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 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch QUALIFIER_1.8.23.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/QUALIFIER.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘QUALIFIER’ can be installed ... [20s/20s] 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
* 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’
save_db: no visible global function definition for ‘l_ply’
saveToDB: no visible binding for global variable ‘name’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] 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
‘/Users/biocbuild/bbs-2.14-bioc/meat/QUALIFIER.Rcheck/00check.log’
for details.