BioC 3.5: CHECK report for ensembldb on tokay2

Package: ensembldb

Version: 2.0.4

Command: rm -rf ensembldb.buildbin-libdir ensembldb.Rcheck && mkdir ensembldb.buildbin-libdir ensembldb.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensembldb.buildbin-libdir ensembldb_2.0.4.tar.gz >ensembldb.Rcheck\00install.out 2>&1 && cp ensembldb.Rcheck\00install.out ensembldb-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ensembldb.buildbin-libdir --install="check:ensembldb-install.out" --force-multiarch --no-vignettes --timings ensembldb_2.0.4.tar.gz

StartedAt: 2017-10-17 23:35:03 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:46:11 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 668.6 seconds

RetCode: 0

Status:  OK

CheckDir: ensembldb.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ensembldb.buildbin-libdir ensembldb.Rcheck && mkdir ensembldb.buildbin-libdir ensembldb.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ensembldb.buildbin-libdir ensembldb_2.0.4.tar.gz >ensembldb.Rcheck\00install.out 2>&1 && cp ensembldb.Rcheck\00install.out ensembldb-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ensembldb.buildbin-libdir --install="check:ensembldb-install.out" --force-multiarch --no-vignettes --timings ensembldb_2.0.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ensembldb.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 'ensembldb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ensembldb' version '2.0.4'
* 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 'ensembldb' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
* 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
Filter-classes      3.67   2.56   39.27
EnsDb-AnnotationDbi 3.83   0.66    9.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
Filter-classes 2.76   2.43    5.19
* 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/ensembldb.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ensembldb' ...
** 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 'ensembldb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ensembldb' as ensembldb_2.0.4.zip
* DONE (ensembldb)

name	user	system	elapsed
EnsDb-AnnotationDbi	3.83	0.66	9.97
EnsDb-class	1.70	0.25	2.26
EnsDb-exonsBy	2.56	1.03	4.13
EnsDb-lengths	0.79	0.19	0.97
EnsDb-seqlevels	1.17	0.09	1.26
EnsDb-sequences	0.01	0.00	0.02
EnsDb-utils	0.44	0.00	0.44
EnsDb	1.50	0.17	1.67
Filter-classes	3.67	2.56	39.27
ProteinFunctionality	0.60	0.52	4.76
hasProteinData-EnsDb-method	0.02	0.00	0.02
listEnsDbs	0	0	0
makeEnsemblDbPackage	1.03	0.07	1.10
useMySQL-EnsDb-method	0.01	0.00	0.02

name	user	system	elapsed
EnsDb-AnnotationDbi	4.24	0.25	4.48
EnsDb-class	2.89	0.09	2.99
EnsDb-exonsBy	2.38	0.66	3.03
EnsDb-lengths	0.97	0.15	1.13
EnsDb-seqlevels	1.39	0.02	1.41
EnsDb-sequences	0.01	0.00	0.01
EnsDb-utils	0.47	0.02	0.49
EnsDb	1.89	0.21	2.16
Filter-classes	2.76	2.43	5.19
ProteinFunctionality	0.35	0.37	0.71
hasProteinData-EnsDb-method	0.01	0.00	0.02
listEnsDbs	0	0	0
makeEnsemblDbPackage	0.93	0.05	0.97
useMySQL-EnsDb-method	0.01	0.00	0.01