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CHECK report for BloodCancerMultiOmics2017 on riesling1

This page was generated on 2021-01-21 16:01:25 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE BloodCancerMultiOmics2017 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 31/386HostnameOS / ArchINSTALLBUILDCHECK
BloodCancerMultiOmics2017 1.11.0
Malgorzata Oles
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017
Branch: master
Last Commit: 7d60da4
Last Changed Date: 2020-10-27 10:26:12 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: BloodCancerMultiOmics2017
Version: 1.11.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BloodCancerMultiOmics2017.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BloodCancerMultiOmics2017_1.11.0.tar.gz
StartedAt: 2021-01-21 11:12:33 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:15:32 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 179.2 seconds
RetCode: 0
Status:  OK  
CheckDir: BloodCancerMultiOmics2017.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BloodCancerMultiOmics2017.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BloodCancerMultiOmics2017_1.11.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/BloodCancerMultiOmics2017.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BloodCancerMultiOmics2017/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BloodCancerMultiOmics2017' version '1.11.0'
* package encoding: UTF-8
* 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 'BloodCancerMultiOmics2017' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 75.4Mb
  sub-directories of 1Mb or more:
    data     66.4Mb
    extdata   8.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
survplot: no visible binding for global variable 's'
survplot: no visible binding for global variable 'cox'
Undefined global functions or variables:
  cox s
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/BloodCancerMultiOmics2017.Rcheck/00check.log'
for details.



Installation output

BloodCancerMultiOmics2017.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/BloodCancerMultiOmics2017_1.11.0.tar.gz && rm -rf BloodCancerMultiOmics2017.buildbin-libdir && mkdir BloodCancerMultiOmics2017.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BloodCancerMultiOmics2017.buildbin-libdir BloodCancerMultiOmics2017_1.11.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BloodCancerMultiOmics2017_1.11.0.zip && rm BloodCancerMultiOmics2017_1.11.0.tar.gz BloodCancerMultiOmics2017_1.11.0.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
 18 36.0M   18 6954k    0     0  25.7M      0  0:00:01 --:--:--  0:00:01 25.6M
100 36.0M  100 36.0M    0     0  59.5M      0 --:--:-- --:--:-- --:--:-- 59.4M

install for i386

* installing *source* package 'BloodCancerMultiOmics2017' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BloodCancerMultiOmics2017'
    finding HTML links ... done
    addNrisk                                html  
REDIRECT:topic	 addNrisk -> addNrisk.html [ SUCCESS ]
    col2hex                                 html  
REDIRECT:topic	 col2hex -> col2hex.html [ SUCCESS ]
    data-conctab                            html  
REDIRECT:topic	 conctab -> data-conctab.html [ SUCCESS ]
REDIRECT:file	 data-conctab.html -> data-conctab.html [ SUCCESS ]
    data-cytokineViab                       html  
REDIRECT:topic	 cytokineViab -> data-cytokineViab.html [ SUCCESS ]
REDIRECT:file	 data-cytokineViab.html -> data-cytokineViab.html [ SUCCESS ]
    data-day23rep                           html  
REDIRECT:topic	 day23rep -> data-day23rep.html [ SUCCESS ]
REDIRECT:file	 data-day23rep.html -> data-day23rep.html [ SUCCESS ]
    finding level-2 HTML links ... done

