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CHECK report for iBBiG on celaya2

This page was generated on 2019-10-16 12:50:03 -0400 (Wed, 16 Oct 2019).

Package 782/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iBBiG 1.28.0
Aedin Culhane
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/iBBiG
Branch: RELEASE_3_9
Last Commit: 69ee95b
Last Changed Date: 2019-05-02 11:53:35 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: iBBiG
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iBBiG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iBBiG_1.28.0.tar.gz
StartedAt: 2019-10-16 03:44:15 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:46:34 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 139.0 seconds
RetCode: 0
Status:  OK 
CheckDir: iBBiG.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iBBiG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iBBiG_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/iBBiG.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iBBiG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iBBiG’ version ‘1.28.0’
* 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 ‘iBBiG’ 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
* 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
'library' or 'require' call to ‘biclust’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addSignal: no visible global function definition for ‘runif’
iBBiG: no visible global function definition for ‘new’
makeArtificial: no visible global function definition for ‘runif’
makeArtificial: no visible global function definition for ‘new’
Clusterscores,iBBiG: no visible global function definition for ‘slot’
Clusterscores<-,iBBiG: no visible global function definition for
  ‘slot<-’
Clusterscores<-,iBBiG: no visible global function definition for
  ‘validObject’
Number,iBBiG: no visible global function definition for ‘slot’
Number<-,iBBiG: no visible global function definition for ‘slot<-’
Number<-,iBBiG: no visible global function definition for ‘validObject’
NumberxCol,iBBiG: no visible global function definition for ‘slot’
NumberxCol<-,iBBiG: no visible global function definition for ‘slot<-’
NumberxCol<-,iBBiG: no visible global function definition for
  ‘validObject’
Parameters,iBBiG: no visible global function definition for ‘slot’
Parameters<-,iBBiG: no visible global function definition for ‘slot<-’
Parameters<-,iBBiG: no visible global function definition for
  ‘validObject’
RowScorexNumber,iBBiG: no visible global function definition for ‘slot’
RowScorexNumber<-,iBBiG: no visible global function definition for
  ‘slot<-’
RowScorexNumber<-,iBBiG: no visible global function definition for
  ‘validObject’
RowxNumber,iBBiG: no visible global function definition for ‘slot’
RowxNumber<-,iBBiG: no visible global function definition for ‘slot<-’
RowxNumber<-,iBBiG: no visible global function definition for
  ‘validObject’
Seeddata,iBBiG: no visible global function definition for ‘slot’
Seeddata<-,iBBiG: no visible global function definition for ‘slot<-’
Seeddata<-,iBBiG: no visible global function definition for
  ‘validObject’
analyzeClust,Biclust-iBBiG: no visible global function definition for
  ‘as’
analyzeClust,list-iBBiG: no visible global function definition for
  ‘new’
coerce,Biclust-iBBiG: no visible global function definition for ‘new’
info,iBBiG: no visible global function definition for ‘slot’
info<-,iBBiG: no visible global function definition for ‘slot<-’
info<-,iBBiG: no visible global function definition for ‘validObject’
plot,iBBiG-ANY: no visible global function definition for ‘layout’
plot,iBBiG-ANY: no visible global function definition for ‘colors’
plot,iBBiG-ANY: no visible global function definition for ‘image’
plot,iBBiG-ANY: no visible global function definition for ‘legend’
plot,iBBiG-ANY: no visible binding for global variable ‘title’
plot,iBBiG-ANY: no visible global function definition for ‘title’
plot,iBBiG-ANY: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  as barplot colors image layout legend new runif slot slot<- title
  validObject
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "barplot", "image", "layout", "legend", "title")
  importFrom("methods", "as", "new", "slot", "slot<-", "validObject")
  importFrom("stats", "runif")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/iBBiG/libs/iBBiG.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
iBBiG-package 26.166  0.258  26.428
iBBiG         25.470  0.180  25.661
iBBiG-class   23.852  0.270  24.127
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/iBBiG.Rcheck/00check.log’
for details.



Installation output

iBBiG.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL iBBiG
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘iBBiG’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_init_iBBiG.c -o R_init_iBBiG.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c iBBiG.c -o iBBiG.o
iBBiG.c:300:22: warning: implicit declaration of function 'time' is invalid in C99 [-Wimplicit-function-declaration]
     srand((unsigned)time(NULL));               
                     ^
1 warning generated.
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 iBBiG.so R_init_iBBiG.o iBBiG.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-iBBiG/00new/iBBiG/libs
** R
** 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 (iBBiG)

Tests output


Example timings

iBBiG.Rcheck/iBBiG-Ex.timings

nameusersystemelapsed
iBBiG-class23.852 0.27024.127
iBBiG-package26.166 0.25826.428
iBBiG25.470 0.18025.661
makeArtificial0.6120.0650.685