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BioC 3.2: CHECK report for qcmetrics on moscato1

This page was generated on 2015-08-20 13:22:08 -0700 (Thu, 20 Aug 2015).

Package 793/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qcmetrics 1.7.0
Laurent Gatto
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/qcmetrics
Last Changed Rev: 102594 / Revision: 107602
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qcmetrics
Version: 1.7.0
Command: rm -rf qcmetrics.buildbin-libdir qcmetrics.Rcheck && mkdir qcmetrics.buildbin-libdir qcmetrics.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qcmetrics.buildbin-libdir qcmetrics_1.7.0.tar.gz >qcmetrics.Rcheck\00install.out 2>&1 && cp qcmetrics.Rcheck\00install.out qcmetrics-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=qcmetrics.buildbin-libdir --install="check:qcmetrics-install.out" --force-multiarch --no-vignettes --timings qcmetrics_1.7.0.tar.gz
StartedAt: 2015-08-20 09:01:56 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 09:03:55 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 119.5 seconds
RetCode: 0
Status:  OK  
CheckDir: qcmetrics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf qcmetrics.buildbin-libdir qcmetrics.Rcheck && mkdir qcmetrics.buildbin-libdir qcmetrics.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=qcmetrics.buildbin-libdir qcmetrics_1.7.0.tar.gz >qcmetrics.Rcheck\00install.out 2>&1 && cp qcmetrics.Rcheck\00install.out qcmetrics-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=qcmetrics.buildbin-libdir --install="check:qcmetrics-install.out" --force-multiarch --no-vignettes --timings qcmetrics_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/qcmetrics.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 'qcmetrics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qcmetrics' version '1.7.0'
* 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 'qcmetrics' 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
* 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
'library' or 'require' calls in package code:
  'affy' 'ggplot2' 'yaqcaffy'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
n15qc: no visible global function definition for 'fvarLabels'
n15qc: no visible global function definition for 'fData'
n15qc : <anonymous>: no visible global function definition for 'ggplot'
n15qc : <anonymous>: no visible global function definition for 'aes'
n15qc : <anonymous>: no visible global function definition for
  'geom_jitter'
n15qc : <anonymous>: no visible global function definition for
  'geom_boxplot'
n15qc : <anonymous>: no visible global function definition for
  'geom_hline'
n15qc : <anonymous>: no visible global function definition for 'labs'
n15qc: no visible global function definition for 'fData<-'
n15qc: no visible global function definition for 'combineFeatures'
n15qc: no visible global function definition for 'exprs'
n15qc: no visible global function definition for 'fileNames'
n15qc: no visible global function definition for 'experimentData'
rnadeg: no visible global function definition for 'ReadAffy'
rnadeg: no visible global function definition for 'AffyRNAdeg'
rnadeg : <anonymous>: no visible global function definition for
  'plotAffyRNAdeg'
rnadeg: no visible global function definition for 'yaqc'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [12s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
qcReport-methods 1.55   0.07    5.25
** running examples for arch 'x64' ... [11s] 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/qcmetrics.Rcheck/00check.log'
for details.


qcmetrics.Rcheck/00install.out:


install for i386

* installing *source* package 'qcmetrics' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'qcmetrics'
Creating a generic function for 'plot' from package 'graphics' in package 'qcmetrics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'qcmetrics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qcmetrics' as qcmetrics_1.7.0.zip
* DONE (qcmetrics)

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

nameusersystemelapsed
QcMetadata-class0.020.000.02
QcMetric-class0.000.010.01
QcMetrics-class0.060.000.06
psm4.010.074.08
qcReport-methods1.550.075.25

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

nameusersystemelapsed
QcMetadata-class0.000.010.02
QcMetric-class0.020.000.01
QcMetrics-class0.080.000.08
psm4.430.144.59
qcReport-methods1.440.053.75