HCsnip 1.10.0
Askar Obulkasim
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/HCsnip | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | 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 HCsnip_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/HCsnip.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HCsnip/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HCsnip’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘HCsnip’ can be installed ... [11s/15s] 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
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
.test_pred: no visible global function definition for ‘coxph’
EnvioPlot: no visible global function definition for ‘exprs’
EnvioPlot: no visible global function definition for ‘hdEntropy’
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: no visible global function definition for ‘coxph’
cluster_pred: no visible global function definition for ‘exprs’
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’
* 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 ... [150s/151s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
TwoHC_perm 89.607 2.125 92.177
TwoHC_assign 42.453 0.306 42.838
* 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/HCsnip.Rcheck/00check.log’
for details.