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BioC 3.6: CHECK report for IHW on veracruz1

This page was generated on 2017-08-16 13:48:13 -0400 (Wed, 16 Aug 2017).

Package 668/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IHW 1.5.0
Nikos Ignatiadis
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IHW
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: IHW
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IHW_1.5.0.tar.gz
StartedAt: 2017-08-16 04:28:06 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:29:04 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 57.7 seconds
RetCode: 0
Status:  OK 
CheckDir: IHW.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IHW_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/IHW.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IHW/DESCRIPTION’ ... OK
* this is package ‘IHW’ version ‘1.5.0’
* 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 ... NOTE
Found the following non-portable file paths:
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_decisionboundary_590d9a0a4410f3408b1d2f616ac3bb8c.RData
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_decisionboundary_590d9a0a4410f3408b1d2f616ac3bb8c.rdb
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_decisionboundary_590d9a0a4410f3408b1d2f616ac3bb8c.rdx
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_rawvsadj_9328823fe5ab47b4077c950928cf9409.RData
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_rawvsadj_9328823fe5ab47b4077c950928cf9409.rdb
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_rawvsadj_9328823fe5ab47b4077c950928cf9409.rdx
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_weights_c49bfd98b1fd6e2e192db36e31fdee5f.RData
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_weights_c49bfd98b1fd6e2e192db36e31fdee5f.rdb
  IHW/vignettes/introduction_to_ihw_cache/html/plot_ihwRes_weights_c49bfd98b1fd6e2e192db36e31fdee5f.rdx

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IHW’ 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
* 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 ... NOTE
filter_pvals_for_optim: no visible global function definition for
  ‘p.adjust’
groups_by_filter: no visible global function definition for ‘runif’
ihw.DESeqResults: no visible global function definition for ‘mcols’
ihw.DESeqResults: no visible global function definition for ‘mcols<-’
ihw.DESeqResults: no visible global function definition for ‘metadata’
ihw.DESeqResults: no visible global function definition for
  ‘metadata<-’
ihw.default: no visible global function definition for ‘runif’
ihw.default: no visible global function definition for ‘p.adjust’
ihw_convex: no visible global function definition for ‘gurobi’
ihw_internal: no visible global function definition for ‘p.adjust’
ihw_milp: no visible global function definition for ‘str’
ihw_milp: no visible global function definition for ‘gurobi’
plot_decisionboundary: no visible binding for global variable ‘stratum’
plot_decisionboundary: no visible binding for global variable
  ‘covariate’
plot_decisionboundary: no visible binding for global variable ‘pvalue’
plot_decisionboundary: no visible binding for global variable ‘fold’
thresholds_ihwResult: no visible global function definition for
  ‘na.exclude’
thresholds,ihwResult: no visible global function definition for
  ‘na.exclude’
Undefined global functions or variables:
  covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude
  p.adjust pvalue runif str stratum
Consider adding
  importFrom("stats", "na.exclude", "p.adjust", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
ihw.default 5.473  0.063   5.747
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/IHW.Rcheck/00check.log’
for details.


IHW.Rcheck/00install.out:

* installing *source* package ‘IHW’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘IHW’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IHW)

IHW.Rcheck/IHW-Ex.timings:

nameusersystemelapsed
get_bh_threshold0.0030.0000.003
groups_by_filter0.0020.0000.002
ihw.DESeqResults0.0010.0010.001
ihw.default5.4730.0635.747
ihwResult-class2.6260.0302.715
plot-ihwResult-method3.6130.0573.743