canceR 1.4.0
Karim Mezhoud
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/canceR | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (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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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.4.0’
* 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 ... 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 38.6Mb
sub-directories of 1Mb or more:
data 7.1Mb
doc 25.5Mb
extdata 5.6Mb
* 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: no visible global function definition for ‘pdf’
GSEA: no visible global function definition for ‘colors’
GSEA: no visible global function definition for ‘dev.cur’
GSEA: no visible global function definition for ‘dev.off’
GSEA.Analyze.Sets: no visible global function definition for ‘pdf’
GSEA.Analyze.Sets: no visible global function definition for ‘dev.cur’
GSEA.Analyze.Sets: no visible global function definition for ‘dev.off’
GSEA.HeatMapPlot2: no visible global function definition for ‘rainbow’
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’
getGenProfs: no visible binding for global variable ‘tl’
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’
plotModel : Save: no visible global function definition for
‘graphics.off’
plotModel : Save: no visible global function definition for ‘jpeg’
plotModel : Save: no visible global function definition for ‘dev.off’
plotModel : Save: no visible global function definition for ‘png’
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 colors
curselectCases dev.cur dev.off devSVG fname.CLS fname.GCT
fname.MSigDB graphics.off jpeg lenght mSigDB_SubName myGlobalEnv pdf
png rainbow tl ttCasesGenProfs ttMain x
Consider adding
importFrom("grDevices", "colors", "dev.cur", "dev.off", "graphics.off",
"jpeg", "pdf", "png", "rainbow")
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 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-3.3-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)