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BioC 3.3: CHECK report for gespeR on oaxaca

This page was generated on 2016-10-13 13:01:13 -0700 (Thu, 13 Oct 2016).

Package 482/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gespeR 1.4.2
Fabian Schmich
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/gespeR
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gespeR
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gespeR_1.4.2.tar.gz
StartedAt: 2016-10-13 02:05:36 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:10:32 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 296.3 seconds
RetCode: 0
Status:  OK 
CheckDir: gespeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gespeR_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/gespeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gespeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gespeR’ version ‘1.4.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gespeR’ 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 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 ... NOTE
.gespeR.cv: no visible global function definition for ‘coef’
.select.model: no visible global function definition for ‘predict’
concordance: no visible global function definition for ‘cor’
lasso.rand: no visible global function definition for ‘runif’
plot.gespeR: no visible global function definition for ‘hist’
stability.selection: no visible global function definition for ‘lm’
Phenotypes,character: no visible global function definition for
  ‘read.delim’
Undefined global functions or variables:
  coef cor hist lm predict read.delim runif
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coef", "cor", "lm", "predict", "runif")
  importFrom("utils", "read.delim")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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
gespeR-package    7.914  0.267  52.584
gespeR-class      0.270  0.013  11.528
stability-methods 0.147  0.010  11.403
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/gespeR.Rcheck/00check.log’
for details.


gespeR.Rcheck/00install.out:

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

gespeR.Rcheck/gespeR-Ex.timings:

nameusersystemelapsed
Phenotypes-class0.0150.0000.015
TargetRelations-class0.0060.0010.007
annotate.gsp-methods0.1380.0070.146
as.data.frame-Phenotypes-method0.0330.0020.034
c-Phenotypes-method0.0320.0010.033
concordance0.4280.0141.257
gespeR-class 0.270 0.01311.528
gespeR-package 7.914 0.26752.584
gspssp-methods0.1610.0120.174
join-methods0.0240.0010.025
lasso.rand0.0060.0010.020
na.rem-methods0.0290.0010.030
path-methods0.0070.0010.008
rbo0.0020.0000.002
scores-methods0.1510.0100.162
simData0.0190.0010.019
stability-methods 0.147 0.01011.403
stabilityfits0.1430.0070.150
target-relations-methods0.1460.0060.152
trmatrix-methods0.1420.0080.150
values-methods0.0310.0060.037