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CHECK report for TurboNorm on machv2

This page was generated on 2020-10-17 11:59:50 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TurboNorm PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1846/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TurboNorm 1.36.0
Maarten van Iterson
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TurboNorm
Branch: RELEASE_3_11
Last Commit: b09fa5a
Last Changed Date: 2020-04-27 14:23:54 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TurboNorm
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TurboNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TurboNorm_1.36.0.tar.gz
StartedAt: 2020-10-17 06:07:32 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:09:25 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 113.3 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 --install=check:TurboNorm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TurboNorm_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TurboNorm.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.36.0’
* 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 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 ‘lines’
turbotrend: no visible global function definition for ‘median’
Undefined global functions or variables:
  as intensity<- layout lines maA maGb<- maM maM<- maRb<- median
Consider adding
  importFrom("graphics", "layout", "lines")
  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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
normalize.pspline 23.863  1.401  25.401
panel.pspline     12.224  0.279  12.523
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/TurboNorm.Rcheck/00check.log’
for details.



Installation output

TurboNorm.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TurboNorm
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘TurboNorm’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
Rinit.c:11:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  NULL
  ^~~~
  {   }
/Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^~~~~~~~~~
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c binners.c -o binners.o
clang -mmacosx-version-min=10.13 -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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-TurboNorm/00new/TurboNorm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TurboNorm)

Tests output


Example timings

TurboNorm.Rcheck/TurboNorm-Ex.timings

nameusersystemelapsed
methylation0.1140.0090.125
normalize.pspline23.863 1.40125.401
panel.pspline12.224 0.27912.523
pspline3.4630.1203.594
turbotrend1.0920.0471.148