Multiple platform build/check report for BioC 3.9 - CHECK report for GenomicDataCommons on tokay2

Package: GenomicDataCommons

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDataCommons.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicDataCommons_1.8.0.tar.gz

StartedAt: 2019-10-16 03:58:35 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:02:47 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 252.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: GenomicDataCommons.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicDataCommons.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicDataCommons_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicDataCommons.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.8.0'
* 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-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/gdc_rnaseq.Rd:28: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/readDNAcopy.Rd:12: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/readDNAcopy.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/readHTSeqFile.Rd:16: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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
* 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 ... NOTE
default_fields.character: no visible binding for global variable
  'defaults'
gdc_rnaseq: no visible binding for global variable 'case_id'
gdc_rnaseq: no visible binding for global variable 'file_id'
Undefined global functions or variables:
  case_id defaults 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 ... WARNING
Undocumented arguments in documentation object '.htseq_importer'
  'fnames'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 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 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicDataCommons.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GenomicDataCommons_1.8.0.tar.gz && rm -rf GenomicDataCommons.buildbin-libdir && mkdir GenomicDataCommons.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GenomicDataCommons_1.8.0.zip && rm GenomicDataCommons_1.8.0.tar.gz GenomicDataCommons_1.8.0.zip
###
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  % 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  536k  100  536k    0     0  7798k      0 --:--:-- --:--:-- --:--:-- 8658k

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  
    dot-htseq_importer                      html  
    entity_name                             html  
    expand                                  html  
    faceting                                html  
    filtering                               html  
    gdc_cache                               html  
    gdc_client                              html  
    gdc_clinical                            html  
    gdc_rnaseq                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/gdc_rnaseq.Rd:28: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    gdc_token                               html  
    gdcdata                                 html  
    grep_fields                             html  
    id_field                                html  
    ids                                     html  
    make_filter                             html  
    manifest                                html  
    mapping                                 html  
    query                                   html  
    readDNAcopy                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/readDNAcopy.Rd:12: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/readDNAcopy.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    readHTSeqFile                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4Iuq2s/R.INSTALL1d24640d24/GenomicDataCommons/man/readHTSeqFile.Rd:16: file link 'read_tsv' in package 'readr' does not exist and so has been treated as a topic
    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_1.8.0.zip
* DONE (GenomicDataCommons)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GenomicDataCommons' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(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: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.51    0.90   18.46


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(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: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.06    0.43   19.87

name	user	system	elapsed
aggregations	0.14	0.00	0.56
available_expand	0.03	0.00	0.08
available_fields	0.05	0.02	0.16
available_values	0.04	0.03	0.37
constants	0	0	0
count	0.14	0.01	0.33
default_fields	0.04	0.03	0.16
entity_name	0.09	0.00	0.19
expand	0.16	0.03	0.39
faceting	0.09	0.04	0.28
filtering	1.08	0.07	2.22
gdc_cache	0	0	0
gdc_client	0	0	0
gdc_clinical	0.72	0.00	1.16
gdc_rnaseq	0.11	0.00	0.31
gdc_token	0.02	0.00	0.02
gdcdata	0.31	0.02	0.68
grep_fields	0.05	0.02	0.10
id_field	0.08	0.00	0.13
ids	0.44	0.00	0.95
manifest	0.15	0.00	0.28
mapping	0.03	0.00	0.07
query	0.16	0.01	0.26
readDNAcopy	0.09	0.00	0.09
readHTSeqFile	0.04	0.00	0.04
response	0.09	0.03	0.23
results	0.11	0.00	0.23
results_all	0.06	0.00	0.27
select	0.11	0.00	0.33
slicing	0	0	0
status	0.00	0.00	0.05
transfer	0	0	0
write_manifest	0.17	0.00	0.37

name	user	system	elapsed
aggregations	0.12	0.00	0.50
available_expand	0.03	0.00	0.08
available_fields	0.06	0.00	0.16
available_values	0.10	0.00	0.34
constants	0	0	0
count	0.13	0.00	0.30
default_fields	0.04	0.00	0.14
entity_name	0.11	0.00	0.19
expand	0.18	0.00	0.35
faceting	0.10	0.00	0.25
filtering	0.99	0.00	2.15
gdc_cache	0.01	0.00	0.01
gdc_client	0	0	0
gdc_clinical	0.69	0.03	1.15
gdc_rnaseq	0.10	0.00	0.33
gdc_token	0	0	0
gdcdata	0.45	0.00	0.86
grep_fields	0.05	0.02	0.09
id_field	0.08	0.00	0.12
ids	0.45	0.02	0.95
manifest	0.72	0.00	0.86
mapping	0.01	0.00	0.05
query	0.17	0.00	0.27
readDNAcopy	0.07	0.01	0.07
readHTSeqFile	0.01	0.02	0.03
response	0.11	0.00	0.24
results	0.11	0.00	0.22
results_all	0.08	0.00	0.29
select	0.14	0.00	0.35
slicing	0	0	0
status	0.02	0.00	0.05
transfer	0	0	0
write_manifest	0.14	0.00	0.35

CHECK report for GenomicDataCommons on tokay2

Summary

Command output

Installation output

Tests output

Example timings