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BioC 3.1: CHECK report for DASiR on moscato2

This page was generated on 2015-10-09 09:30:18 -0700 (Fri, 09 Oct 2015).

Package 239/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DASiR 1.8.0
Oscar Flores , Anna Mantsoki
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/DASiR
Last Changed Rev: 106568 / Revision: 109384
Last Changed Date: 2015-07-20 04:51:15 -0700 (Mon, 20 Jul 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: DASiR
Version: 1.8.0
Command: rm -rf DASiR.buildbin-libdir DASiR.Rcheck && mkdir DASiR.buildbin-libdir DASiR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DASiR.buildbin-libdir DASiR_1.8.0.tar.gz >DASiR.Rcheck\00install.out 2>&1 && cp DASiR.Rcheck\00install.out DASiR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DASiR.buildbin-libdir --install="check:DASiR-install.out" --force-multiarch --no-vignettes --timings DASiR_1.8.0.tar.gz
StartedAt: 2015-10-09 01:00:05 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:02:47 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 162.4 seconds
RetCode: 0
Status:  OK  
CheckDir: DASiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DASiR.buildbin-libdir DASiR.Rcheck && mkdir DASiR.buildbin-libdir DASiR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DASiR.buildbin-libdir DASiR_1.8.0.tar.gz >DASiR.Rcheck\00install.out 2>&1 && cp DASiR.Rcheck\00install.out DASiR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DASiR.buildbin-libdir --install="check:DASiR-install.out" --force-multiarch --no-vignettes --timings DASiR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/DASiR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DASiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DASiR' version '1.8.0'
* 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 whether package 'DASiR' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages in Depends field not imported from:
  'Biostrings' 'GenomicRanges' 'IRanges' 'XML'
  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
.getCapabilities: no visible global function definition for 'xmlSize'
.getCapabilities: no visible global function definition for 'xmlAttrs'
.getFeature: no visible global function definition for 'xmlAttrs'
.getFeature: no visible global function definition for 'xmlSApply'
.getFeature: no visible binding for global variable 'xmlValue'
.getGroup: no visible global function definition for 'xmlAttrs'
.getSequence: no visible global function definition for 'xmlValue'
.getStructure: no visible global function definition for 'xmlAttrs'
.makeSegments: no visible global function definition for 'seqnames'
getDasDsn: no visible global function definition for 'xmlTreeParse'
getDasDsn: no visible global function definition for 'xmlRoot'
getDasDsn: no visible global function definition for 'xmlSApply'
getDasDsn : <anonymous>: no visible global function definition for
  'xmlAttrs'
getDasEntries: no visible global function definition for 'xmlTreeParse'
getDasEntries : <anonymous>: no visible global function definition for
  'htmlTreeParse'
getDasEntries: no visible global function definition for 'xmlRoot'
getDasEntries: no visible global function definition for 'xmlApply'
getDasEntries: no visible binding for global variable 'xmlAttrs'
getDasEntries: no visible global function definition for 'GRanges'
getDasEntries: no visible global function definition for 'IRanges'
getDasEntries: no visible global function definition for
  'elementMetadata<-'
getDasFeature: no visible global function definition for 'xmlTreeParse'
getDasFeature: no visible global function definition for 'xmlRoot'
getDasFeature: no visible global function definition for 'xmlSize'
getDasFeature: no visible global function definition for 'xmlApply'
getDasSequence: no visible global function definition for
  'xmlTreeParse'
getDasSequence: no visible global function definition for 'xmlRoot'
getDasSequence: no visible global function definition for 'xmlApply'
getDasSource: no visible global function definition for 'xmlTreeParse'
getDasSource: no visible global function definition for 'xmlRoot'
getDasSource: no visible global function definition for 'xmlSApply'
getDasSource : <anonymous>: no visible global function definition for
  'xmlAttrs'
getDasStructure: no visible global function definition for
  'xmlTreeParse'
getDasStructure: no visible global function definition for 'xmlRoot'
getDasStructure: no visible global function definition for 'xmlSApply'
getDasStructure: no visible binding for global variable 'xmlAttrs'
getDasTypes: no visible global function definition for 'xmlTreeParse'
getDasTypes: no visible global function definition for 'xmlRoot'
getDasTypes: no visible global function definition for 'xmlSApply'
getDasTypes : <anonymous>: no visible global function definition for
  'xmlAttrs'
plotFeatures: no visible global function definition for 'IRanges'
plotFeatures: no visible global function definition for 'disjointBins'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [21s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getDasStructure 2.53   0.02    5.19
DASiR-package   0.81   0.00    6.72
** running examples for arch 'x64' ... [23s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getDasStructure 4.14   0.02    5.30
DASiR-package   1.34   0.00    8.68
* 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/DASiR.Rcheck/00check.log'
for details.


DASiR.Rcheck/00install.out:


install for i386

* installing *source* package 'DASiR' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'DASiR' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'DASiR' as DASiR_1.8.0.zip
* DONE (DASiR)

DASiR.Rcheck/examples_i386/DASiR-Ex.timings:

nameusersystemelapsed
DASiR-package0.810.006.72
getDas-functions0.080.003.37
getDasFeature0.060.000.35
getDasSequence0.050.000.35
getDasStructure2.530.025.19
plotFeatures0.010.010.59

DASiR.Rcheck/examples_x64/DASiR-Ex.timings:

nameusersystemelapsed
DASiR-package1.340.008.68
getDas-functions0.160.001.95
getDasFeature0.060.000.36
getDasSequence0.060.000.36
getDasStructure4.140.025.30
plotFeatures0.040.000.58