canceR 1.2.0
Karim Mezhoud
| 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/canceR | | 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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/canceR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.2.0’
* 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 ‘canceR’ can be installed ... [23s/24s] OK
* checking installed package size ... NOTE
installed size is 13.1Mb
sub-directories of 1Mb or more:
data 7.1Mb
doc 2.6Mb
extdata 3.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Formula’ ‘rpart’ ‘Biobase’
A package should be listed in only one of these fields.
* 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’
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 binding for global variable
‘mSigDB_SubName’
getGSEAlm_Variables: no visible binding for global variable
‘GenesDetails’
getGeneExpMatrix: no visible binding for global variable ‘ttMain’
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’
plotModel : Save: no visible global function definition for ‘devSVG’
testCheckedCaseGenProf: no visible binding for global variable
‘ttCasesGenProfs’
* 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 ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘canceR_unit_tests.R’ [11s/21s]
[11s/21s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-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)