Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:07:02 -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 RbcBook1 on palomino4


To the developers/maintainers of the RbcBook1 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RbcBook1.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 1554/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RbcBook1 1.65.0  (landing page)
Vince Carey
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/RbcBook1
git_branch: master
git_last_commit: 89f8404
git_last_commit_date: 2022-04-26 10:58:53 -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: RbcBook1
Version: 1.65.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RbcBook1.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings RbcBook1_1.65.0.tar.gz
StartedAt: 2022-06-24 04:49:59 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:50:45 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 45.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RbcBook1.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:RbcBook1.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings RbcBook1_1.65.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/RbcBook1.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 'RbcBook1/DESCRIPTION' ... OK
* this is package 'RbcBook1' version '1.65.0'
* 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 'RbcBook1' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to 'graph' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'graph' 'rpart'
  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
bcSweave: no visible global function definition for
  'Sweave'
remapAff: no visible binding for global variable
  'hgu95av2SYMBOL'
rpart2gNEL: no visible global function definition for
  'new'
rpart2gNEL: no visible global function definition for
  'edgemode<-'
rpart2gNEL: no visible global function definition for
  'addEdge'
Undefined global functions or variables:
  Sweave addEdge edgemode<- hgu95av2SYMBOL new
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "Sweave")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: requireAllBook1.Rd:9-10: Dropping empty section \arguments
* 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
* 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: 5 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/RbcBook1.Rcheck/00check.log'
for details.



Installation output

RbcBook1.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/RbcBook1_1.65.0.tar.gz && rm -rf RbcBook1.buildbin-libdir && mkdir RbcBook1.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RbcBook1.buildbin-libdir RbcBook1_1.65.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL RbcBook1_1.65.0.zip && rm RbcBook1_1.65.0.tar.gz RbcBook1_1.65.0.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 6534k  100 6534k    0     0  16.5M      0 --:--:-- --:--:-- --:--:-- 16.5M
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'RbcBook1' ...
** using staged installation
** R
** data
** 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
** 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 'RbcBook1' as RbcBook1_1.65.0.zip
* DONE (RbcBook1)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'RbcBook1' successfully unpacked and MD5 sums checked

Tests output


Example timings

RbcBook1.Rcheck/RbcBook1-Ex.timings

nameusersystemelapsed
bcStangle000
bcSweave000
bcr0.620.030.66
checkVerbatimLines0.020.000.02
imageSize000
perf000
requireAllBook1000
rpart2gNEL0.080.020.14