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### Running command:
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### /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_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/farms.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘farms’ version ‘1.52.0’
* 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 startup messages can be suppressed ... 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-3.17-bioc-mac-arm64/meat/farms.Rcheck/00check.log’
for details.
