BioC 3.5: CHECK report for SummarizedExperiment on tokay2

Package: SummarizedExperiment

Version: 1.6.3

Command: rm -rf SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && mkdir SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.6.3.tar.gz >SummarizedExperiment.Rcheck\00install.out 2>&1 && cp SummarizedExperiment.Rcheck\00install.out SummarizedExperiment-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SummarizedExperiment.buildbin-libdir --install="check:SummarizedExperiment-install.out" --force-multiarch --no-vignettes --timings SummarizedExperiment_1.6.3.tar.gz

StartedAt: 2017-08-16 03:12:35 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:17:16 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 280.3 seconds

RetCode: 0

Status:  OK

CheckDir: SummarizedExperiment.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && mkdir SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.6.3.tar.gz >SummarizedExperiment.Rcheck\00install.out 2>&1 && cp SummarizedExperiment.Rcheck\00install.out SummarizedExperiment-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=SummarizedExperiment.buildbin-libdir --install="check:SummarizedExperiment-install.out" --force-multiarch --no-vignettes --timings SummarizedExperiment_1.6.3.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SummarizedExperiment.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SummarizedExperiment/DESCRIPTION' ... OK
* this is package 'SummarizedExperiment' version '1.6.3'
* package encoding: UTF-8
* 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 'SummarizedExperiment' 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
* 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 ... NOTE
'library' or 'require' calls in package code:
  'HDF5Array' 'rhdf5'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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
makeSummarizedExperimentFromExpressionSet 6.58   0.25    7.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                          user system elapsed
makeSummarizedExperimentFromExpressionSet  7.1   0.27    7.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.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/SummarizedExperiment.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SummarizedExperiment' ...
** 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 'SummarizedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SummarizedExperiment' as SummarizedExperiment_1.6.3.zip
* DONE (SummarizedExperiment)

name	user	system	elapsed
Assays-class	0.64	0.02	0.66
RangedSummarizedExperiment-class	0.58	0.03	0.61
SummarizedExperiment-class	0.68	0.02	0.73
coverage-methods	0.36	0.00	0.36
findOverlaps-methods	0.28	0.00	0.28
inter-range-methods	0.24	0.00	0.23
intra-range-methods	0.32	0.00	0.31
makeSummarizedExperimentFromDataFrame	0.28	0.00	0.28
makeSummarizedExperimentFromExpressionSet	6.58	0.25	7.44
nearest-methods	1.04	0.03	1.08
readKallisto	0.81	0.04	0.86
saveHDF5SummarizedExperiment	0.66	0.02	0.67

name	user	system	elapsed
Assays-class	1.07	0.03	1.09
RangedSummarizedExperiment-class	0.74	0.00	0.74
SummarizedExperiment-class	0.88	0.05	0.93
coverage-methods	0.33	0.00	0.33
findOverlaps-methods	0.31	0.00	0.31
inter-range-methods	0.25	0.00	0.25
intra-range-methods	0.36	0.00	0.36
makeSummarizedExperimentFromDataFrame	0.28	0.00	0.28
makeSummarizedExperimentFromExpressionSet	7.10	0.27	7.36
nearest-methods	0.89	0.06	0.96
readKallisto	0.81	0.00	0.82
saveHDF5SummarizedExperiment	0.59	0.05	0.64