BioC 3.5: CHECK report for GenomicDataCommons on malbec2

Package: GenomicDataCommons

Version: 1.0.5

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomicDataCommons_1.0.5.tar.gz

StartedAt: 2017-10-17 23:30:06 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:31:40 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 93.6 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicDataCommons.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomicDataCommons_1.0.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.Rcheck/00check.log’
for details.

* 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
* DONE (GenomicDataCommons)

name	user	system	elapsed
aggregations	0.576	0.012	0.915
as.data.frame.GDCResults	0.336	0.000	0.558
available_expand	0.020	0.000	0.078
available_fields	0.056	0.000	0.148
available_values	0.048	0.000	0.201
constants	0.000	0.000	0.001
count	0.088	0.000	0.259
default_fields	0.052	0.004	0.147
entity_name	0.048	0.004	0.127
expand	0.140	0.000	0.333
faceting	0.080	0.000	0.206
filtering	0.184	0.000	0.436
gdc_client	0.000	0.012	0.016
gdc_token	0.000	0.000	0.001
gdcdata	0.008	0.008	0.473
grep_fields	0.028	0.004	0.080
id_field	0.036	0.000	0.079
ids	0.448	0.028	1.070
manifest	0.208	0.012	0.357
mapping	0.020	0.000	0.055
query	0.060	0.004	0.155
rbindlist2	0.004	0.000	0.004
readDNAcopy	0.344	0.004	0.349
readHTSeqFile	0.352	0.000	0.351
response	0.048	0.000	0.218
results	0.052	0.000	0.229
results_all	0.088	0.000	0.310
select	0.136	0.000	0.349
slicing	0	0	0
status	0.020	0.000	0.049
transfer	0.000	0.000	0.001
write_manifest	0.072	0.004	0.207