Karim Mezhoud
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/canceR |
| Branch: master |
| Last Commit: d0e4002 |
| Last Changed Date: 2019-02-21 17:03:40 -0400 (Thu, 21 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:23:00 -0400 (Tue, 09 Apr 2019).
| Package 202/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| canceR 1.17.1 Karim Mezhoud
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: canceR |
| Version: 1.17.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:canceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings canceR_1.17.1.tar.gz |
| StartedAt: 2019-04-09 01:31:35 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:42:10 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 635.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: canceR.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:canceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings canceR_1.17.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'canceR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'canceR' version '1.17.1'
* package encoding: UTF-8
* 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 whether package 'canceR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.1Mb
sub-directories of 1Mb or more:
data 7.1Mb
extdata 2.9Mb
* 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
* 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 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 'windows'
GSEA: no visible global function definition for 'savePlot'
GSEA: no visible global function definition for 'dev.new'
GSEA.Analyze.Sets: no visible global function definition for 'savePlot'
GSEA.Analyze.Sets: no visible global function definition for 'windows'
Undefined global functions or variables:
dev.new savePlot windows
Consider adding
importFrom("grDevices", "dev.new", "savePlot", "windows")
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 ... NOTE
S3 methods shown with full name in documentation object 'cbind.na':
'cbind.na'
S3 methods shown with full name in documentation object 'rbind.na':
'rbind.na'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... WARNING
'data/datalist' is a directory
Output for data("Circos", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Output for data("brca_tcga73genes", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Output for data("brca_tcgaClassifier223", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Output for data("brca_tcgaGSEAlm1021", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Output for data("gbm_tcgaPlotTwoGenProf", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Output for data("prad_michPhenoTest1021", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
Output for data("ucec_tcga_pubGSEA1021", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck/00check.log'
for details.
canceR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/canceR_1.17.1.tar.gz && rm -rf canceR.buildbin-libdir && mkdir canceR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=canceR.buildbin-libdir canceR_1.17.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL canceR_1.17.1.zip && rm canceR_1.17.1.tar.gz canceR_1.17.1.zip
###
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install for i386
* installing *source* package 'canceR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
converting help for package 'canceR'
finding HTML links ... done
ClinicalData html
GSEA.Analyze.Sets html
GSEA.ConsPlot html
GSEA.EnrichmentScore html
GSEA.EnrichmentScore2 html
GSEA.Gct2Frame html
GSEA.Gct2Frame2 html
GSEA.GeneRanking html
GSEA.HeatMapPlot html
GSEA.HeatMapPlot2 html
GSEA.NormalizeCols html
GSEA.NormalizeRows html
GSEA html
GSEA.ReadClsFile html
GSEA.Res2Frame html
GSEA.Threshold html
GSEA.VarFilter html
GSEA.write.gct html
GeneExpMatrix html
Match_GeneList_MSigDB html
OLD.GSEA.EnrichmentScore html
Run.GSEA html
about html
canceR html
canceRHelp html
canceR_Vignette html
cbind.na html
dialogGeneClassifier html
dialogMetOption html
dialogMut html
dialogOptionCircos html
dialogOptionGSEAlm html
dialogOptionPhenoTest html
dialogPlotOption_SkinCor html
dialogSamplingGSEA html
dialogSelectFiles_GSEA html
dialogSpecificMut html
dialogSummary_GSEA html
dialoggetGeneListMSigDB html
displayInTable html
getCases html
getCasesGenProfs html
getCircos html
getClinicData_MultipleCases html
getClinicalDataMatrix html
getCor_ExpCNAMet html
getGCTCLSExample html
getGCT_CLSfiles html
getGSEAlm_Diseases html
getGSEAlm_Variables html
getGenProfs html
getGeneExpMatrix html
getGeneList html
getGeneListExample html
getGeneListFromMSigDB html
getGenesClassifier html
getGenesTree_MultipleCases html
getGenesTree_SingleCase html
getInTable html
getListProfData html
getMSigDB html
getMSigDBExample html
getMSigDBfile html
getMegaProfData html
getMetDataMultipleGenes html
getMutData html
getPhenoTest html
getProfilesDataMultipleGenes html
getProfilesDataSingleGene html
getSpecificMut html
getSummaryGSEA html
getSurvival html
getTextWin html
geteSet html
modalDialog html
myGlobalEnv html
plotModel html
plot_1Gene_2GenProfs html
plot_2Genes_1GenProf html
rbind.na html
setWorkspace html
testCheckedCaseGenProf html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'canceR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* MD5 sums
packaged installation of 'canceR' as canceR_1.17.1.zip
* DONE (canceR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'canceR' successfully unpacked and MD5 sums checked
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canceR.Rcheck/tests_i386/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(canceR) Loading required package: tcltk Loading required package: tcltk2 Loading required package: cgdsr Please send questions to [email protected] ///////////////////////////////////////////////////////////////////////////// //------------------ Thanks for using HTSanalyzeR -------------------// //------------please use function changes() to see new changes-------------// //------------please report any bug to [email protected]// ///////////////////////////////////////////////////////////////////////////// Warning message: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR' > > test_check("canceR") getCancerStudies... OK getCaseLists (1/2) ... OK getCaseLists (2/2) ... OK getGeneticProfiles (1/2) ... OK getGeneticProfiles (2/2) ... OK getClinicalData (1/1) ... OK getProfileData (1/6) ... OK getProfileData (2/6) ... OK getProfileData (3/6) ... OK getProfileData (4/6) ... OK getProfileData (5/6) ... OK getProfileData (6/6) ... OK == testthat results =========================================================== OK: 0 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 14.60 1.82 18.64 |
canceR.Rcheck/tests_x64/testthat.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(canceR) Loading required package: tcltk Loading required package: tcltk2 Loading required package: cgdsr Please send questions to [email protected] ///////////////////////////////////////////////////////////////////////////// //------------------ Thanks for using HTSanalyzeR -------------------// //------------please use function changes() to see new changes-------------// //------------please report any bug to [email protected]// ///////////////////////////////////////////////////////////////////////////// Warning message: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR' > > test_check("canceR") getCancerStudies... OK getCaseLists (1/2) ... OK getCaseLists (2/2) ... OK getGeneticProfiles (1/2) ... OK getGeneticProfiles (2/2) ... OK getClinicalData (1/1) ... OK getProfileData (1/6) ... OK getProfileData (2/6) ... OK getProfileData (3/6) ... OK getProfileData (4/6) ... OK getProfileData (5/6) ... OK getProfileData (6/6) ... OK == testthat results =========================================================== OK: 0 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 18.68 1.62 22.59 |
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canceR.Rcheck/examples_i386/canceR-Ex.timings
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canceR.Rcheck/examples_x64/canceR-Ex.timings
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