canceR 1.5.2
Karim Mezhoud
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR | | Last Changed Rev: 120682 / Revision: 121152 | | Last Changed Date: 2016-09-02 07:18:27 -0700 (Fri, 02 Sep 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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/canceR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘canceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘canceR’ version ‘1.5.2’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘canceR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 36.2Mb
sub-directories of 1Mb or more:
data 7.1Mb
doc 25.7Mb
extdata 3.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSEA.HeatMapPlot2: possible error in rainbow(100, s = 1, v = 0.75,
start = 0, end = 0.75, gamma = 1.5): unused argument (gamma = 1.5)
canceR : loadAllStudies: no visible binding for global variable ‘Li’
canceR : loadMatchStudies: no visible binding for global variable ‘A’
cbind.na: no visible global function definition for ‘cbind2’
dialogOptionPhenoTest: no visible binding for global variable
‘EventTime’
dialogOptionPhenoTest: no visible binding for global variable
‘Category’
dialogOptionPhenoTest: no visible binding for global variable ‘Continu’
dialogOptionPhenoTest : loadCategorical: no visible binding for global
variable ‘Category’
getClinicalDataMatrix: no visible binding for global variable ‘ttMain’
getCor_ExpCNAMet : getMatrices: no visible binding for global variable
‘x’
getGCTCLSExample: no visible binding for global variable ‘fname.GCT’
getGCTCLSExample: no visible binding for global variable ‘fname.CLS’
getGSEAlm_Diseases: no visible global function definition for ‘new’
getGSEAlm_Diseases: no visible binding for global variable
‘mSigDB_SubName’
getGSEAlm_Variables: no visible global function definition for ‘new’
getGSEAlm_Variables: no visible binding for global variable
‘GenesDetails’
getGeneExpMatrix: no visible binding for global variable ‘ttMain’
getGenesClassifier: no visible global function definition for ‘new’
getGenesClassifier: no visible binding for global variable
‘GenesDetails’
getGenesTree_MultipleCases: no visible binding for global variable
‘CaseChoice’
getListProfData: no visible binding for global variable ‘ListProfData’
getListProfData: no visible binding for global variable ‘ListMetData’
getListProfData: no visible binding for global variable ‘ListMutData’
getListProfData: no visible global function definition for ‘lenght’
getMSigDBExample : ifrm: no visible global function definition for
‘myGlobalEnv’
getMSigDBExample: no visible binding for global variable ‘MSigDB’
getMSigDBExample: no visible binding for global variable ‘MSigDBFile’
getMSigDBExample: no visible binding for global variable ‘fname.MSigDB’
getMegaProfData: no visible global function definition for ‘lenght’
getSurvival: no visible binding for global variable ‘age’
geteSet: no visible binding for global variable ‘CasesStudies’
geteSet: no visible binding for global variable ‘curselectCases’
geteSet: no visible global function definition for ‘new’
plotModel : Save: no visible global function definition for ‘devSVG’
rbind.na: no visible global function definition for ‘rbind2’
testCheckedCaseGenProf: no visible binding for global variable
‘ttCasesGenProfs’
Undefined global functions or variables:
A CaseChoice CasesStudies Category Continu EventTime GenesDetails Li
ListMetData ListMutData ListProfData MSigDB MSigDBFile age cbind2
curselectCases devSVG fname.CLS fname.GCT fname.MSigDB lenght
mSigDB_SubName myGlobalEnv new rbind2 ttCasesGenProfs ttMain x
Consider adding
importFrom("methods", "cbind2", "new", "rbind2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/canceR.Rcheck/00check.log’
for details.
* installing *source* package ‘canceR’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (canceR)