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This page was generated on 2021-11-26 15:05:49 -0500 (Fri, 26 Nov 2021).

CHECK results for farms on machv2

To the developers/maintainers of the farms package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/farms.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 624/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
farms 1.46.0  (landing page)
Djork-Arne Clevert
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/farms
git_branch: RELEASE_3_14
git_last_commit: a3cde8d
git_last_commit_date: 2021-10-26 11:56:52 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: farms
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:farms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings farms_1.46.0.tar.gz
StartedAt: 2021-11-25 16:32:35 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 16:33:28 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 53.3 seconds
RetCode: 0
Status:   OK  
CheckDir: farms.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:farms.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings farms_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/farms.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘farms’ version ‘1.46.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘methods’
* 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 ‘farms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘MASS’ ‘methods’ ‘Biobase’
A package should be listed in only one of these fields.
* 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' calls to packages already attached by Depends:
  ‘affy’ ‘methods’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Biobase’ ‘utils’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘MASS’
  All declared Imports should be used.
Package in Depends field not imported from: ‘MASS’
  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
File ‘farms/R/zzz.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)
    packageStartupMessage(" _                             ", "\n",     "| |                            ", "\n", "| |  __,   ,_    _  _  _    ,  ",     "\n", "|/  /  |  /  |  / |/ |/ |  / \\_", "\n", "|__/\\_/|_/   |_/  |  |  |_/ \\/ ",     "\n", "|\\                             ", "\n", "|/   ",     "\n")
    require(utils)
    require(Biobase, quietly = TRUE)
    require(affy, quietly = TRUE)
    packageStartupMessage("Citation: S. Hochreiter et al.,", "\n",     "A new summarization method for affymetrix probe level data,",     "\n", "Bioinformatics, 22, 8, 943-949, 2006", "\n", "\n",     "Citation: W. Talloen et al.,", "\n", "I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data,",     "\n", "Bioinformatics, 23, 21, 2897-2902, 2007", "\n", "BibTex: enter 'toBibtex(citation(\"farms\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/farms/farms.html",     "\n\n", "FARMS Package Version ", version, "\n")
    packageStartupMessage("\n", "Changes in FARMS:", "\n", "For all changes previous to 1.3.0, see the farms vignette.",     "\n", "Version 1.3.0: Added I/NI-calls for filtering", "\n",     "               Adjusted Hyperparameters for alternative CDFs,",     "\n", "               probes set standardized, weighted mean",     "\n", "               Works now with R >= 2.8 and Bioconductor 2.3,",     "\n", "               Changed termination criterion, initialization values,",     "\n", "               factors and loadings scaled, added argument robust",     "\n", "               Update for R-2.11", "\n", "               Updated I/NI-Call for Laplace-FARMS version,",     "\n", "               Maximum likelihood correlation structure given",     "\n", "               non-negative constraints", "\n", "Version 1.4.0: Default centering changed to median",     "\n", "Version 1.8.x: Suppression of spurious correlation (Laplace-FARMS)",     "\n")

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

plot,INI_Calls-missing: no visible global function definition for
  ‘truehist’
Undefined global functions or variables:
  truehist
* 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 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/farms.Rcheck/00check.log’
for details.



Installation output

farms.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL farms
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘farms’ ...
** 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
* DONE (farms)

Tests output


Example timings

farms.Rcheck/farms-Ex.timings

nameusersystemelapsed
INI_Calls-class0.1860.0190.205
INIcalls-methods0.2310.0050.236
expFarms0.0300.0030.033
generateExprVal.method.farms0.0040.0030.007
getI_Eset-methods0.0570.0040.061
getI_ProbeSets-methods0.0500.0040.055
getNI_Eset-methods0.0510.0030.054
getNI_ProbeSets-methods0.0560.0020.059
lFarms0.0470.0030.051
plot-methods0.0480.0030.052
qFarms0.0250.0030.027
summary-methods0.0410.0020.045