Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:14 -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 Risa on tokay2


To the developers/maintainers of the Risa package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Risa.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 1613/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.36.0  (landing page)
Alejandra Gonzalez-Beltran
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Risa
git_branch: RELEASE_3_14
git_last_commit: e0c196c
git_last_commit_date: 2021-10-26 12:04:36 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Risa
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Risa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Risa_1.36.0.tar.gz
StartedAt: 2022-04-13 01:45:21 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:52:15 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 413.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Risa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Risa.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Risa_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Risa.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 'Risa/DESCRIPTION' ... OK
* this is package 'Risa' version '1.36.0'
* 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 'Risa' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPackagesInBiocView: no visible global function definition for 'data'
readISAtabZip: no visible global function definition for 'unzip'
suggestBiocPackage: no visible global function definition for
  'read.csv'
write.assay.file: no visible global function definition for
  'write.table'
write.investigation.file: no visible global function definition for
  'write.table'
write.study.file: no visible global function definition for
  'write.table'
initialize,ISATab: no visible global function definition for
  'count.fields'
initialize,ISATab: no visible global function definition for
  'read.table'
initialize,ISATab : <anonymous>: no visible global function definition
  for 'read.table'
initialize,ISATab : <anonymous> : <anonymous>: no visible global
  function definition for 'read.table'
initialize,ISATab: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  count.fields data na.omit read.csv read.table unzip write.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "count.fields", "data", "read.csv", "read.table",
             "unzip", "write.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
processAssayXcmsSet.1factor 1.37   0.03   30.95
Risa-package                0.57   0.31   10.60
processAssayXcmsSet         0.81   0.00   29.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
processAssayXcmsSet.1factor 1.51   0.00   29.93
processAssayXcmsSet         0.94   0.02   26.41
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/Risa.Rcheck/00check.log'
for details.



Installation output

Risa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Risa_1.36.0.tar.gz && rm -rf Risa.buildbin-libdir && mkdir Risa.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Risa.buildbin-libdir Risa_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Risa_1.36.0.zip && rm Risa_1.36.0.tar.gz Risa_1.36.0.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
 30 2202k   30  664k    0     0   855k      0  0:00:02 --:--:--  0:00:02  856k
100 2202k  100 2202k    0     0  1321k      0  0:00:01  0:00:01 --:--:-- 1322k

install for i386

* installing *source* package 'Risa' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Risa'
    finding HTML links ... done
    AssayTab-class                          html  
    ISAtab-class                            html  
    Risa-package                            html  
    getAnnotatedDataFrameAssay              html  
    getAssayRawDataFilenames-methods        html  
    getExpressionSet                        html  
    getMIAMEMetadata                        html  
    getMSAssayFilenames                     html  
    getMicroarrayAssayFilenames             html  
    getRawDataFilenames-methods             html  
    getStudyFilename                        html  
    isMSAssay                               html  
    isMicroarrayAssay                       html  
    processAssayXcmsSet.1factor             html  
    processAssayXcmsSet                     html  
    readISAtab                              html  
    suggestBiocPackage                      html  
    updateAssayMetadata                     html  
    write.assay.file                        html  
    write.investigation.file                html  
    write.isatab                            html  
    write.study.file                        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 'Risa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Risa' as Risa_1.36.0.zip
* DONE (Risa)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Risa' successfully unpacked and MD5 sums checked

Tests output


Example timings

Risa.Rcheck/examples_i386/Risa-Ex.timings

nameusersystemelapsed
AssayTab-class000
ISAtab-class000
Risa-package 0.57 0.3110.60
getAnnotatedDataFrameAssay0.250.071.19
getExpressionSet0.070.030.09
getMIAMEMetadata0.060.060.13
getMSAssayFilenames0.050.000.04
getMicroarrayAssayFilenames0.060.030.10
getStudyFilename0.030.020.04
isMSAssay0.020.000.02
isMicroarrayAssay0.050.030.08
processAssayXcmsSet.1factor 1.37 0.0330.95
processAssayXcmsSet 0.81 0.0029.44
readISAtab0.110.150.26
updateAssayMetadata0.070.040.10
write.assay.file0.030.000.03
write.investigation.file0.030.000.03
write.isatab0.010.040.09
write.study.file0.050.000.05

Risa.Rcheck/examples_x64/Risa-Ex.timings

nameusersystemelapsed
AssayTab-class000
ISAtab-class000
Risa-package0.350.130.47
getAnnotatedDataFrameAssay0.120.000.12
getExpressionSet0.060.000.06
getMIAMEMetadata0.080.010.10
getMSAssayFilenames0.020.000.01
getMicroarrayAssayFilenames0.060.020.08
getStudyFilename0.010.000.02
isMSAssay0.000.010.01
isMicroarrayAssay0.070.000.07
processAssayXcmsSet.1factor 1.51 0.0029.93
processAssayXcmsSet 0.94 0.0226.41
readISAtab0.090.170.26
updateAssayMetadata0.100.020.11
write.assay.file0.030.000.04
write.investigation.file0.010.010.03
write.isatab0.040.000.03
write.study.file0.030.000.03