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BioC 3.2: CHECK report for biobroom on zin1

This page was generated on 2016-04-23 10:15:08 -0700 (Sat, 23 Apr 2016).

Package 94/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biobroom 1.2.0
John D. Storey and Andrew J. Bass
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/biobroom
Last Changed Rev: 112908 / Revision: 116712
Last Changed Date: 2016-01-26 08:12:47 -0800 (Tue, 26 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: biobroom
Version: 1.2.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biobroom_1.2.0.tar.gz
StartedAt: 2016-04-22 22:28:43 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:29:38 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 55.4 seconds
RetCode: 0
Status:  OK 
CheckDir: biobroom.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biobroom_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/biobroom.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biobroom/DESCRIPTION’ ... OK
* this is package ‘biobroom’ version ‘1.2.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biobroom’ can be installed ... [3s/3s] 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
tidy.DESeqDataSet: no visible binding for global variable ‘term’
tidy.DESeqDataSet: no visible binding for global variable ‘.’
tidy.DESeqDataSet: no visible global function definition for ‘counts’
tidy.DESeqDataSet: no visible binding for global variable ‘gene’
tidy.DGEList: no visible binding for global variable ‘sample.id’
tidy.DGEList: no visible binding for global variable ‘value’
tidy.DGEList: no visible binding for global variable ‘gene’
tidy.ExpressionSet: no visible binding for global variable ‘sample.id’
tidy.ExpressionSet: no visible binding for global variable ‘value’
tidy.ExpressionSet: no visible binding for global variable ‘gene’
tidy.ExpressionSet: no visible global function definition for ‘pData’
tidy.MArrayLM: no visible binding for global variable ‘term’
tidy.MArrayLM: no visible binding for global variable ‘estimate’
tidy.MArrayLM: no visible binding for global variable ‘gene’
tidy.MSnSet: no visible binding for global variable ‘sample.id’
tidy.MSnSet: no visible binding for global variable ‘value’
tidy.MSnSet: no visible binding for global variable ‘protein’
tidy.MSnSet: no visible global function definition for ‘pData’
tidy.qvalue: no visible binding for global variable ‘smoothed’
tidy.qvalue: no visible binding for global variable ‘pi0’
tidy.qvalue: no visible binding for global variable ‘lambda’
tidy_matrix: no visible binding for global variable ‘value’
tidy_matrix: no visible binding for global variable ‘gene’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
DESeq2_tidiers 8.656  0.175   8.839
edgeR_tidiers  5.591  0.016   5.624
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/biobroom.Rcheck/00check.log’
for details.


biobroom.Rcheck/00install.out:

* installing *source* package ‘biobroom’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biobroom)

biobroom.Rcheck/biobroom-Ex.timings:

nameusersystemelapsed
DESeq2_tidiers8.6560.1758.839
ExpressionSet_tidiers1.5510.0281.589
MSnSet_tidiers2.1640.0362.209
edgeR_tidiers5.5910.0165.624
limma_tidiers0.2920.0040.297
qvalue_tidiers0.6330.0000.633