Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-12 11:06:37 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4167
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 PADOG on palomino4


To the developers/maintainers of the PADOG package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PADOG.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 1397/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PADOG 1.39.0  (landing page)
Adi L. Tarca
Snapshot Date: 2022-08-11 14:00:04 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/PADOG
git_branch: master
git_last_commit: 3d62408
git_last_commit_date: 2022-04-26 11:11:39 -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: PADOG
Version: 1.39.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PADOG.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PADOG_1.39.0.tar.gz
StartedAt: 2022-08-12 04:18:35 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 04:22:49 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 254.3 seconds
RetCode: 0
Status:   OK  
CheckDir: PADOG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PADOG.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PADOG_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/PADOG.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PADOG/DESCRIPTION' ... OK
* this is package 'PADOG' version '1.39.0'
* 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 'PADOG' 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
compPADOG: no visible global function definition for 'data'
compPADOG : padogF: no visible global function definition for
  'p.adjust'
compPADOG : gsaF: no visible global function definition for 'p.adjust'
compPADOG : <anonymous>: no visible global function definition for
  'complete.cases'
compPADOG : wi: no visible global function definition for 'wilcox.test'
compPADOG: no visible binding for global variable 'median'
compPADOG: no visible global function definition for 'colors'
compPADOG: no visible global function definition for 'par'
compPADOG: no visible global function definition for 'boxplot'
compPADOG: no visible global function definition for 'abline'
filteranot: no visible global function definition for 'model.matrix'
padog: no visible global function definition for 'quantile'
padog: no visible global function definition for 'sd'
padog : combFun: no visible global function definition for 'combn'
padog : gsScoreFun: no visible global function definition for
  'model.matrix'
padog : gsScoreFun : <anonymous>: no visible global function definition
  for 'na.omit'
padog: no visible global function definition for 'par'
padog: no visible global function definition for 'boxplot'
padog: no visible global function definition for 'points'
padog: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline boxplot colors combn complete.cases data median model.matrix
  na.omit p.adjust par points quantile sd wilcox.test
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "boxplot", "par", "points")
  importFrom("stats", "complete.cases", "median", "model.matrix",
             "na.omit", "p.adjust", "quantile", "sd", "wilcox.test")
  importFrom("utils", "combn", "data")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
compPADOG 13.92   2.08   84.53
padog     10.47   1.17   29.05
* 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/PADOG.Rcheck/00check.log'
for details.



Installation output

PADOG.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/PADOG_1.39.0.tar.gz && rm -rf PADOG.buildbin-libdir && mkdir PADOG.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PADOG.buildbin-libdir PADOG_1.39.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL PADOG_1.39.0.zip && rm PADOG_1.39.0.tar.gz PADOG_1.39.0.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 37689  100 37689    0     0   807k      0 --:--:-- --:--:-- --:--:--  817k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'PADOG' ...
** using staged installation
** R
** 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
** 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 'PADOG' as PADOG_1.39.0.zip
* DONE (PADOG)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'PADOG' successfully unpacked and MD5 sums checked

Tests output


Example timings

PADOG.Rcheck/PADOG-Ex.timings

nameusersystemelapsed
compPADOG13.92 2.0884.53
filteranot1.660.121.92
padog10.47 1.1729.05