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BioC 3.4: CHECK report for oligoClasses on malbec1

This page was generated on 2017-04-15 16:09:30 -0400 (Sat, 15 Apr 2017).

Package 860/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligoClasses 1.36.0
Benilton Carvalho and Robert Scharpf
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/oligoClasses
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  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: oligoClasses
Version: 1.36.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.36.0.tar.gz
StartedAt: 2017-04-15 00:12:33 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:15:47 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 193.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: oligoClasses.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/oligoClasses.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 ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doRedis’
* 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 ‘oligoClasses’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSequenceLengths: no visible binding for global variable ‘seqlengths’
pdPkgFromBioC: no visible binding for global variable ‘contrib.url’
pdPkgFromBioC: no visible global function definition for
  ‘available.packages’
pdPkgFromBioC: no visible global function definition for
  ‘install.packages’
chromosome,gSetList: no visible global function definition for
  ‘chromosomeList’
coerce,CNSet-CopyNumberSet: no visible global function definition for
  ‘totalCopynumber’
geometry,FeatureSet: no visible global function definition for ‘getPD’
Undefined global functions or variables:
  available.packages chromosomeList contrib.url getPD install.packages
  seqlengths totalCopynumber
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "install.packages")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY,ANY,ANY'
  generic '[' and siglist 'gSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
GenomeAnnotatedDataFrame-class 0.88   0.12   5.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.


oligoClasses.Rcheck/00install.out:

* installing *source* package ‘oligoClasses’ ...
** 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 (oligoClasses)

oligoClasses.Rcheck/oligoClasses-Ex.timings:

nameusersystemelapsed
AlleleSet-class0.3600.0000.361
AssayData-methods0.8520.0240.888
AssayDataList0.0040.0000.001
BeadStudioSet-class0.3520.0000.351
CNSet-class0.0360.0000.037
CopyNumberSet-class0.0280.0000.028
CopyNumberSet-methods0.1240.0280.155
FeatureSetExtensions-class0.1080.0000.110
GRanges-methods0.2520.0200.270
GenomeAnnotatedDataFrame-class0.8800.1205.696
GenomeAnnotatedDataFrameFrom-methods1.2760.0201.377
SnpSet-methods0.0400.0000.038
SnpSet2-class0.0280.0000.028
SnpSuperSet-class0.0600.0000.057
affyPlatforms0.0000.0000.001
batch0.0320.0000.033
celfileDate0.0240.0040.078
celfileName0.0000.0000.001
checkExists0.0080.0000.009
checkOrder0.3120.0040.328
chromosome-methods0.0040.0000.001
chromosome2integer0.0000.0000.001
clusterOpts0.0000.0000.001
data-efsExample0.0000.0000.002
data-scqsExample0.0000.0000.002
data-sfsExample0.0040.0000.001
data-sqsExample0.0000.0000.003
db000
ff_matrix0.0000.0000.001
ff_or_matrix-class0.0040.0000.001
fileConnections0.0000.0000.001
flags0.0400.0080.047
gSet-class0.0000.0000.001
gSetList-class0.0040.0000.001
genomeBuild0.0040.0000.003
geometry-methods0.6320.0000.633
getBar0.0040.0000.000
getSequenceLengths0.0960.0000.099
i2p_p2i0.0000.0000.001
integerMatrix0.0040.0000.000
is.ffmatrix0.0000.0000.001
isPackageLoaded0.0000.0000.001
kind0.1520.0040.158
largeObjects0.0000.0000.003
ldOpts0.0000.0000.001
library20.0320.0000.030
list.celfiles0.0120.0040.095
locusLevelData0.0880.0040.094
makeFeatureGRanges0.3760.0080.383
oligoSetExample0.1760.0040.179
pdPkgFromBioC0.0040.0000.001
requireAnnotation0.0000.0000.001
splitVec0.0040.0000.003