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This page was generated on 2021-12-03 13:05:40 -0500 (Fri, 03 Dec 2021).

CHECK results for BicARE on machv2

To the developers/maintainers of the BicARE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BicARE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 145/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BicARE 1.52.0  (landing page)
Pierre Gestraud
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/BicARE
git_branch: RELEASE_3_14
git_last_commit: 1c04ed8
git_last_commit_date: 2021-10-26 11:53:14 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BicARE
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BicARE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BicARE_1.52.0.tar.gz
StartedAt: 2021-12-02 12:02:56 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 12:14:30 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 694.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BicARE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BicARE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BicARE_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BicARE.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BicARE/DESCRIPTION’ ... OK
* this is package ‘BicARE’ version ‘1.52.0’
* 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 ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BicARE/libs/BicARE.so’:
  Found ‘_printf’, 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 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
testSet 493.159  1.688 496.612
FLOC     30.611  0.051  30.699
* 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-3.14-bioc/meat/BicARE.Rcheck/00check.log’
for details.



Installation output

BicARE.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BicARE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BicARE’ ...
** 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 BicARE.c -o BicARE.o
BicARE.c:439:12: warning: unused variable 'invk' [-Wunused-variable]
    double invk = 1/(double)*k;
           ^
1 warning generated.
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 BicARE.so BicARE.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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
FLOC30.611 0.05130.699
bicluster0.4550.0100.466
makeReport3.7980.2294.053
residue0.0050.0020.006
testAnnot0.0210.0030.024
testSet493.159 1.688496.612