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BioC 3.5: CHECK report for RNAprobR on tokay2

This page was generated on 2017-08-16 13:24:19 -0400 (Wed, 16 Aug 2017).

Package 1130/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAprobR 1.8.0
Nikos Sidiropoulos
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/RNAprobR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAprobR
Version: 1.8.0
Command: rm -rf RNAprobR.buildbin-libdir RNAprobR.Rcheck && mkdir RNAprobR.buildbin-libdir RNAprobR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAprobR.buildbin-libdir RNAprobR_1.8.0.tar.gz >RNAprobR.Rcheck\00install.out 2>&1 && cp RNAprobR.Rcheck\00install.out RNAprobR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RNAprobR.buildbin-libdir --install="check:RNAprobR-install.out" --force-multiarch --no-vignettes --timings RNAprobR_1.8.0.tar.gz
StartedAt: 2017-08-16 02:32:21 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:37:23 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 301.7 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAprobR.buildbin-libdir RNAprobR_1.8.0.tar.gz >RNAprobR.Rcheck\00install.out 2>&1 && cp RNAprobR.Rcheck\00install.out RNAprobR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RNAprobR.buildbin-libdir --install="check:RNAprobR-install.out" --force-multiarch --no-vignettes --timings RNAprobR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/RNAprobR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.8.0'
* 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 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 ... 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'
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 segments write.table
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "aggregate", "lm", "pnorm", "quantile")
  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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RNAprobR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAprobR' as RNAprobR_1.8.0.zip
* DONE (RNAprobR)

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

nameusersystemelapsed
BED2txDb1.160.041.20
GR2norm_df0.380.000.38
bedgraph2norm1.870.021.92
comp0.130.000.13
compdata0.210.000.21
correct_oversaturation0.050.000.05
dtcr0.330.000.33
k2n_calc0.090.000.09
norm2bedgraph0.550.000.55
norm_df2GR0.020.000.02
plotRNA0.140.000.14
plotReads0.130.000.13
readsamples0.010.000.01
slograt0.190.000.19
swinsor0.120.020.14
swinsor_vector0.040.000.03
winsor000

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

nameusersystemelapsed
BED2txDb1.480.031.54
GR2norm_df0.420.000.42
bedgraph2norm2.210.002.20
comp0.170.000.17
compdata0.230.000.24
correct_oversaturation0.130.000.23
dtcr0.450.000.46
k2n_calc0.190.000.37
norm2bedgraph0.780.000.78
norm_df2GR0.050.000.05
plotRNA0.280.000.28
plotReads0.220.000.22
readsamples0.010.000.01
slograt0.420.000.43
swinsor0.220.000.21
swinsor_vector0.050.000.05
winsor000