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BioC 2.14: CHECK report for QUALIFIER on moscato2

This page was generated on 2014-10-08 08:54:32 -0700 (Wed, 08 Oct 2014).

Package 619/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QUALIFIER 1.8.23
Mike Jiang
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/QUALIFIER
Last Changed Rev: 91344 / Revision: 95116
Last Changed Date: 2014-06-12 16:06:19 -0700 (Thu, 12 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: QUALIFIER
Version: 1.8.23
Command: rm -rf QUALIFIER.buildbin-libdir && mkdir QUALIFIER.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QUALIFIER.buildbin-libdir QUALIFIER_1.8.23.tar.gz >QUALIFIER-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=QUALIFIER.buildbin-libdir --install="check:QUALIFIER-install.out" --force-multiarch --no-vignettes --timings QUALIFIER_1.8.23.tar.gz
StartedAt: 2014-10-08 04:10:01 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 04:12:43 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 162.0 seconds
RetCode: 0
Status:  OK  
CheckDir: QUALIFIER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QUALIFIER.buildbin-libdir && mkdir QUALIFIER.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QUALIFIER.buildbin-libdir QUALIFIER_1.8.23.tar.gz >QUALIFIER-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=QUALIFIER.buildbin-libdir --install="check:QUALIFIER-install.out" --force-multiarch --no-vignettes --timings QUALIFIER_1.8.23.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/QUALIFIER.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QUALIFIER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QUALIFIER' version '1.8.23'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'flowCore' 'flowViz' 'ncdfFlow' 'flowWorkspace' 'data.table'
  'reshape'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'QUALIFIER' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'flowCore' 'flowViz' 'flowWorkspace'
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  'flowViz' 'grDevices' 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'data.table' 'flowCore' 'flowViz' 'ncdfFlow' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'flowWorkspace:::mkformula'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'flowCore:::findTimeChannel' 'flowCore:::prepareSet'
  'flowWorkspace:::.formulaParser' 'flowWorkspace:::.getNodeInd'
  'flowWorkspace:::.getPopStat' 'lattice:::calculateGridLayout'
  'lattice:::checkArgsAndCall' 'lattice:::chooseFace'
  'lattice:::compute.layout' 'lattice:::drawInViewport'
  'lattice:::evaluate.legend' 'lattice:::getFunctionOrName'
  'lattice:::getLabelList' 'lattice:::grobFromLabelList'
  'lattice:::lattice.getStatus' 'lattice:::lattice.setStatus'
  'lattice:::layoutNCol' 'lattice:::layoutNRow'
  'lattice:::paste.and.draw' 'lattice:::updateList'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'getName' 'height' 'width'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
.addStats: no visible binding for global variable 'value'
.addStats: no visible binding for global variable 'stats'
.addStats: no visible binding for global variable 'sid'
.addStats: no visible binding for global variable 'channel'
.addStats: no visible binding for global variable 'stain'
.addStats: no visible binding for global variable 'population'
.addStats: no visible binding for global variable 'node'
.getQAStats.env: no visible binding for global variable 'sid'
.getQAStats.gh : <anonymous>: no visible binding for global variable
  'node'
.getQAStats.gh : <anonymous>: no visible binding for global variable
  'population'
.qaCheck : .funcOutlierGrp: no visible binding for global variable 'V1'
.qaCheck : .funcOutlierGrp: no visible binding for global variable
  'sid'
.qaCheck: no visible binding for global variable 'V1'
.qaCheck : .funcOutlier: no visible binding for global variable 'sid'
.queryStats: no visible binding for global variable 'stats'
.read.qaTask : <anonymous>: no visible binding for global variable
  'aoutlierFunc_args'
load_db: no visible global function definition for 'l_ply'
panel.bwplotEx: no visible binding for global variable 'outlier'
panel.bwplotEx: no visible binding for global variable 'gOutlier'
plot.qaTask: no visible binding for global variable 'outlier'
plot.qaTask: no visible binding for global variable 'gOutlier'
qa.GroupPlot : <anonymous>: no visible binding for global variable
  'channel'
qa.GroupPlot: no visible binding for global variable 'name'
saveToDB: no visible binding for global variable 'name'
save_db: no visible global function definition for 'l_ply'
* 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' ... [6s] OK
** running examples for arch 'x64' ... [5s] 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

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/QUALIFIER.Rcheck/00check.log'
for details.

QUALIFIER.Rcheck/00install.out:


install for i386

* installing *source* package 'QUALIFIER' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'QUALIFIER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QUALIFIER' as QUALIFIER_1.8.23.zip
* DONE (QUALIFIER)

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

nameusersystemelapsed
getQAStats000
initDB000
plot-methods000
qaCheck-methods000
qaPreprocess000
qaReport000
read.qaTask000
saveToDB000
save_db000

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

nameusersystemelapsed
getQAStats000
initDB000
plot-methods0.020.000.02
qaCheck-methods000
qaPreprocess000
qaReport000
read.qaTask000
saveToDB000
save_db000