    data-dds                                html  
REDIRECT:topic	 dds -> data-dds.html [ SUCCESS ]
REDIRECT:file	 data-dds.html -> data-dds.html [ SUCCESS ]
    data-drpar                              html  
REDIRECT:topic	 drpar -> data-drpar.html [ SUCCESS ]
REDIRECT:file	 data-drpar.html -> data-drpar.html [ SUCCESS ]
    data-drugs                              html  
REDIRECT:topic	 drugs -> data-drugs.html [ SUCCESS ]
REDIRECT:file	 data-drugs.html -> data-drugs.html [ SUCCESS ]
    data-exprTreat                          html  
REDIRECT:topic	 exprTreat -> data-exprTreat.html [ SUCCESS ]
REDIRECT:file	 data-exprTreat.html -> data-exprTreat.html [ SUCCESS ]
    data-lpdAll                             html  
REDIRECT:topic	 lpdAll -> data-lpdAll.html [ SUCCESS ]
REDIRECT:file	 data-lpdAll.html -> data-lpdAll.html [ SUCCESS ]
    data-methData                           html  
REDIRECT:topic	 methData -> data-methData.html [ SUCCESS ]
REDIRECT:file	 data-methData.html -> data-methData.html [ SUCCESS ]
    data-mutCOM                             html  
REDIRECT:topic	 mutCOM -> data-mutCOM.html [ SUCCESS ]
REDIRECT:file	 data-mutCOM.html -> data-mutCOM.html [ SUCCESS ]
    data-patmeta                            html  
REDIRECT:topic	 patmeta -> data-patmeta.html [ SUCCESS ]
REDIRECT:file	 data-patmeta.html -> data-patmeta.html [ SUCCESS ]
    data-validateExp                        html  
REDIRECT:topic	 validateExp -> data-validateExp.html [ SUCCESS ]
REDIRECT:file	 data-validateExp.html -> data-validateExp.html [ SUCCESS ]
    deckel                                  html  
REDIRECT:topic	 deckel -> deckel.html [ SUCCESS ]
    defineResponseGroups                    html  
REDIRECT:topic	 defineResponseGroups -> defineResponseGroups.html [ SUCCESS ]
    exp10div                                html  
REDIRECT:topic	 exp10div -> exp10div.html [ SUCCESS ]
    giveDrugLabel                           html  
REDIRECT:topic	 giveDrugLabel -> giveDrugLabel.html [ SUCCESS ]
    log10div                                html  
REDIRECT:topic	 log10div -> log10div.html [ SUCCESS ]
    meltWholeDF                             html  
REDIRECT:topic	 meltWholeDF -> meltWholeDF.html [ SUCCESS ]
    moround                                 html  
REDIRECT:topic	 moround -> moround.html [ SUCCESS ]
    nrisk                                   html  
REDIRECT:topic	 nrisk -> nrisk.html [ SUCCESS ]
    percentAxisScale                        html  
REDIRECT:topic	 percentAxisScale -> percentAxisScale.html [ SUCCESS ]
    pheatmapwh                              html  
REDIRECT:topic	 pheatmapwh -> pheatmapwh.html [ SUCCESS ]
    safeMatch                               html  
REDIRECT:topic	 safeMatch -> safeMatch.html [ SUCCESS ]
    scientific_10                           html  
REDIRECT:topic	 scientific_10 -> scientific_10.html [ SUCCESS ]
    smunlist                                html  
REDIRECT:topic	 smunlist -> smunlist.html [ SUCCESS ]
    stripConc                               html  
REDIRECT:topic	 stripConc -> stripConc.html [ SUCCESS ]
    survplot                                html  
REDIRECT:topic	 survplot -> survplot.html [ SUCCESS ]
    toCaps                                  html  
REDIRECT:topic	 toCaps -> toCaps.html [ SUCCESS ]
    whichInGrob                             html  
REDIRECT:topic	 whichInGrob -> whichInGrob.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'BloodCancerMultiOmics2017' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BloodCancerMultiOmics2017' as BloodCancerMultiOmics2017_1.11.0.zip
* DONE (BloodCancerMultiOmics2017)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'BloodCancerMultiOmics2017' successfully unpacked and MD5 sums checked

Tests output


Example timings

BloodCancerMultiOmics2017.Rcheck/examples_i386/BloodCancerMultiOmics2017-Ex.timings

nameusersystemelapsed
addNrisk0.030.020.04
col2hex000
deckel000
exp10div000
giveDrugLabel000
log10div000
meltWholeDF000
moround000
nrisk0.030.000.03
percentAxisScale000
pheatmapwh0.500.030.72
safeMatch000
scientific_10000
smunlist0.000.020.02
stripConc000
survplot0.090.000.09
toCaps000
whichInGrob0.070.000.06

BloodCancerMultiOmics2017.Rcheck/examples_x64/BloodCancerMultiOmics2017-Ex.timings

nameusersystemelapsed
addNrisk0.050.000.06
col2hex000
deckel0.010.000.01
exp10div000
giveDrugLabel000
log10div000
meltWholeDF000
moround000
nrisk0.020.000.02
percentAxisScale000
pheatmapwh0.560.080.76
safeMatch000
scientific_10000
smunlist000
stripConc000
survplot0.080.000.08
toCaps000
whichInGrob0.450.000.46