siggenes 1.43.0
Holger Schwender
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/siggenes | | Last Changed Rev: 102594 / Revision: 107696 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings siggenes_1.43.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/siggenes.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘siggenes/DESCRIPTION’ ... OK
* this is package ‘siggenes’ version ‘1.43.0’
* checking package namespace information ... OK
* 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 ‘siggenes’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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' call to ‘splines’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘KernSmooth’ ‘affy’ ‘annotate’ ‘scrime’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘annotate:::getTDRows’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.C("get_stat_num_denum", ..., PACKAGE = "multtest")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
checkDBs: no visible global function definition for ‘getAnnMap’
chisqEbamMissing: no visible global function definition for
‘rowChisq2Class’
chisqEbamMissing: no visible global function definition for
‘rowChisqMultiClass’
chisqStatMissing: no visible global function definition for
‘rowChisq2Class’
chisqStatMissing: no visible global function definition for
‘rowChisqMultiClass’
fuzzy.ebam: no visible global function definition for ‘rowTrendFuzzy’
fuzzy.ebam: no visible global function definition for ‘abf’
fuzzy.stat: no visible global function definition for ‘rowTrendFuzzy’
fuzzy.stat: no visible global function definition for ‘abf’
make.tablecode: no visible global function definition for
‘cleancdfname’
make.tablecode: no visible global function definition for ‘geneNames’
make.tablecode: no visible global function definition for ‘lookUp’
make.tablecode: no visible global function definition for
‘shortenGeneDescription’
nclass.wand: no visible global function definition for ‘dpih’
trend.ebam.list: no visible global function definition for ‘rowCATTs’
trend.ebam.list: no visible global function definition for
‘rowMsquares’
trend.stat.list: no visible global function definition for ‘rowCATTs’
trend.stat.list: no visible global function definition for
‘rowMsquares’
identify,SAM : .local: no visible global function definition for
‘lookUp’
identify,SAM : .local: no visible global function definition for
‘getSYMBOL’
summary,EBAM : .local: no visible global function definition for
‘lookUp’
summary,EBAM : .local: no visible global function definition for
‘getSYMBOL’
summary,SAM : .local: no visible global function definition for
‘lookUp’
summary,SAM : .local: no visible global function definition for
‘getSYMBOL’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/siggenes.Rcheck/00check.log’
for details.
* installing *source* package ‘siggenes’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘siggenes’
Creating a generic function for ‘identify’ from package ‘graphics’ in package ‘siggenes’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (siggenes)