XhybCasneuf 1.8.0
Tineke Casneuf
| Snapshot Date: 2016-04-20 09:20:20 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/XhybCasneuf | | Last Changed Rev: 3460 / Revision: 3730 | | Last Changed Date: 2015-10-13 13:14:23 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings XhybCasneuf_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/XhybCasneuf.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XhybCasneuf/DESCRIPTION’ ... OK
* this is package ‘XhybCasneuf’ version ‘1.8.0’
* 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 ‘XhybCasneuf’ can be installed ... [6s/6s] 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.
* 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
Packages in Depends field not imported from:
‘RColorBrewer’ ‘affy’ ‘ath1121501cdf’ ‘grid’ ‘methods’ ‘tinesath1cdf’
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
runSimulation: no visible binding for global variable
‘generateExprVal.method.mas’
runSimulation: no visible binding for global variable
‘generateExprVal.method.liwong’
plotExample,XhybExamples : .local: no visible global function
definition for ‘brewer.pal’
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
AffysTissue.noBl.rda 202Kb 154Kb xz
AffysTissue.rda 741Kb 491Kb xz
AffysTissueMC.rda 886Kb 589Kb xz
CustomsTissue.noBl.rda 153Kb 120Kb xz
CustomsTissue.rda 552Kb 372Kb xz
CustomsTissueMC.rda 688Kb 462Kb xz
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-data-experiment/meat/XhybCasneuf.Rcheck/00check.log’
for details.
* installing *source* package ‘XhybCasneuf’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ath1121501cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘ath1121501cdf’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ath1121501cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘ath1121501cdf’
* DONE (XhybCasneuf)