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BioC 3.1: CHECK report for RNAprobR on moscato2

This page was generated on 2015-10-09 09:32:08 -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: rm -rf RNAprobR.buildbin-libdir RNAprobR.Rcheck && mkdir RNAprobR.buildbin-libdir RNAprobR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAprobR.buildbin-libdir RNAprobR_1.0.2.tar.gz >RNAprobR.Rcheck\00install.out 2>&1 && cp RNAprobR.Rcheck\00install.out RNAprobR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RNAprobR.buildbin-libdir --install="check:RNAprobR-install.out" --force-multiarch --no-vignettes --timings RNAprobR_1.0.2.tar.gz
StartedAt: 2015-10-09 05:41:17 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:45:38 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 261.3 seconds
RetCode: 0
Status:  OK  
CheckDir: RNAprobR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RNAprobR.buildbin-libdir RNAprobR.Rcheck && mkdir RNAprobR.buildbin-libdir RNAprobR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAprobR.buildbin-libdir RNAprobR_1.0.2.tar.gz >RNAprobR.Rcheck\00install.out 2>&1 && cp RNAprobR.Rcheck\00install.out RNAprobR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RNAprobR.buildbin-libdir --install="check:RNAprobR-install.out" --force-multiarch --no-vignettes --timings RNAprobR_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/RNAprobR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [12s] OK
** running examples for arch 'x64' ... [15s] 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
  'E:/biocbld/bbs-3.1-bioc/meat/RNAprobR.Rcheck/00check.log'
for details.


RNAprobR.Rcheck/00install.out:


install for i386

* 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'

install for x64

* installing *source* package 'RNAprobR' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'RNAprobR' as RNAprobR_1.0.2.zip
* DONE (RNAprobR)

RNAprobR.Rcheck/examples_i386/RNAprobR-Ex.timings:

nameusersystemelapsed
BED2txDb0.730.210.93
GR2norm_df0.250.000.25
bedgraph2norm1.290.001.31
comp0.140.000.15
compdata0.270.000.26
correct_oversaturation0.060.000.06
dtcr0.30.00.3
k2n_calc0.010.000.01
norm2bedgraph0.550.000.55
norm_df2GR0.030.000.03
plotRNA0.230.000.24
plotReads0.130.000.12
readsamples0.020.000.02
slograt0.310.000.31
swinsor0.220.000.22
swinsor_vector0.040.000.04
winsor000

RNAprobR.Rcheck/examples_x64/RNAprobR-Ex.timings:

nameusersystemelapsed
BED2txDb0.820.271.09
GR2norm_df0.390.000.39
bedgraph2norm1.290.001.31
comp0.30.00.3
compdata0.510.000.51
correct_oversaturation0.080.000.08
dtcr0.480.000.49
k2n_calc0.020.010.03
norm2bedgraph0.640.000.64
norm_df2GR0.050.000.04
plotRNA0.260.000.27
plotReads0.130.020.14
readsamples0.030.000.03
slograt0.340.000.34
swinsor0.250.000.25
swinsor_vector0.050.000.05
winsor000