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This page was generated on 2022-06-24 11:07:13 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 SigCheck on palomino4


To the developers/maintainers of the SigCheck package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SigCheck.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1814/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SigCheck 2.29.0  (landing page)
Rory Stark
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/SigCheck
git_branch: master
git_last_commit: 4acc7ba
git_last_commit_date: 2022-04-26 11:22:17 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SigCheck
Version: 2.29.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SigCheck.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SigCheck_2.29.0.tar.gz
StartedAt: 2022-06-24 05:49:29 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:55:14 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 345.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SigCheck.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SigCheck.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SigCheck_2.29.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SigCheck.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SigCheck/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SigCheck' version '2.29.0'
* 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 'SigCheck' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sigCheckKnown: no visible binding for global variable 'knownSignatures'
Undefined global functions or variables:
  knownSignatures
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
sigCheckAll      96.53   2.85   99.39
sigCheckKnown    47.53   1.11   48.65
sigCheckPermuted 13.92   0.42   14.35
sigCheck         12.03   0.75   12.89
sigCheckPlot     11.00   0.55   11.54
sigCheckRandom    7.74   0.36    8.10
* 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 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/SigCheck.Rcheck/00check.log'
for details.



Installation output

SigCheck.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/SigCheck_2.29.0.tar.gz && rm -rf SigCheck.buildbin-libdir && mkdir SigCheck.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SigCheck.buildbin-libdir SigCheck_2.29.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL SigCheck_2.29.0.zip && rm SigCheck_2.29.0.tar.gz SigCheck_2.29.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  111k  100  111k    0     0  1639k      0 --:--:-- --:--:-- --:--:-- 1664k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'SigCheck' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'signature' in package 'SigCheck'
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'SigCheck' as SigCheck_2.29.0.zip
* DONE (SigCheck)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'SigCheck' successfully unpacked and MD5 sums checked

Tests output


Example timings

SigCheck.Rcheck/SigCheck-Ex.timings

nameusersystemelapsed
SigCheckObject-class000
classifyResults0.030.000.03
knownSignatures0.040.040.08
nkiResults0.030.000.03
sigCheck12.03 0.7512.89
sigCheckAll96.53 2.8599.39
sigCheckKnown47.53 1.1148.65
sigCheckPermuted13.92 0.4214.35
sigCheckPlot11.00 0.5511.54
sigCheckRandom7.740.368.10