chroGPS 1.17.0
Oscar Reina
| Snapshot Date: 2016-06-06 16:20:08 -0700 (Mon, 06 Jun 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chroGPS | | Last Changed Rev: 117081 / Revision: 118222 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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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### rm -rf chroGPS.buildbin-libdir chroGPS.Rcheck && mkdir chroGPS.buildbin-libdir chroGPS.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chroGPS.buildbin-libdir chroGPS_1.17.0.tar.gz >chroGPS.Rcheck\00install.out 2>&1 && cp chroGPS.Rcheck\00install.out chroGPS-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=chroGPS.buildbin-libdir --install="check:chroGPS-install.out" --force-multiarch --no-vignettes --timings chroGPS_1.17.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/chroGPS.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chroGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chroGPS' version '1.17.0'
* 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 '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
* 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
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 'arrows'
addVar: no visible global function definition for 'text'
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> : <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 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'
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'
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'
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'
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 'mahalanobis'
gps2xgmml,mds: no visible global function definition for 'col2hex'
mds,distGPS-mds: no visible global function definition for 'dist'
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'
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'
Undefined global functions or variables:
Rle abline arrows as.dist as.hclust axis boxplot chisq.test cmdscale
col2hex colors contour cutree dist download.file filled.contour
fitted hclust installed.packages lm mahalanobis mclapply na.omit
plot3d points rainbow read.csv read.table saveXML spheres3d state
tail terrain.colors text text3d u 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",
"cutree", "dist", "fitted", "hclust", "lm", "mahalanobis",
"na.omit", "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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
'D:/biocbld/bbs-3.4-bioc/meat/chroGPS.Rcheck/00check.log'
for details.