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This page was generated on 2022-01-21 11:08:43 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for StarBioTrek on riesling1


To the developers/maintainers of the StarBioTrek package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/StarBioTrek.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1879/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
StarBioTrek 1.21.0  (landing page)
Claudia Cava
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/StarBioTrek
git_branch: master
git_last_commit: 186561c
git_last_commit_date: 2021-10-26 12:31:11 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'SpidermiR' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'SpidermiR' which is not available

Summary

Package: StarBioTrek
Version: 1.21.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:StarBioTrek.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings StarBioTrek_1.21.0.tar.gz
StartedAt: 2022-01-20 20:12:03 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:14:14 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 131.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: StarBioTrek.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:StarBioTrek.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings StarBioTrek_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/StarBioTrek.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'StarBioTrek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'StarBioTrek' version '1.21.0'
* 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 whether package 'StarBioTrek' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'AnnotationDbi'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
svm_classification: no visible binding for global variable 'Target'
Undefined global functions or variables:
  Target
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'svm_classification':
  'Target'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 5.4 MB without LazyDataCompression set
  See ยง1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... 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: 2 WARNINGs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/StarBioTrek.Rcheck/00check.log'
for details.



Installation output

StarBioTrek.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL StarBioTrek
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'StarBioTrek' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'StarBioTrek'
    finding HTML links ... done
    ConvertedIDgenes                        html  
    Data_CANCER_normUQ_fil                  html  
    GE_matrix                               html  
    GE_matrix_mean                          html  
    GOChord                                 html  
    GetData                                 html  
    GetPathData                             html  
    GetPathNet                              html  
    IPPI                                    html  
    SelectedSample                          html  
    StarBioTrek                             html  
    average                                 html  
    circleplot                              html  
    dsscorecrtlk                            html  
    eucdistcrtlk                            html  
    getNETdata                              html  
    listpathnet                             html  
    netw                                    html  
    netw_IPPI                               html  
    norm                                    html  
    path                                    html  
    path_KEGG                               html  
    pathnet                                 html  
    pathway                                 html  
    pathway_matrix                          html  
    plotcrosstalk                           html  
    score_euc_dista                         html  
    select_class                            html  
    stdv                                    html  
    svm_classification                      html  
    tumo                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (StarBioTrek)
Making 'packages.html' ... done

Tests output


Example timings

StarBioTrek.Rcheck/StarBioTrek-Ex.timings

nameusersystemelapsed
ConvertedIDgenes3.390.033.42
GE_matrix0.030.000.03
GE_matrix_mean0.030.010.05
GetData000
GetPathData000
GetPathNet000
IPPI000
SelectedSample0.110.020.13
average0.820.080.89
circleplot0.710.030.75
dsscorecrtlk0.050.000.04
eucdistcrtlk0.000.030.03
getNETdata000
listpathnet0.450.020.47
pathnet0.220.010.23
plotcrosstalk0.010.000.02
stdv0.020.000.01
svm_classification000