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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 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


CHECK results for StarBioTrek on nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings StarBioTrek_1.30.0.tar.gz
StartedAt: 2024-06-13 04:06:13 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:09:20 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 187.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: StarBioTrek.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:StarBioTrek.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings StarBioTrek_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/StarBioTrek.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘StarBioTrek’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  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 loading without being on the library search path ... 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 §1.1.6 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 4.886   0.16   5.048
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/StarBioTrek.Rcheck/00check.log’
for details.


Installation output

StarBioTrek.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL StarBioTrek
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
ConvertedIDgenes4.8860.1605.048
GE_matrix0.0450.0000.044
GE_matrix_mean0.0420.0000.042
GetData000
GetPathData0.0040.0000.003
GetPathNet0.0320.0000.032
IPPI0.0000.0000.001
SelectedSample0.0900.0160.106
average0.9370.0721.008
circleplot0.9710.0080.978
dsscorecrtlk0.0300.0000.031
eucdistcrtlk0.0610.0000.061
getNETdata000
listpathnet0.3610.0040.365
pathnet0.3540.0120.365
plotcrosstalk0.0050.0030.009
stdv0.0210.0090.028
svm_classification000