GRridge 1.0.0
Mark A. van de Wiel
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/GRridge | | Branch: RELEASE_3_5 | | Last Commit: 0209390 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | 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 GRridge_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GRridge.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 ‘GRridge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRridge’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘penalized’ ‘Iso’ ‘survival’ ‘GSEABase’ ‘BiocGenerics’ ‘Biobase’
‘annotate’ ‘graph’
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 ‘GRridge’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
See ‘/home/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 8.5Mb
* 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
* 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
dataFarkas.rda 3.4Mb 2.5Mb bzip2
dataWurdinger.rda 1.9Mb 1.2Mb xz
* 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
predict.grridge 174.956 0.184 175.255
grridgeCV 74.048 0.480 74.567
* 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: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck/00check.log’
for details.
* installing *source* package ‘GRridge’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
* DONE (GRridge)