HCsnip 1.16.0
Askar Obulkasim
| Snapshot Date: 2017-06-22 17:17:32 -0400 (Thu, 22 Jun 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/HCsnip | | Last Changed Rev: 129126 / Revision: 130624 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf HCsnip.buildbin-libdir HCsnip.Rcheck && mkdir HCsnip.buildbin-libdir HCsnip.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HCsnip.buildbin-libdir HCsnip_1.16.0.tar.gz >HCsnip.Rcheck\00install.out 2>&1 && cp HCsnip.Rcheck\00install.out HCsnip-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=HCsnip.buildbin-libdir --install="check:HCsnip-install.out" --force-multiarch --no-vignettes --timings HCsnip_1.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/HCsnip.Rcheck'
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HCsnip/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HCsnip' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'survival' 'coin' 'fpc' 'clusterRepro' 'impute' 'randomForestSRC'
'sm' 'sigaR' 'Biobase'
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 'HCsnip' 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
Packages in Depends field not imported from:
'Biobase' 'clusterRepro' 'coin' 'fpc' 'impute' 'randomForestSRC'
'sigaR' 'sm' 'survival'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plot_KM: no visible global function definition for 'lines'
.plot_KM: no visible global function definition for 'plot'
.plot_KM: no visible global function definition for 'legend'
.test_pred: no visible global function definition for 'cor'
.test_pred: no visible global function definition for 'coxph'
.test_pred: no visible global function definition for 'coef'
EnvioPlot: no visible global function definition for 'exprs'
EnvioPlot: no visible global function definition for 'hdEntropy'
EnvioPlot: no visible global function definition for 'quantile'
EnvioPlot: no visible global function definition for 'median'
EnvioPlot: no visible global function definition for 'plot.new'
EnvioPlot: no visible global function definition for 'plot.window'
EnvioPlot: no visible global function definition for 'axis'
EnvioPlot: no visible global function definition for 'box'
EnvioPlot: no visible global function definition for 'polygon'
EnvioPlot: no visible global function definition for 'lines'
EnvioPlot: no visible global function definition for 'rect'
EnvioPlot: no visible global function definition for 'points'
EnvioPlot: no visible global function definition for 'title'
HCsnipper: no visible global function definition for 'hclust'
HCsnipper: no visible global function definition for 'as.dist'
HCsnipper: no visible global function definition for 'cor'
HCsnipper: no visible global function definition for 'dist'
HCsnipper: no visible global function definition for 'tail'
HCsnipper: no visible global function definition for 'cutree'
RSF_eval: no visible global function definition for 'rfsrc'
RSF_eval: no visible global function definition for 'predict.rfsrc'
TwoHC_assign: no visible global function definition for 'exprs'
TwoHC_perm : wrapper: no visible global function definition for 'coxph'
TwoHC_perm : wrapper: no visible global function definition for 'coef'
TwoHC_perm: no visible global function definition for 'coxph'
TwoHC_perm : <anonymous>: no visible global function definition for
'median'
TwoHC_perm: no visible global function definition for 'sd'
cluster_pred: no visible global function definition for 'exprs'
cluster_pred: no visible global function definition for 'as.dist'
cluster_pred: no visible global function definition for 'cor'
cluster_pred: no visible global function definition for 'hclust'
cluster_pred : <anonymous>: no visible global function definition for
'cor'
cluster_pred: no visible global function definition for 'pvalue'
cluster_pred: no visible global function definition for 'surv_test'
measure: no visible global function definition for 'cluster.stats'
measure: no visible global function definition for 'IGP.clusterRepro'
perm_test: no visible global function definition for 'pvalue'
perm_test: no visible global function definition for 'surv_test'
surv_measure: no visible global function definition for 'coxph'
Undefined global functions or variables:
IGP.clusterRepro as.dist axis box cluster.stats coef cor coxph cutree
dist exprs hclust hdEntropy legend lines median plot plot.new
plot.window points polygon predict.rfsrc pvalue quantile rect rfsrc
sd surv_test tail title
Consider adding
importFrom("graphics", "axis", "box", "legend", "lines", "plot",
"plot.new", "plot.window", "points", "polygon", "rect",
"title")
importFrom("stats", "as.dist", "coef", "cor", "cutree", "dist",
"hclust", "median", "quantile", "sd")
importFrom("utils", "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
Examples with CPU or elapsed time > 5s
user system elapsed
TwoHC_perm 57.53 0.27 57.80
TwoHC_assign 11.69 0.03 11.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TwoHC_perm 64.09 0.35 64.44
TwoHC_assign 14.11 0.04 14.15
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/HCsnip.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'HCsnip' ...
** 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 'HCsnip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HCsnip' as HCsnip_1.16.0.zip
* DONE (HCsnip)