  
    readDNAcopy                             html  
    readHTSeqFile                           html  
    response                                html  
    results                                 html  
    results_all                             html  
    select                                  html  
    slicing                                 html  
    status                                  html  
    transfer                                html  
    write_manifest                          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 'GenomicDataCommons' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicDataCommons' as GenomicDataCommons_1.18.0.zip
* DONE (GenomicDataCommons)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GenomicDataCommons' successfully unpacked and MD5 sums checked

Tests output

GenomicDataCommons.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(GenomicDataCommons)
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not


Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':

    filter

> 
> test_check("GenomicDataCommons")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
   8.06    0.51   19.45 

GenomicDataCommons.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(GenomicDataCommons)
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not


Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':

    filter

> 
> test_check("GenomicDataCommons")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
   8.10    0.45   19.53 

Example timings

GenomicDataCommons.Rcheck/examples_i386/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.130.020.71
available_expand0.040.000.11
available_fields0.050.000.22
available_values0.060.000.61
constants000
count0.170.000.44
default_fields0.060.000.23
entity_name0.110.000.24
expand0.140.000.50
faceting0.100.020.30
field_description0.490.030.81
filtering1.110.032.69
gdc_cache000
gdc_client000
gdc_clinical0.710.021.31
gdc_token000
gdcdata0.750.021.37
grep_fields0.060.000.12
id_field0.100.000.16
ids0.540.001.26
manifest0.320.000.52
mapping0.030.000.09
query0.200.000.33
readDNAcopy0.200.030.22
readHTSeqFile0.110.020.11
response0.130.000.30
results0.140.000.29
results_all0.090.000.41
select0.140.000.62
slicing000
status0.020.000.08
transfer000
write_manifest0.280.010.50

GenomicDataCommons.Rcheck/examples_x64/GenomicDataCommons-Ex.timings

nameusersystemelapsed
aggregations0.120.000.74
available_expand0.050.000.11
available_fields0.050.000.22
available_values0.060.000.59
constants0.020.000.02
count0.150.010.44
default_fields0.050.000.22
entity_name0.110.020.23
expand0.170.000.52
faceting0.110.000.31
field_description0.410.010.79
filtering1.080.022.61
gdc_cache0.010.000.02
gdc_client000
gdc_clinical0.660.001.27
gdc_token000
gdcdata0.810.011.32
grep_fields0.060.000.13
id_field0.100.000.15
ids0.500.001.24
manifest0.290.000.51
mapping0.020.000.08
query0.200.000.35
readDNAcopy0.240.000.23
readHTSeqFile0.140.000.14
response0.110.000.27
results0.110.000.28
results_all0.060.000.43
select0.180.000.65
slicing000
status0.010.000.08
transfer000
write_manifest0.280.020.50