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BioC 3.3: CHECK report for Biobase on zin2

This page was generated on 2016-10-13 12:40:29 -0700 (Thu, 13 Oct 2016).

Package 99/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.32.0
Bioconductor Package Maintainer
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/Biobase
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biobase
Version: 2.32.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.32.0.tar.gz
StartedAt: 2016-10-12 23:50:10 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:51:23 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 73.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.32.0’
* 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 ‘Biobase’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
openVignette: no visible global function definition for ‘menu’
package.version: no visible global function definition for
  ‘packageDescription’
read.AnnotatedDataFrame: no visible global function definition for
  ‘read.table’
readExpressionSet: no visible binding for global variable ‘read.table’
write.AnnotatedDataFrame: no visible global function definition for
  ‘write.table’
write.exprs,ExpressionSet: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  menu packageDescription read.table write.table
Consider adding
  importFrom("utils", "menu", "packageDescription", "read.table",
             "write.table")
to your NAMESPACE file.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
  Running ‘test-rowMedians.R’
 OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck/00check.log’
for details.


Biobase.Rcheck/00install.out:

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biobase)

Biobase.Rcheck/Biobase-Ex.timings:

nameusersystemelapsed
Aggregate0.0060.0030.008
ScalarObject-class0.0090.0010.010
addVig2Menu000
anyMissing0.0010.0030.002
cache0.0010.0010.004
channel0.0910.0000.091
channelNames0.0450.0070.053
class.AnnotatedDataFrame0.0210.0040.025
class.ExpressionSet0.1900.0040.194
class.MIAxE0.0150.0000.015
class.MultiSet0.0260.0000.026
class.NChannelSet0.1400.0120.152
class.Versioned0.050.000.05
class.VersionedBiobase0.0230.0000.023
class.Versions0.0120.0040.016
class.VersionsNull0.0010.0000.001
class.container0.0010.0030.003
class.eSet0.0700.0010.073
classVersion0.0060.0000.006
contents0.0010.0000.001
copyEnv000
copySubstitute0.0100.0000.011
createPackage0.0060.0000.005
data.aaMap0.0020.0000.002
data.geneData0.0270.0000.027
data.reporter0.0020.0000.001
data.sample.ExpressionSet0.060.000.06
data.sample.MultiSet0.0040.0000.005
dumpPackTxt0.0020.0000.008
esApply1.1200.0361.155
getPkgVigs0.0060.0040.730
isCurrent0.0270.0000.026
isUnique000
isVersioned0.010.000.01
lcSuffix0.0020.0000.002
listLen0.0010.0000.001
makeDataPackage0.0600.0000.059
matchpt0.0040.0000.005
multiassign0.0010.0000.002
note0.0010.0000.001
openPDF0.0010.0000.000
openVignette000
package.version0.0010.0000.001
read.AnnotatedDataFrame0.0140.0000.014
read.MIAME0.0010.0000.002
readExpressionSet0.0460.0000.046
reverseSplit0.0010.0000.001
rowMedians0.0450.0000.045
rowQ0.0120.0070.018
selectChannels0.0390.0000.040
selectSome0.0010.0010.000
strbreak0.0010.0000.001
subListExtract0.7700.0000.769
testBioCConnection0.0100.0000.492
updateOldESet0.0000.0000.001
validMsg000