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This page was generated on 2023-10-16 11:37:27 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 1725/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.42.0  (landing page)
Alejandra Gonzalez-Beltran
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Risa
git_branch: RELEASE_3_17
git_last_commit: e3766f1
git_last_commit_date: 2023-04-25 10:24:06 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for Risa on merida1


To the developers/maintainers of the Risa package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Risa
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Risa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Risa_1.42.0.tar.gz
StartedAt: 2023-10-16 06:08:19 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 06:18:45 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 626.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Risa.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Risa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Risa_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Risa.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Risa/DESCRIPTION’ ... OK
* this is package ‘Risa’ version ‘1.42.0’
* 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 for sufficient/correct file permissions ... 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Changes for 1.9.1
    1. Added citation information.
    2. The identification of investigation files now avoids editor backup files (ignoring files like  "i_Investigation~")
    3. Fixed issue where the investigation file wasn't fully read, due to the number of columns in higher rows being greater than the first five rows (as used by read.table)
    4. Moved inst/doc to vignettes folder as required since R 3.1.0
    5. Imported packages in Depends
    6. Removed 'library' or 'require' calls to packages already attached by Depends.
    7. Fixed no visible binding for global variable.
  Cannot process chunk/lines:
    Changes for 1.3.3
    1. Fixed definitions of assay.filenames.per.sample and factors.
    2. Fixed regulession of investigation file (i_) to be considered at the beginning of the string. 
    3. Added CITATION file.
  Cannot process chunk/lines:
    Changes for 1.1.0
    1. The ISAtab-class was extended to include the definition of assay.names, factors, treatments and groups.
    2. The previous processAssayXcmsSet method was split into processAssayXcmsSet.1factor and processAssayXcmsSet to consider the first factor only (as it was in the previous definition) or all the factors, respectively.
    3. More methods for processing mass spectrometry assays were added:
      - the method getMSAssayFilenames retrieves a list with the mass spectrometry assay filenames 
      - the method getRawDataFiles retrieves a list with all the files listed under the column 'Raw Spectral Data File' within the mass spectrometry assays.
      - the method is.ms receives an object from the ISAtab-class and an assay filename as parameter, and retrieves TRUE if the assay filename is a mass spectrometry assay, or FALSE otherwise.
    4. A method called suggestBiocPackage was added, which retrieves a list of packages in Bioconductor that might be relevant to the ISAtab dataset, according to its assays' mesaurement and technology types. This method relies on the BiocViews annotations for each of the packages available in Bioconductor in a specific version.
    5. Added AssayTab-class and subclasses for MS, Microarray, Seq and NMR.
    6. Defined method getAssayRawDataFilenames and getRawDataFilenames
    7. Defined method getExpressionSet for microarray assays relying on affy package.
  Cannot process chunk/lines:
    This is the first release version of the package. It contains functionality to parse ISAtab datasets into an R object from the ISAtab class. It also provides functionality to save the ISA-tab dataset, or each of its individual files. Additionally, it is also possible to update assay files. Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into an xcmsSet object (from the xcms R package).
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet         70.010 11.346  29.819
processAssayXcmsSet.1factor 38.308  5.739  33.616
readISAtab                  35.142  5.857   0.478
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/Risa.Rcheck/00check.log’
for details.



Installation output

Risa.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Risa
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Risa’ ...
** using staged installation
** R
** 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
* DONE (Risa)

Tests output


Example timings

Risa.Rcheck/Risa-Ex.timings

nameusersystemelapsed
AssayTab-class0.0070.0060.021
ISAtab-class0.0020.0020.008
Risa-package0.9300.5032.006
getAnnotatedDataFrameAssay0.2510.0880.477
getExpressionSet0.1050.0570.217
getMIAMEMetadata0.1560.0730.301
getMSAssayFilenames0.0500.0130.086
getMicroarrayAssayFilenames0.1070.0550.216
getStudyFilename0.0440.0080.066
isMSAssay0.0450.0080.073
isMicroarrayAssay0.1030.0440.197
processAssayXcmsSet.1factor38.308 5.73933.616
processAssayXcmsSet70.01011.34629.819
readISAtab35.142 5.857 0.478
updateAssayMetadata0.1440.0770.286
write.assay.file0.0480.0090.078
write.investigation.file0.0450.0070.071
write.isatab0.0510.0130.085
write.study.file0.0440.0070.069