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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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.15.11.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/minfi.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 ‘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 ... [19s/19s] WARNING
Found the following significant warnings:
Warning: /home/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck/00_pkg_src/minfi/man/mdsPlot.Rd:68: unexpected END_OF_INPUT '}
See ‘/home/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 ... [393s/394s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gaphunter 270.293 0.132 271.053
bumphunter 37.531 0.843 38.484
compartments 30.410 0.008 30.425
detectionP 5.794 0.000 5.818
read.450k.exp 5.377 0.016 5.389
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [178s/224s]
[179s/224s] 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
‘/home/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck/00check.log’
for details.
* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading
** help
Warning: /home/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
* DONE (minfi)