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BioC 3.4: CHECK report for RiboProfiling on moscato1

This page was generated on 2016-09-21 03:47:42 -0700 (Wed, 21 Sep 2016).

Package 1020/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RiboProfiling 1.3.2
A. Popa
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RiboProfiling
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  TIMEOUT  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  TIMEOUT  skipped  skipped 

Summary

Package: RiboProfiling
Version: 1.3.2
Command: rm -rf RiboProfiling.buildbin-libdir RiboProfiling.Rcheck && mkdir RiboProfiling.buildbin-libdir RiboProfiling.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RiboProfiling.buildbin-libdir RiboProfiling_1.3.2.tar.gz >RiboProfiling.Rcheck\00install.out 2>&1 && cp RiboProfiling.Rcheck\00install.out RiboProfiling-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RiboProfiling.buildbin-libdir --install="check:RiboProfiling-install.out" --force-multiarch --no-vignettes --timings RiboProfiling_1.3.2.tar.gz
StartedAt: 2016-09-20 15:27:17 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:49:01 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1303.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RiboProfiling.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RiboProfiling.buildbin-libdir RiboProfiling.Rcheck && mkdir RiboProfiling.buildbin-libdir RiboProfiling.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RiboProfiling.buildbin-libdir RiboProfiling_1.3.2.tar.gz >RiboProfiling.Rcheck\00install.out 2>&1 && cp RiboProfiling.Rcheck\00install.out RiboProfiling-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RiboProfiling.buildbin-libdir --install="check:RiboProfiling-install.out" --force-multiarch --no-vignettes --timings RiboProfiling_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RiboProfiling.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RiboProfiling/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RiboProfiling' version '1.3.2'
* 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 'RiboProfiling' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling'
See 'D:/biocbld/bbs-3.4-bioc/meat/RiboProfiling.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data      2.9Mb
    extdata   6.9Mb
* 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
applyShiftFeature: no visible global function definition for 'is'
aroundPromoter: no visible global function definition for 'is'
codonInfo: no visible global function definition for 'is'
countShiftReads: no visible global function definition for 'is'
histMatchLength: no visible global function definition for 'is'
orfRelativePos: no visible global function definition for 'is'
plotSummarizedCov: no visible global function definition for 'is'
readStartCov: no visible global function definition for 'is'
readsToStartOrEnd: no visible global function definition for 'is'
riboSeqFromBAM: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
countShiftReads   79.84   1.00   80.98
countsPlot        73.60   0.36   74.07
riboSeqFromBAM    67.69   0.35   68.08
orfRelativePos    38.36   0.06   38.44
codonInfo         33.84   0.44   34.37
aroundPromoter    11.45   0.36   11.81
plotSummarizedCov 10.11   0.25   10.36
readStartCov       8.53   0.17    8.70
histMatchLength    5.09   0.08    5.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
countShiftReads   81.69   1.07   82.88
countsPlot        78.70   0.38   79.08
riboSeqFromBAM    72.57   0.16   72.75
orfRelativePos    38.78   0.04   38.83
codonInfo         27.35   0.52   28.57
aroundPromoter    11.20   0.51   11.72
plotSummarizedCov 10.98   0.07   11.35
readStartCov       7.84   0.18    8.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/RiboProfiling.Rcheck/00check.log'
for details.


RiboProfiling.Rcheck/00install.out:


install for i386

* installing *source* package 'RiboProfiling' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling'

install for x64

* installing *source* package 'RiboProfiling' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling'
* MD5 sums
packaged installation of 'RiboProfiling' as RiboProfiling_1.3.2.zip
* DONE (RiboProfiling)

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

nameusersystemelapsed
aroundPromoter11.45 0.3611.81
codonInfo33.84 0.4434.37
codonPCA2.200.062.26
countShiftReads79.84 1.0080.98
countsPlot73.60 0.3674.07
histMatchLength5.090.085.18
orfRelativePos38.36 0.0638.44
plotSummarizedCov10.11 0.2510.36
printPCA1.840.001.84
readStartCov8.530.178.70
readsToStartOrEnd3.940.144.08
riboSeqFromBAM67.69 0.3568.08

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

nameusersystemelapsed
aroundPromoter11.20 0.5111.72
codonInfo27.35 0.5228.57
codonPCA2.210.052.37
countShiftReads81.69 1.0782.88
countsPlot78.70 0.3879.08
histMatchLength4.430.004.43
orfRelativePos38.78 0.0438.83
plotSummarizedCov10.98 0.0711.35
printPCA2.240.032.27
readStartCov7.840.188.03
readsToStartOrEnd3.500.113.60
riboSeqFromBAM72.57 0.1672.75