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BioC 3.4: CHECK report for iBBiG on malbec1

This page was generated on 2017-04-15 16:10:51 -0400 (Sat, 15 Apr 2017).

Package 609/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iBBiG 1.18.0
Aedin Culhane
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/iBBiG
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: iBBiG
Version: 1.18.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iBBiG_1.18.0.tar.gz
StartedAt: 2017-04-14 23:14:55 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:16:36 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 101.3 seconds
RetCode: 0
Status:  OK 
CheckDir: iBBiG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iBBiG_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/iBBiG.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 loading without being on the library search path ... 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
File ‘iBBiG/libs/iBBiG.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘iBBiG.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘iBBiG.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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
iBBiG         27.428  0.008  27.457
iBBiG-class   23.884  0.008  23.908
iBBiG-package 22.724  0.012  22.752
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/iBBiG.Rcheck/00check.log’
for details.

iBBiG.Rcheck/00install.out:

* installing *source* package ‘iBBiG’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_iBBiG.c -o R_init_iBBiG.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c iBBiG.c -o iBBiG.o
iBBiG.c: In function ‘clusterCovsC’:
iBBiG.c:300:22: warning: implicit declaration of function ‘time’ [-Wimplicit-function-declaration]
      srand((unsigned)time(NULL));     
                      ^
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o iBBiG.so R_init_iBBiG.o iBBiG.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/iBBiG.Rcheck/iBBiG/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iBBiG)

iBBiG.Rcheck/iBBiG-Ex.timings:

nameusersystemelapsed
iBBiG-class23.884 0.00823.908
iBBiG-package22.724 0.01222.752
iBBiG27.428 0.00827.457
makeArtificial0.6480.0160.665