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This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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

Package 2082/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
StarBioTrek 1.30.0  (landing page)
Claudia Cava
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/StarBioTrek
git_branch: RELEASE_3_19
git_last_commit: ab618a7
git_last_commit_date: 2024-04-30 10:54:49 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  NO, package depends on 'SpidermiR' which is not available
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'SpidermiR' which is not available
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'SpidermiR' which is not available
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'SpidermiR' which is not available
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


CHECK results for StarBioTrek on palomino3

To the developers/maintainers of the StarBioTrek package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: StarBioTrek
Version: 1.30.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:StarBioTrek.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings StarBioTrek_1.30.0.tar.gz
StartedAt: 2024-06-27 06:40:13 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 06:43:19 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 186.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: StarBioTrek.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:StarBioTrek.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings StarBioTrek_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/StarBioTrek.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'StarBioTrek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'StarBioTrek' version '1.30.0'
* 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  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
* 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 code 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 whether startup messages can be suppressed ... 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 Rd file 'svm_classification.Rd':
  '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 5.3 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ConvertedIDgenes 6.03   0.22    6.27
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/StarBioTrek.Rcheck/00check.log'
for details.


Installation output

StarBioTrek.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL StarBioTrek
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'StarBioTrek' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'StarBioTrek' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (StarBioTrek)

Tests output


Example timings

StarBioTrek.Rcheck/StarBioTrek-Ex.timings

nameusersystemelapsed
ConvertedIDgenes6.030.226.27
GE_matrix0.060.000.06
GE_matrix_mean0.050.020.06
GetData000
GetPathData0.010.000.02
GetPathNet0.050.000.04
IPPI000
SelectedSample0.090.000.09
average1.480.181.69
circleplot1.390.071.45
dsscorecrtlk0.050.000.05
eucdistcrtlk0.110.000.11
getNETdata000
listpathnet0.430.000.43
pathnet0.460.050.50
plotcrosstalk0.010.000.02
stdv0.050.000.04
svm_classification000