BioC 3.5: CHECK report for SummarizedExperiment on tokay2

Package: SummarizedExperiment

Version: 1.6.5

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_1.6.5.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_1.6.5.tar.gz

StartedAt: 2017-10-18 03:18:30 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:22:57 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 267.1 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_1.6.5.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_1.6.5.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/SummarizedExperiment.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 'SummarizedExperiment/DESCRIPTION' ... OK
* this is package 'SummarizedExperiment' version '1.6.5'
* 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 5.56   0.11    5.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                          user system elapsed
makeSummarizedExperimentFromExpressionSet 6.28   0.09    6.38
* 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_1.6.5.zip
* DONE (SummarizedExperiment)

name	user	system	elapsed
Assays-class	0.46	0.00	0.45
RangedSummarizedExperiment-class	0.54	0.08	0.63
SummarizedExperiment-class	0.53	0.03	0.57
coverage-methods	0.17	0.00	0.17
findOverlaps-methods	0.16	0.00	0.15
inter-range-methods	0.15	0.00	0.16
intra-range-methods	0.25	0.00	0.25
makeSummarizedExperimentFromDataFrame	0.21	0.00	0.20
makeSummarizedExperimentFromExpressionSet	5.56	0.11	5.91
nearest-methods	0.57	0.01	0.59
readKallisto	0.96	0.02	0.97
saveHDF5SummarizedExperiment	0.47	0.06	0.53

name	user	system	elapsed
Assays-class	0.27	0.00	0.27
RangedSummarizedExperiment-class	0.98	0.00	0.98
SummarizedExperiment-class	0.64	0.00	0.64
coverage-methods	0.18	0.00	0.18
findOverlaps-methods	0.19	0.00	0.19
inter-range-methods	0.19	0.00	0.19
intra-range-methods	0.31	0.00	0.31
makeSummarizedExperimentFromDataFrame	0.25	0.00	0.25
makeSummarizedExperimentFromExpressionSet	6.28	0.09	6.38
nearest-methods	0.67	0.00	0.67
readKallisto	0.85	0.04	0.87
saveHDF5SummarizedExperiment	0.70	0.01	0.72