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CHECK report for BicARE on malbec1

This page was generated on 2020-10-21 12:05:42 -0400 (Wed, 21 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BicARE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 140/1939HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BicARE 1.47.0
Pierre Gestraud
Snapshot Date: 2020-10-20 14:40:34 -0400 (Tue, 20 Oct 2020)
URL: https://git.bioconductor.org/packages/BicARE
Branch: master
Last Commit: 45cb7bc
Last Changed Date: 2020-04-27 14:18:27 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BicARE
Version: 1.47.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BicARE.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BicARE_1.47.0.tar.gz
StartedAt: 2020-10-21 00:23:20 -0400 (Wed, 21 Oct 2020)
EndedAt: 2020-10-21 00:34:10 -0400 (Wed, 21 Oct 2020)
EllapsedTime: 650.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BicARE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BicARE.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BicARE_1.47.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BicARE.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BicARE/DESCRIPTION’ ... OK
* this is package ‘BicARE’ version ‘1.47.0’
* 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 ‘BicARE’ 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘GSEABase’ ‘multtest’
  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
FLOC: no visible global function definition for ‘new’
FLOC: no visible global function definition for ‘exprs’
FLOC: no visible global function definition for ‘runif’
FLOC: no visible binding for global variable ‘var’
bicluster: no visible global function definition for ‘exprs’
bicluster: no visible global function definition for ‘featureNames’
bicluster: no visible global function definition for ‘sampleNames’
makeReport: no visible global function definition for ‘annotation’
makeReport: no visible global function definition for ‘png’
makeReport: no visible global function definition for ‘dev.off’
makeReport: no visible global function definition for ‘getSYMBOL’
makeReport: no visible global function definition for ‘setName’
makeReport: no visible global function definition for ‘browseURL’
plot.bicluster: no visible global function definition for ‘par’
plot.bicluster: no visible global function definition for ‘matplot’
plot.bicluster: no visible global function definition for ‘axis’
residue: no visible global function definition for ‘new’
residue: no visible global function definition for ‘exprs’
testAnnot: no visible global function definition for ‘pData’
testAnnot: no visible global function definition for ‘phenoData’
testAnnot: no visible global function definition for ‘chisq.test’
testAnnot: no visible global function definition for ‘mt.rawp2adjp’
testSet: no visible global function definition for ‘exprs’
testSet: no visible global function definition for ‘GeneSet’
testSet: no visible global function definition for ‘geneIdType’
testSet: no visible global function definition for ‘geneIds’
testSet: no visible global function definition for ‘mapIdentifiers’
testSet: no visible global function definition for ‘phyper’
testSet: no visible global function definition for ‘mt.rawp2adjp’
Undefined global functions or variables:
  GeneSet annotation axis browseURL chisq.test dev.off exprs
  featureNames geneIdType geneIds getSYMBOL mapIdentifiers matplot
  mt.rawp2adjp new pData par phenoData phyper png runif sampleNames
  setName var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "chisq.test", "phyper", "runif", "var")
  importFrom("utils", "browseURL")
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
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/BicARE/libs/BicARE.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
testSet 496.920  0.340 504.680
FLOC     34.224  0.008  34.321
* 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-3.12-bioc/meat/BicARE.Rcheck/00check.log’
for details.



Installation output

BicARE.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BicARE
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BicARE’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c BicARE.c -o BicARE.o
BicARE.c: In function ‘floc’:
BicARE.c:439:12: warning: unused variable ‘invk’ [-Wunused-variable]
     double invk = 1/(double)*k;
            ^~~~
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o BicARE.so BicARE.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-BicARE/00new/BicARE/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 (BicARE)

Tests output


Example timings

BicARE.Rcheck/BicARE-Ex.timings

nameusersystemelapsed
FLOC34.224 0.00834.321
bicluster0.3000.0000.301
makeReport2.7400.1043.008
residue0.0040.0000.003
testAnnot0.0160.0000.014
testSet496.92 0.34504.68