Multiple platform build/check report for BioC 3.6 - CHECK report for GenomicDataCommons on tokay1

Package: GenomicDataCommons

Version: 1.2.0

Command: rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.2.0.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.2.0.tar.gz

StartedAt: 2018-04-12 00:17:23 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:19:54 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 151.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: GenomicDataCommons.Rcheck

Warnings: 1

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### Running command:
###
###   rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.2.0.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicDataCommons.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.2.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqGxIyD/R.INSTALL2bbc448b386c/GenomicDataCommons/man/readDNAcopy.Rd:12: missing file link 'read_tsv'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqGxIyD/R.INSTALL2bbc448b386c/GenomicDataCommons/man/readDNAcopy.Rd:15: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqGxIyD/R.INSTALL2bbc448b386c/GenomicDataCommons/man/readHTSeqFile.Rd:16: missing file link 'read_tsv'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicDataCommons.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
default_fields.character: no visible binding for global variable
  'defaults'
Undefined global functions or variables:
  defaults
* 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 ... NOTE
S3 methods shown with full name in documentation object 'as.data.frame.GDCResults':
  'as.data.frame.GDCResults'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicDataCommons.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'GenomicDataCommons' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicDataCommons'
    finding HTML links ... done
    GenomicDataCommons                      html  
    aggregations                            html  
    as.data.frame.GDCResults                html  
    available_expand                        html  
    available_fields                        html  
    available_values                        html  
    constants                               html  
    count                                   html  
    default_fields                          html  
    entity_name                             html  
    expand                                  html  
    faceting                                html  
    filtering                               html  
    gdc_client                              html  
    gdc_token                               html  
    gdcdata                                 html  
    grep_fields                             html  
    id_field                                html  
    ids                                     html  
    make_filter                             html  
    manifest                                html  
    mapping                                 html  
    query                                   html  
    rbindlist2                              html  
    readDNAcopy                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqGxIyD/R.INSTALL2bbc448b386c/GenomicDataCommons/man/readDNAcopy.Rd:12: missing file link 'read_tsv'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqGxIyD/R.INSTALL2bbc448b386c/GenomicDataCommons/man/readDNAcopy.Rd:15: missing file link 'GRanges'
    readHTSeqFile                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqGxIyD/R.INSTALL2bbc448b386c/GenomicDataCommons/man/readHTSeqFile.Rd:16: missing file link 'read_tsv'
    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
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicDataCommons' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicDataCommons' as GenomicDataCommons_1.2.0.zip
* DONE (GenomicDataCommons)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(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")
== testthat results  ===========================================================
OK: 40 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.54    0.21    8.57


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(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")
== testthat results  ===========================================================
OK: 40 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.14    0.14    9.20

name	user	system	elapsed
aggregations	0.49	0.00	0.78
as.data.frame.GDCResults	0.39	0.01	0.62
available_expand	0.03	0.00	0.08
available_fields	0.04	0.02	0.14
available_values	0.04	0.00	0.23
constants	0	0	0
count	0.09	0.00	0.25
default_fields	0.06	0.00	0.16
entity_name	0.10	0.00	0.17
expand	0.09	0.00	0.28
faceting	0.06	0.00	0.19
filtering	0.18	0.00	0.42
gdc_client	0	0	0
gdc_token	0	0	0
gdcdata	0.00	0.01	1.44
grep_fields	0.02	0.00	0.06
id_field	0.05	0.00	0.09
ids	0.20	0.00	0.85
manifest	0.62	0.03	0.78
mapping	0.02	0.00	0.04
query	0.08	0.00	0.19
rbindlist2	0	0	0
readDNAcopy	0.2	0.0	0.2
readHTSeqFile	0.2	0.0	0.2
response	0.05	0.00	0.25
results	0.05	0.00	0.24
results_all	0.04	0.00	0.23
select	0.07	0.00	0.28
slicing	0	0	0
status	0.00	0.00	0.04
transfer	0	0	0
write_manifest	0.08	0.00	0.22

name	user	system	elapsed
aggregations	0.36	0.00	0.69
as.data.frame.GDCResults	0.27	0.00	0.59
available_expand	0.02	0.00	0.09
available_fields	0.05	0.00	0.14
available_values	0.03	0.00	0.24
constants	0	0	0
count	0.06	0.00	0.21
default_fields	0.01	0.00	0.15
entity_name	0.07	0.00	0.14
expand	0.09	0.00	0.28
faceting	0.04	0.00	0.19
filtering	0.16	0.00	0.44
gdc_client	0	0	0
gdc_token	0	0	0
gdcdata	0.01	0.00	0.94
grep_fields	0.02	0.00	0.06
id_field	0.03	0.00	0.09
ids	0.28	0.00	1.00
manifest	0.90	0.03	1.07
mapping	0.03	0.00	0.06
query	0.09	0.00	0.20
rbindlist2	0	0	0
readDNAcopy	0.28	0.00	0.28
readHTSeqFile	0.28	0.00	0.28
response	0.05	0.00	0.24
results	0.05	0.00	0.25
results_all	0.07	0.00	0.25
select	0.11	0.00	0.36
slicing	0	0	0
status	0.00	0.00	0.04
transfer	0	0	0
write_manifest	0.08	0.00	0.24

CHECK report for GenomicDataCommons on tokay1

Summary

Command output

Installation output

Tests output

Example timings