curatedMetagenomicData 1.2.2
Lucas Schiffer
| Snapshot Date: 2017-10-18 09:00:07 -0400 (Wed, 18 Oct 2017) | | URL: https://git.bioconductor.org/packages/curatedMetagenomicData | | Branch: RELEASE_3_5 | | Last Commit: b353a12 | | Last Changed Date: 2017-10-17 08:32:53 -0400 (Tue, 17 Oct 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings curatedMetagenomicData_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/curatedMetagenomicData.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 ‘curatedMetagenomicData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedMetagenomicData’ version ‘1.2.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘dplyr’ ‘phyloseq’ ‘Biobase’ ‘ExperimentHub’ ‘AnnotationHub’
‘magrittr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘curatedMetagenomicData’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.6Mb
sub-directories of 1Mb or more:
help 7.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocInstaller’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘BiocInstaller’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ExpressionSet2MRexperiment: no visible global function definition for
‘AnnotatedDataFrame’
ExpressionSet2MRexperiment: no visible global function definition for
‘phenoData’
curatedMetagenomicData : <anonymous>: no visible global function
definition for ‘exprs<-’
Undefined global functions or variables:
AnnotatedDataFrame exprs<- phenoData
* checking Rd files ... NOTE
prepare_Rd: HMP_2012.Rd:540-542: Dropping empty section \seealso
prepare_Rd: KarlssonFH_2013.Rd:90-92: Dropping empty section \seealso
prepare_Rd: LeChatelierE_2013.Rd:86-88: Dropping empty section \seealso
prepare_Rd: LomanNJ_2013_Hi.Rd:82-84: Dropping empty section \seealso
prepare_Rd: LomanNJ_2013_Mi.Rd:82-84: Dropping empty section \seealso
prepare_Rd: NielsenHB_2014.Rd:94-96: Dropping empty section \seealso
prepare_Rd: Obregon_TitoAJ_2015.Rd:94-96: Dropping empty section \seealso
prepare_Rd: OhJ_2014.Rd:86-88: Dropping empty section \seealso
prepare_Rd: QinJ_2012.Rd:106-108: Dropping empty section \seealso
prepare_Rd: QinN_2014.Rd:94-96: Dropping empty section \seealso
prepare_Rd: RampelliS_2015.Rd:90-92: Dropping empty section \seealso
prepare_Rd: TettAJ_2016.Rd:184-186: Dropping empty section \seealso
prepare_Rd: ZellerG_2014.Rd:94-96: Dropping empty section \seealso
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
NielsenHB_2014 238.432 8.540 247.739
LeChatelierE_2013 175.888 5.676 181.933
KarlssonFH_2013 80.644 3.192 84.674
OhJ_2014 56.712 10.488 67.606
HMP_2012 53.200 2.804 56.096
QinJ_2012 25.972 5.600 31.993
QinN_2014 18.496 3.944 22.699
ZellerG_2014 14.384 2.884 17.427
LomanNJ_2013_Hi 11.896 0.512 12.560
Obregon_TitoAJ_2015 4.696 0.256 5.201
* 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: 6 NOTEs
See
‘/home/biocbuild/bbs-3.5-data-experiment/meat/curatedMetagenomicData.Rcheck/00check.log’
for details.
* installing *source* package ‘curatedMetagenomicData’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (curatedMetagenomicData)