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BioC 3.5: CHECK report for chroGPS on oaxaca

This page was generated on 2017-03-04 16:44:48 -0500 (Sat, 04 Mar 2017).

Package 204/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 1.23.0
Oscar Reina
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chroGPS
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / 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 

Summary

Package: chroGPS
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chroGPS_1.23.0.tar.gz
StartedAt: 2017-03-04 00:33:23 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 00:35:59 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 155.1 seconds
RetCode: 0
Status:  OK 
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chroGPS_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chroGPS.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chroGPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chroGPS’ version ‘1.23.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘chroGPS’ 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
* 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
Missing or unexported object: ‘changepoint::cpt.method’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addVar: no visible global function definition for ‘lm’
addVar: no visible global function definition for ‘fitted’
addVar: no visible global function definition for ‘var’
addVar: no visible global function definition for ‘arrows’
addVar: no visible global function definition for ‘text’
avgdistpair: no visible global function definition for ‘%over%’
boostMDS: no visible global function definition for ‘cmdscale’
boostMDS : targetf: no visible global function definition for ‘dist’
boostMDS: no visible global function definition for ‘dist’
boostMDS: no visible global function definition for ‘lm’
chisqdist : <anonymous>: no visible global function definition for
  ‘RleList’
chisqdist : <anonymous> : <anonymous>: no visible global function
  definition for ‘Rle’
chisqdist2: no visible global function definition for ‘mclapply’
chisqdist2 : <anonymous> : <anonymous>: no visible global function
  definition for ‘chisq.test’
contour2dDP: no visible global function definition for ‘colors’
contour2dDP: no visible global function definition for ‘var’
contour2dDP: no visible binding for global variable ‘state’
contour2dDP: no visible binding for global variable ‘na.omit’
contour2dDP: no visible global function definition for ‘contour’
contour2dDP: no visible global function definition for ‘filled.contour’
domainDist: no visible global function definition for ‘boxplot’
getURL: no visible global function definition for ‘download.file’
getmodEncodeBS: no visible global function definition for
  ‘download.file’
getmodEncodeBS: no visible global function definition for ‘read.csv’
gff2RDList: no visible global function definition for ‘GenomicRanges’
gffRead: no visible global function definition for ‘read.table’
gps2xgmml: no visible global function definition for ‘col2hex’
plotContour: no visible global function definition for ‘contour’
preCalcGrid: no visible global function definition for ‘quantile’
preCalcGrid: no visible global function definition for ‘var’
premergeClusters: no visible global function definition for ‘dist’
premergeClusters: no visible global function definition for ‘points’
rdldist: no visible global function definition for ‘installed.packages’
realtanipair: no visible global function definition for ‘%over%’
splitMDS: no visible global function definition for ‘tail’
uniqueCount: no visible binding for global variable ‘u’
xgmml2d: no visible global function definition for ‘xmlOutputDOM’
xgmml2d: no visible global function definition for ‘saveXML’
xgmml3d: no visible global function definition for ‘xmlOutputDOM’
xgmml3d: no visible global function definition for ‘saveXML’
adjustPeaks,GRangesList: no visible binding for global variable ‘var’
clusGPS,distGPS-mds: no visible global function definition for
  ‘as.hclust’
clusGPS,distGPS-mds: no visible global function definition for ‘hclust’
clusGPS,distGPS-mds: no visible global function definition for
  ‘as.dist’
clusGPS,distGPS-mds : <anonymous>: no visible global function
  definition for ‘cutree’
distGPS,matrix: no visible global function definition for ‘dist’
distGPS,matrix: no visible global function definition for ‘cov’
distGPS,matrix: no visible global function definition for ‘mahalanobis’
gps2xgmml,mds: no visible global function definition for ‘col2hex’
mds,distGPS-mds: no visible global function definition for ‘dist’
mds,distGPS-mds: no visible global function definition for ‘cor’
mds,distGPS-missing: no visible global function definition for
  ‘cmdscale’
mds,distGPS-missing: no visible global function definition for
  ‘as.dist’
mds,distGPS-missing: no visible global function definition for ‘dist’
mds,distGPS-missing: no visible global function definition for ‘cor’
mergeClusters,list: no visible global function definition for ‘text’
mergeClusters,list: no visible global function definition for ‘axis’
mergeClusters,list: no visible global function definition for ‘points’
mergeClusters,list: no visible global function definition for ‘abline’
plot,clusGPS-ANY: no visible global function definition for
  ‘weighted.mean’
plot,clusGPS-ANY: no visible global function definition for ‘abline’
plot,clusGPS-ANY : <anonymous>: no visible global function definition
  for ‘weighted.mean’
plot,clusGPS-ANY: no visible global function definition for ‘rainbow’
plot,clusGPS-ANY: no visible global function definition for ‘contour’
plot,mds-ANY: no visible global function definition for
  ‘terrain.colors’
plot,mds-ANY: no visible global function definition for ‘text’
plot,mds-ANY: no visible global function definition for ‘plot3d’
plot,mds-ANY: no visible global function definition for ‘text3d’
plot,mds-ANY: no visible global function definition for ‘spheres3d’
procrustesAdj,mds-distGPS: no visible global function definition for
  ‘dist’
procrustesAdj,mds-distGPS: no visible global function definition for
  ‘cor’
Undefined global functions or variables:
  %over% GenomicRanges Rle RleList abline arrows as.dist as.hclust axis
  boxplot chisq.test cmdscale col2hex colors contour cor cov cutree
  dist download.file filled.contour fitted hclust installed.packages lm
  mahalanobis mclapply na.omit plot3d points quantile rainbow read.csv
  read.table saveXML spheres3d state tail terrain.colors text text3d u
  var weighted.mean xmlOutputDOM
Consider adding
  importFrom("grDevices", "colors", "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "arrows", "axis", "boxplot",
             "contour", "filled.contour", "points", "text")
  importFrom("stats", "as.dist", "as.hclust", "chisq.test", "cmdscale",
             "cor", "cov", "cutree", "dist", "fitted", "hclust", "lm",
             "mahalanobis", "na.omit", "quantile", "var",
             "weighted.mean")
  importFrom("utils", "download.file", "installed.packages", "read.csv",
             "read.table", "tail")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘gplots’
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/chroGPS.Rcheck/00check.log’
for details.


chroGPS.Rcheck/00install.out:

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

chroGPS.Rcheck/chroGPS-Ex.timings:

nameusersystemelapsed
addVar000
adjustPeaks0.0010.0000.000
boostMDS000
clusGPS-class0.0010.0010.001
clusGPS0.0010.0000.001
distGPS-class0.0010.0000.001
distGPS0.2750.0120.288
domainDist000
geneSetGPS0.0010.0000.001
getURL0.0010.0000.001
gff2RDList0.0010.0000.001
gps2xgmml0.0010.0000.000
mds-class0.0020.0010.001
mds0.0240.0030.027
mergeClusters0.0010.0000.001
procrustesAdj2.6170.0582.687
profileClusters0.0010.0010.001
s20.1840.0050.189
splitDistGPS-class0.0010.0000.001