Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:57 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 MultiDataSet on tokay2


To the developers/maintainers of the MultiDataSet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/MultiDataSet.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 1242/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiDataSet 1.22.0  (landing page)
Xavier EscribĂ  Montagut
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MultiDataSet
git_branch: RELEASE_3_14
git_last_commit: d737fbe
git_last_commit_date: 2021-10-26 12:27:30 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MultiDataSet
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiDataSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MultiDataSet_1.22.0.tar.gz
StartedAt: 2022-04-12 23:26:25 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:30:20 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 235.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MultiDataSet.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiDataSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MultiDataSet_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiDataSet.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MultiDataSet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MultiDataSet' version '1.22.0'
* 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 'MultiDataSet' 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
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  'Biobase:::assayDataEnvLock' 'Biobase:::assayDataStorageMode'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
downloadGEO : <anonymous>: no visible global function definition for
  'methylationSet'
lambdaClayton: no visible global function definition for 'qnorm'
lambdaClayton: no visible global function definition for 'qchisq'
qq_plot: no visible global function definition for 'qbeta'
Undefined global functions or variables:
  methylationSet qbeta qchisq qnorm
Consider adding
  importFrom("stats", "qbeta", "qchisq", "qnorm")
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 ... WARNING
Codoc mismatches from documentation object 'ResultSet':
\S4method{getAssociation}{ResultSet}
  Code: function(object, rid = 1, coef = 2, contrast = NULL, fNames =
                 NULL, robust = FALSE, ...)
  Docs: function(object, rid = 1, coef = 2, contrast = NULL, fNames =
                 NULL, ...)
  Argument names in code not in docs:
    robust
  Mismatches in argument names:
    Position: 6 Code: robust Docs: ...

* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
add_methy 14.37   2.39   27.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
add_methy 15.8   0.81   16.64
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiDataSet.Rcheck/00check.log'
for details.



Installation output

MultiDataSet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MultiDataSet_1.22.0.tar.gz && rm -rf MultiDataSet.buildbin-libdir && mkdir MultiDataSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MultiDataSet.buildbin-libdir MultiDataSet_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MultiDataSet_1.22.0.zip && rm MultiDataSet_1.22.0.tar.gz MultiDataSet_1.22.0.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 65355  100 65355    0     0   147k      0 --:--:-- --:--:-- --:--:--  147k

install for i386

* installing *source* package 'MultiDataSet' ...
** using staged installation
Warning in .write_description(db, file.path(outDir, "DESCRIPTION")) :
  Unknown encoding with non-ASCII data: converting to ASCII
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for 'add_methy' with signature '"MultiDataSet","GenomicRatioSet"': no definition for class "GenomicRatioSet"
** help
*** installing help indices
  converting help for package 'MultiDataSet'
    finding HTML links ... done
    MultiDataSet-class                      html  
    MultiDataSet                            html  
    ResultSet-class                         html  
    add_eset                                html  
    add_genexp                              html  
    add_methy                               html  
    add_rnaseq-methods                      html  
    add_rse                                 html  
    add_se                                  html  
    add_snps                                html  
    add_table                               html  
    chrNumToChar                            html  
    commonIds                               html  
    commonSamples                           html  
    getAssociation-methods                  html  
    lambdaClayton                           html  
    mae2mds                                 html  
    mds2mae                                 html  
    opt-methods                             html  
    qq_plot                                 html  
    rowRangesElements                       html  
    rset                                    html  
    volcano_plot                            html  
    w_iclusterplus                          html  
    w_mcia                                  html  
** 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 'MultiDataSet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiDataSet' as MultiDataSet_1.22.0.zip
* DONE (MultiDataSet)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MultiDataSet' successfully unpacked and MD5 sums checked

Tests output


Example timings

MultiDataSet.Rcheck/examples_i386/MultiDataSet-Ex.timings

nameusersystemelapsed
MultiDataSet-class000
ResultSet-class000
add_eset0.060.030.09
add_genexp0.110.040.16
add_methy14.37 2.3927.12
add_rnaseq-methods0.090.000.09
add_rse0.240.020.25
add_se0.060.000.06
add_snps0.050.000.05
add_table000
chrNumToChar000
commonIds0.100.000.09
commonSamples0.220.000.22
getAssociation-methods0.030.000.03
lambdaClayton000
opt-methods000
qq_plot0.300.030.33
rowRangesElements0.080.000.08
volcano_plot0.130.000.12

MultiDataSet.Rcheck/examples_x64/MultiDataSet-Ex.timings

nameusersystemelapsed
MultiDataSet-class000
ResultSet-class000
add_eset0.110.000.11
add_genexp0.150.000.16
add_methy15.80 0.8116.64
add_rnaseq-methods0.100.000.11
add_rse0.250.000.25
add_se0.050.020.06
add_snps0.030.030.07
add_table000
chrNumToChar000
commonIds0.110.010.12
commonSamples0.140.020.16
getAssociation-methods0.030.000.03
lambdaClayton000
opt-methods000
qq_plot0.500.060.56
rowRangesElements0.130.020.14
volcano_plot0.190.000.19