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BioC 3.2: CHECK report for farms on perceval

This page was generated on 2015-11-10 14:46:43 -0800 (Tue, 10 Nov 2015).

Package 335/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
farms 1.22.0
Djork-Arne Clevert
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/farms
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: farms
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings farms_1.22.0.tar.gz
StartedAt: 2015-11-10 04:40:22 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 04:41:04 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 42.1 seconds
RetCode: 0
Status:  OK 
CheckDir: farms.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings farms_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/farms.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.22.0’
* 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 ... [3s/3s] 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 : .local: no visible global function definition
  for ‘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 ... [2s/2s] 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-3.2-bioc/meat/farms.Rcheck/00check.log’
for details.


farms.Rcheck/00install.out:

* 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)

farms.Rcheck/farms-Ex.timings:

nameusersystemelapsed
INI_Calls-class0.1990.0100.209
INIcalls-methods0.0590.0010.061
expFarms0.0360.0000.037
generateExprVal.method.farms0.0050.0010.021
getI_Eset-methods0.0590.0010.062
getI_ProbeSets-methods0.0640.0020.066
getNI_Eset-methods0.0610.0010.063
getNI_ProbeSets-methods0.0580.0010.060
lFarms0.0350.0020.036
plot-methods0.0610.0020.063
qFarms0.0370.0010.037
summary-methods0.0650.0020.067