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BioC 3.5: CHECK report for TurboNorm on oaxaca

This page was generated on 2017-03-04 16:40:19 -0500 (Sat, 04 Mar 2017).

Package 1300/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TurboNorm 1.23.0
Maarten van Iterson
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TurboNorm
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: TurboNorm
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TurboNorm_1.23.0.tar.gz
StartedAt: 2017-03-04 10:16:07 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 10:17:36 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 89.2 seconds
RetCode: 0
Status:  OK 
CheckDir: TurboNorm.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TurboNorm_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TurboNorm.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TurboNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TurboNorm’ version ‘1.23.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TurboNorm’ 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
* 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
Packages in Depends field not imported from:
  ‘convert’ ‘limma’ ‘marray’
  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
normalize.AffyBatch.pspline: no visible global function definition for
  ‘intensity<-’
pspline: no visible global function definition for ‘as’
pspline: no visible global function definition for ‘maRb<-’
pspline: no visible global function definition for ‘maGb<-’
pspline: no visible global function definition for ‘maA’
pspline: no visible global function definition for ‘maM’
pspline: no visible global function definition for ‘layout’
pspline: no visible global function definition for ‘maM<-’
pspline: no visible global function definition for ‘plot’
pspline: no visible global function definition for ‘lines’
turbotrend: no visible global function definition for ‘median’
Undefined global functions or variables:
  as intensity<- layout lines maA maGb<- maM maM<- maRb<- median plot
Consider adding
  importFrom("graphics", "layout", "lines", "plot")
  importFrom("methods", "as")
  importFrom("stats", "median")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
normalize.pspline 25.37  0.902  26.619
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/TurboNorm.Rcheck/00check.log’
for details.


TurboNorm.Rcheck/00install.out:

* installing *source* package ‘TurboNorm’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Rinit.c -o Rinit.o
Rinit.c:11:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  NULL
  ^˜˜˜
  {   }
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stddef.h:77:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c binners.c -o binners.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o TurboNorm.so Rinit.o binners.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/TurboNorm.Rcheck/TurboNorm/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TurboNorm)

TurboNorm.Rcheck/TurboNorm-Ex.timings:

nameusersystemelapsed
methylation0.0910.0070.097
normalize.pspline25.370 0.90226.619
panel.pspline2.2630.1972.712
pspline2.0310.1252.176
turbotrend0.5650.0610.633