farms 1.35.0
Djork-Arne Clevert
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/farms |
| Branch: master |
| Last Commit: de025b6 |
| Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:farms.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings farms_1.35.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/farms.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'farms' version '1.35.0'
* 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 whether package 'farms' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/INI_Calls-class.rd:6: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/INIcalls-methods.rd:20: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/INIcalls-methods.rd:22: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/INIcalls-methods.rd:14: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/expFarms.rd:5: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/expFarms.rd:35: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/generateExprVal.method.farms.rd:39: file link 'li.wong' in package 'affy' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/generateExprVal.method.farms.rd:39: file link 'medianpolish' in package 'affy' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/getI_Eset-methods.rd:8: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/getI_Eset-methods.rd:18: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/getNI_Eset-methods.rd:10: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/getNI_Eset-methods.rd:20: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/lFarms.rd:6: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/lFarms.rd:32: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/plot-methods.rd:20: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/qFarms.rd:6: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/qFarms.rd:33: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZUZlR/R.INSTALL1ab86e271bf2/farms/man/summary-methods.rd:19: file link 'exprSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/farms.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/farms.Rcheck/00check.log'
for details.