BioC 3.5: CHECK report for farms on oaxaca

Package: farms

Version: 1.27.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings farms_1.27.0.tar.gz

StartedAt: 2017-03-04 02:40:02 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:40:54 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 52.0 seconds

RetCode: 0

Status:  OK

CheckDir: farms.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings farms_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/farms.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.27.0’
* 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 loading without being on the library search path ... 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 installed files from ‘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-3.5-bioc/meat/farms.Rcheck/00check.log’
for details.

* installing *source* package ‘farms’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (farms)

name	user	system	elapsed
INI_Calls-class	0.489	0.011	0.500
INIcalls-methods	0.392	0.003	0.395
expFarms	0.022	0.001	0.022
generateExprVal.method.farms	0.005	0.001	0.059
getI_Eset-methods	0.041	0.001	0.042
getI_ProbeSets-methods	0.034	0.002	0.036
getNI_Eset-methods	0.043	0.001	0.045
getNI_ProbeSets-methods	0.041	0.002	0.042
lFarms	0.035	0.002	0.037
plot-methods	0.039	0.001	0.041
qFarms	0.056	0.001	0.057
summary-methods	0.044	0.001	0.046