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BioC 3.4: CHECK report for RNAprobR on malbec1

This page was generated on 2017-04-15 16:12:49 -0400 (Sat, 15 Apr 2017).

Package 1062/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAprobR 1.6.0
Nikos Sidiropoulos
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/RNAprobR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAprobR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.6.0.tar.gz
StartedAt: 2017-04-15 00:59:24 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:02:10 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 166.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAprobR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RNAprobR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAprobR/DESCRIPTION’ ... OK
* this is package ‘RNAprobR’ version ‘1.6.0’
* 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 ‘RNAprobR’ 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
.all_dc: no visible binding for global variable ‘depth_correction’
.compare_prop: no visible global function definition for ‘pnorm’
.compare_prop_slograt: no visible global function definition for
  ‘pnorm’
.process_oneRNA_euc: no visible global function definition for
  ‘IRanges’
.remove_unannotated: no visible binding for global variable ‘Pos’
.save_bedgraph: no visible global function definition for ‘write.table’
BED2txDb: no visible global function definition for ‘IRanges’
bam2bedgraph: no visible global function definition for ‘aggregate’
comp: no visible global function definition for ‘endoapply’
correct_oversaturation: no visible global function definition for ‘lm’
k2n_calc: no visible global function definition for ‘read.table’
k2n_calc: no visible binding for global variable ‘Barcodes’
k2n_calc: no visible global function definition for ‘quantile’
norm2bedgraph: no visible global function definition for ‘runValue’
norm_df2GR: no visible global function definition for ‘IRanges’
plotRNA: no visible global function definition for ‘plot’
plotRNA: no visible global function definition for ‘points’
plotReads: no visible global function definition for ‘plot’
plotReads: no visible global function definition for ‘segments’
readsamples: no visible binding for global variable ‘read.table’
readsamples: no visible global function definition for ‘IRanges’
swinsor_vector: no visible binding for global variable ‘sd’
winsor: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  Barcodes IRanges Pos aggregate depth_correction endoapply lm plot
  pnorm points quantile read.table runValue sd segments write.table
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "aggregate", "lm", "pnorm", "quantile", "sd")
  importFrom("utils", "read.table", "write.table")
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
* 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-3.4-bioc/meat/RNAprobR.Rcheck/00check.log’
for details.


RNAprobR.Rcheck/00install.out:

* installing *source* package ‘RNAprobR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RNAprobR)

RNAprobR.Rcheck/RNAprobR-Ex.timings:

nameusersystemelapsed
BED2txDb1.0760.0401.121
GR2norm_df0.1960.0120.209
bedgraph2norm0.9280.0440.973
comp0.1240.0000.126
compdata0.1920.0000.190
correct_oversaturation0.0440.0000.042
dtcr0.2400.0000.239
k2n_calc0.0120.0000.011
norm2bedgraph0.5720.0000.573
norm_df2GR0.0240.0000.023
plotRNA0.1960.0000.195
plotReads0.0760.0040.079
readsamples0.0160.0000.015
slograt0.2680.0000.268
swinsor0.1640.0000.164
swinsor_vector0.0280.0000.026
winsor0.0040.0000.003