BioC 3.5: CHECK report for annotatr on tokay2

Package: annotatr

Version: 1.2.1

Command: rm -rf annotatr.buildbin-libdir annotatr.Rcheck && mkdir annotatr.buildbin-libdir annotatr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotatr.buildbin-libdir annotatr_1.2.1.tar.gz >annotatr.Rcheck\00install.out 2>&1 && cp annotatr.Rcheck\00install.out annotatr-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=annotatr.buildbin-libdir --install="check:annotatr-install.out" --force-multiarch --no-vignettes --timings annotatr_1.2.1.tar.gz

StartedAt: 2017-10-17 22:02:32 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:12:16 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 584.2 seconds

RetCode: 0

Status:  OK

CheckDir: annotatr.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf annotatr.buildbin-libdir annotatr.Rcheck && mkdir annotatr.buildbin-libdir annotatr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotatr.buildbin-libdir annotatr_1.2.1.tar.gz >annotatr.Rcheck\00install.out 2>&1 && cp annotatr.Rcheck\00install.out annotatr-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=annotatr.buildbin-libdir --install="check:annotatr-install.out" --force-multiarch --no-vignettes --timings annotatr_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/annotatr.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 'annotatr/DESCRIPTION' ... OK
* this is package 'annotatr' version '1.2.1'
* 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 'annotatr' 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
plot_coannotations: no visible binding for global variable '.'
plot_numerical_coannotations: no visible binding for global variable
  '.'
Undefined global functions or variables:
  .
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
Examples with CPU or elapsed time > 5s
                  user system elapsed
build_annotations 5.11   0.15    5.27
build_ah_annots   3.89   0.17    5.09
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/annotatr.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'annotatr' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'annotatr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotatr' as annotatr_1.2.1.zip
* DONE (annotatr)

name	user	system	elapsed
annotate_regions	0.95	0.02	0.97
annotatr_cache	1.11	0.23	1.39
build_ah_annots	3.22	0.31	4.36
build_annotations	4.66	0.18	4.83
builtin_annotations	0.02	0.00	0.02
builtin_genomes	0	0	0
plot_annotation	2.62	0.10	3.70
plot_categorical	2.09	0.10	2.91
plot_coannotations	2.08	0.01	2.09
plot_numerical	0.46	0.02	0.47
plot_numerical_coannotations	1.32	0.02	1.34
randomize_regions	1.08	0.06	1.95
read_annotations	0.35	0.00	0.35
read_regions	0.42	0.01	0.44
summarize_annotations	1.44	0.05	2.24
summarize_categorical	0.38	0.05	0.42
summarize_numerical	0.89	0.01	0.90

name	user	system	elapsed
annotate_regions	1.41	0.01	1.42
annotatr_cache	1.31	0.43	1.73
build_ah_annots	3.89	0.17	5.09
build_annotations	5.11	0.15	5.27
builtin_annotations	0.01	0.00	0.01
builtin_genomes	0	0	0
plot_annotation	3.79	0.05	4.43
plot_categorical	2.13	0.11	3.03
plot_coannotations	1.92	0.03	1.96
plot_numerical	1.15	0.00	1.15
plot_numerical_coannotations	1.08	0.00	1.08
randomize_regions	1.39	0.06	2.09
read_annotations	0.41	0.04	0.44
read_regions	0.41	0.03	0.44
summarize_annotations	1.75	0.06	2.48
summarize_categorical	0.43	0.02	0.46
summarize_numerical	0.51	0.03	0.56