BioC 3.5: CHECK report for GenomicDataCommons on tokay2

Package: GenomicDataCommons

Version: 1.0.5

Command: rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.0.5.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.0.5.tar.gz

StartedAt: 2017-10-18 00:04:49 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:07:33 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 163.8 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicDataCommons.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.0.5.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.0.5.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.0.5'
* 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
** 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GenomicDataCommons' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicDataCommons' as GenomicDataCommons_1.0.5.zip
* DONE (GenomicDataCommons)

name	user	system	elapsed
aggregations	0.50	0.00	0.75
as.data.frame.GDCResults	0.36	0.03	1.92
available_expand	0.03	0.02	0.08
available_fields	0.05	0.00	0.14
available_values	0.06	0.00	0.18
constants	0	0	0
count	0.11	0.00	0.29
default_fields	0.05	0.00	0.17
entity_name	0.09	0.00	0.15
expand	0.11	0.00	0.30
faceting	0.06	0.00	0.17
filtering	0.24	0.00	0.47
gdc_client	0	0	0
gdc_token	0	0	0
gdcdata	0.03	0.00	0.53
grep_fields	0.06	0.00	0.10
id_field	0.09	0.00	0.14
ids	0.39	0.01	1.14
manifest	0.22	0.02	0.39
mapping	0.02	0.00	0.05
query	0.14	0.00	0.23
rbindlist2	0	0	0
readDNAcopy	0.37	0.00	0.50
readHTSeqFile	0.28	0.00	0.29
response	0.08	0.00	0.25
results	0.10	0.00	0.26
results_all	0.09	0.00	0.27
select	0.11	0.00	0.36
slicing	0	0	0
status	0.02	0.00	0.04
transfer	0	0	0
write_manifest	0.10	0.01	0.29

name	user	system	elapsed
aggregations	0.61	0.01	0.86
as.data.frame.GDCResults	0.45	0.00	0.85
available_expand	0.01	0.00	0.06
available_fields	0.01	0.02	0.12
available_values	0.08	0.00	0.21
constants	0	0	0
count	0.13	0.01	0.34
default_fields	0.05	0.00	0.15
entity_name	0.09	0.00	0.17
expand	0.13	0.00	0.33
faceting	0.06	0.02	0.19
filtering	0.23	0.00	0.48
gdc_client	0	0	0
gdc_token	0	0	0
gdcdata	0.03	0.00	0.76
grep_fields	0.04	0.00	0.09
id_field	0.07	0.00	0.11
ids	0.42	0.00	1.05
manifest	0.25	0.03	0.42
mapping	0.03	0.00	0.07
query	0.19	0.00	0.26
rbindlist2	0	0	0
readDNAcopy	0.54	0.03	0.64
readHTSeqFile	0.36	0.00	0.36
response	0.08	0.00	0.25
results	0.11	0.00	0.28
results_all	0.10	0.00	0.27
select	0.09	0.00	0.32
slicing	0	0	0
status	0.02	0.00	0.05
transfer	0	0	0
write_manifest	0.12	0.00	0.26