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BioC 3.2: CHECK report for RNAprobR on linux1.bioconductor.org

This page was generated on 2015-10-27 17:27:04 -0400 (Tue, 27 Oct 2015).

Package 895/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAprobR 1.2.0
Nikos Sidiropoulos
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RNAprobR
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: RNAprobR
Version: 1.2.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.2.0.tar.gz
StartedAt: 2015-10-27 07:37:54 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 07:40:36 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 161.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAprobR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RNAprobR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ‘RNAprobR’ can be installed ... [15s/15s] 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’
.process_oneRNA_euc: no visible global function definition for
  ‘IRanges’
.remove_unannotated: no visible binding for global variable ‘Pos’
BED2txDb: no visible global function definition for ‘IRanges’
comp: no visible global function definition for ‘endoapply’
k2n_calc: no visible binding for global variable ‘Barcodes’
norm2bedgraph: no visible global function definition for ‘runValue’
norm_df2GR: no visible global function definition for ‘IRanges’
readsamples: no visible global function definition for ‘IRanges’
* 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 ... [11s/11s] 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-3.2-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
BED2txDb0.5820.0280.609
GR2norm_df0.2050.0040.209
bedgraph2norm0.8550.0040.858
comp0.1180.0010.119
compdata0.220.000.22
correct_oversaturation0.0550.0000.055
dtcr0.2550.0000.255
k2n_calc0.0100.0000.011
norm2bedgraph0.4370.0030.442
norm_df2GR0.0260.0000.026
plotRNA0.1830.0010.182
plotReads0.0710.0000.072
readsamples0.0240.0000.023
slograt0.2630.0000.263
swinsor0.1690.0000.170
swinsor_vector0.2990.0000.298
winsor0.0020.0000.003