minfi 1.15.11
Kasper Daniel Hansen
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/minfi | | Last Changed Rev: 106951 / Revision: 107696 | | Last Changed Date: 2015-07-31 08:51:31 -0700 (Fri, 31 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.15.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.15.11’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘GenomicRanges’
‘SummarizedExperiment’ ‘Biostrings’ ‘bumphunter’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘minfi’ can be installed ... [26s/26s] WARNING
Found the following significant warnings:
Warning: /Users/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck/00_pkg_src/minfi/man/mdsPlot.Rd:68: unexpected END_OF_INPUT '}
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck/00install.out’ for details.
* 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
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’
‘SummarizedExperiment:::.valid.SummarizedExperiment0.assays_ncol’
‘bumphunter:::.getEstimate’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
prepare_Rd: mdsPlot.Rd:68: unexpected END_OF_INPUT '}
'
* 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 ... [461s/537s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gaphunter 245.513 2.262 285.126
bumphunter 46.337 9.663 58.389
compartments 43.219 2.391 45.869
detectionP 22.426 0.771 23.271
read.450k.exp 8.807 0.354 11.741
read.450k 7.530 0.479 10.474
preprocessIllumina 7.659 0.349 14.111
minfiQC 7.129 0.645 15.292
densityBeanPlot 7.053 0.360 7.523
densityPlot 6.130 0.588 6.746
preprocessRaw 6.172 0.326 9.385
getSex 5.565 0.408 11.734
getAnnotation 2.899 0.123 5.967
makeGenomicRatioSetFromMatrix 2.200 0.176 5.132
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [223s/331s]
[223s/332s] 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: 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck/00check.log’
for details.
* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
Warning: /Users/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck/00_pkg_src/minfi/man/mdsPlot.Rd:68: unexpected END_OF_INPUT '}
'
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (minfi)