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BioC 3.1: CHECK report for RNAprobR on zin2

This page was generated on 2015-10-09 09:26:49 -0700 (Fri, 09 Oct 2015).

Package 833/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAprobR 1.0.2
Nikos Sidiropoulos
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/RNAprobR
Last Changed Rev: 107292 / Revision: 109384
Last Changed Date: 2015-08-10 06:47:27 -0700 (Mon, 10 Aug 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]NO, built version is LOWER than in internal repository!!!
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK NO, built version is LOWER than in internal repository!!!

Summary

Package: RNAprobR
Version: 1.0.2
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.0.2.tar.gz
StartedAt: 2015-10-09 05:03:03 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:05:25 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 141.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAprobR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.0.2’
* 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 ‘RNAprobR’ can be installed ... [13s/13s] 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 ... NOTE
Package in Depends field not imported from: ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/RNAprobR.Rcheck/00check.log’
for details.


RNAprobR.Rcheck/00install.out:

* installing *source* package ‘RNAprobR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (RNAprobR)

RNAprobR.Rcheck/RNAprobR-Ex.timings:

nameusersystemelapsed
BED2txDb0.5780.0360.625
GR2norm_df0.2750.0000.276
bedgraph2norm1.1250.0001.127
comp0.1590.0000.158
compdata0.2730.0000.272
correct_oversaturation0.0690.0000.068
dtcr0.3170.0000.317
k2n_calc0.0110.0000.011
norm2bedgraph0.5080.0000.508
norm_df2GR0.0350.0000.035
plotRNA0.2120.0000.212
plotReads0.1050.0000.106
readsamples0.0230.0000.022
slograt0.3110.0000.310
swinsor0.1990.0000.199
swinsor_vector0.0370.0000.037
winsor0.0040.0000.004