Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-06 11:07:00 -0400 (Sat, 06 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4371
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4155
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4155
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 sscore on palomino4


To the developers/maintainers of the sscore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sscore.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 1922/2137HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sscore 1.69.0  (landing page)
Richard Kennedy
Snapshot Date: 2022-08-05 14:00:05 -0400 (Fri, 05 Aug 2022)
git_url: https://git.bioconductor.org/packages/sscore
git_branch: master
git_last_commit: cc3c875
git_last_commit_date: 2022-04-26 10:57:59 -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    NA  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sscore
Version: 1.69.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sscore.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sscore_1.69.0.tar.gz
StartedAt: 2022-08-06 06:21:15 -0400 (Sat, 06 Aug 2022)
EndedAt: 2022-08-06 06:21:54 -0400 (Sat, 06 Aug 2022)
EllapsedTime: 38.6 seconds
RetCode: 0
Status:   OK  
CheckDir: sscore.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:sscore.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings sscore_1.69.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/sscore.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 'sscore/DESCRIPTION' ... OK
* this is package 'sscore' version '1.69.0'
* 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 'sscore' 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 ... NOTE
Package in Depends field not imported from: 'affyio'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
OneStepBiweightAlgorithm: no visible global function definition for
  'median'
SScore: no visible global function definition for 'read.celfile'
SScore: no visible global function definition for 'new'
SScore: no visible global function definition for 'annotation'
SScoreBatch: no visible global function definition for 'read.celfile'
SScoreBatch: no visible global function definition for 'new'
SScoreBatch: no visible global function definition for 'annotation'
computeAffxSFandSDT: no visible binding for global variable 'var'
computeAffxSFandSDT: no visible global function definition for 'x11'
computeAffxSFandSDT: no visible global function definition for 'par'
computeSFandSDT: no visible binding for global variable 'var'
computeSFandSDT: no visible global function definition for 'x11'
computeSFandSDT: no visible global function definition for 'par'
Undefined global functions or variables:
  annotation median new par read.celfile var x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("methods", "new")
  importFrom("stats", "median", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
* 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 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/sscore.Rcheck/00check.log'
for details.



Installation output

sscore.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/sscore_1.69.0.tar.gz && rm -rf sscore.buildbin-libdir && mkdir sscore.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sscore.buildbin-libdir sscore_1.69.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL sscore_1.69.0.zip && rm sscore_1.69.0.tar.gz sscore_1.69.0.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  209k  100  209k    0     0  2469k      0 --:--:-- --:--:-- --:--:-- 2496k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'sscore' ...
** 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 'sscore' as sscore_1.69.0.zip
* DONE (sscore)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'sscore' successfully unpacked and MD5 sums checked

Tests output


Example timings

sscore.Rcheck/sscore-Ex.timings

nameusersystemelapsed
SScore000
SScoreBatch000
computeAffxSFandSDT0.020.000.01
computeOutlier000
computeSFandSDT000