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BioC 3.4: CHECK report for massiR on moscato1

This page was generated on 2016-09-21 03:45:39 -0700 (Wed, 21 Sep 2016).

Package 693/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
massiR 1.9.0
Sam Buckberry
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/massiR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: massiR
Version: 1.9.0
Command: rm -rf massiR.buildbin-libdir massiR.Rcheck && mkdir massiR.buildbin-libdir massiR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=massiR.buildbin-libdir massiR_1.9.0.tar.gz >massiR.Rcheck\00install.out 2>&1 && cp massiR.Rcheck\00install.out massiR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=massiR.buildbin-libdir --install="check:massiR-install.out" --force-multiarch --no-vignettes --timings massiR_1.9.0.tar.gz
StartedAt: 2016-09-20 11:31:32 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:32:34 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 62.2 seconds
RetCode: 0
Status:  OK  
CheckDir: massiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf massiR.buildbin-libdir massiR.Rcheck && mkdir massiR.buildbin-libdir massiR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=massiR.buildbin-libdir massiR_1.9.0.tar.gz >massiR.Rcheck\00install.out 2>&1 && cp massiR.Rcheck\00install.out massiR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=massiR.buildbin-libdir --install="check:massiR-install.out" --force-multiarch --no-vignettes --timings massiR_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/massiR.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 'massiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'massiR' version '1.9.0'
* 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 'massiR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
massi_cluster: no visible binding for global variable 'sd'
massi_cluster_plot: no visible global function definition for 'dev.new'
massi_cluster_plot: no visible global function definition for 'barplot'
massi_cluster_plot: no visible global function definition for
  'segments'
massi_cluster_plot: no visible global function definition for 'legend'
massi_dip: no visible global function definition for 'density'
massi_select : cal.cv: no visible global function definition for 'sd'
massi_select: no visible global function definition for 'quantile'
massi_y : cal.cv: no visible global function definition for 'sd'
massi_y: no visible global function definition for 'quantile'
massi_y_plot: no visible global function definition for 'dev.new'
massi_y_plot: no visible global function definition for 'barplot'
massi_y_plot: no visible global function definition for 'abline'
massi_y_plot: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline barplot density dev.new legend quantile sd segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "segments")
  importFrom("stats", "density", "quantile", "sd")
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 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/massiR.Rcheck/00check.log'
for details.


massiR.Rcheck/00install.out:


install for i386

* installing *source* package 'massiR' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'massiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'massiR' as massiR_1.9.0.zip
* DONE (massiR)

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

nameusersystemelapsed
massi.test.dataset0.000.020.10
massi.test.probes000
massiR-package0.140.000.22
massi_cluster0.030.010.05
massi_cluster_plot0.190.020.20
massi_dip0.030.010.08
massi_select0.030.000.03
massi_y0.020.000.02
massi_y_plot0.030.020.08
y_probes000

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

nameusersystemelapsed
massi.test.dataset0.010.010.17
massi.test.probes000
massiR-package0.140.030.30
massi_cluster0.030.000.03
massi_cluster_plot0.210.030.24
massi_dip0.010.020.03
massi_select0.030.020.04
massi_y0.020.000.02
massi_y_plot0.050.000.06
y_probes000