chipenrich 1.8.0
Raymond G. Cavalcante , Chee Lee
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/chipenrich | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf chipenrich.buildbin-libdir chipenrich.Rcheck && mkdir chipenrich.buildbin-libdir chipenrich.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_1.8.0.tar.gz >chipenrich.Rcheck\00install.out 2>&1 && cp chipenrich.Rcheck\00install.out chipenrich-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_1.8.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/chipenrich.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chipenrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chipenrich' 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 whether package 'chipenrich' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Chee Lee <cheelee@umich.edu> [aut, cre]
Raymond G. Cavalcante <rcavalca@umich.edu> [aut, cre]
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chipenrich: no visible binding for global variable 'P.value'
load_peaks: no visible binding for global variable 'chrom'
randomize_locusdef : <anonymous>: no visible binding for global
variable 'chrom'
read_bed: no visible binding for global variable 'chrom'
read_bedgff: no visible binding for global variable 'chrom'
read_peaks: no visible binding for global variable 'chrom'
setup_ldef: no visible binding for global variable 'chrom'
test_approx: no visible binding for global variable 'geneid'
test_binomial: no visible binding for global variable 'geneid'
test_fisher_exact: no visible binding for global variable 'geneid'
test_gam: no visible binding for global variable 'geneid'
test_gam_ratio: no visible binding for global variable 'geneid'
test_gam_ratio_splineless: no visible binding for global variable
'geneid'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [95s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
chipenrich 39.50 0.05 40.68
plot_spline_length 22.34 0.15 22.50
plot_expected_peaks 21.31 0.06 21.37
** running examples for arch 'x64' ... [104s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
chipenrich 40.79 0.08 40.87
plot_spline_length 25.75 0.16 25.91
plot_expected_peaks 24.68 0.02 24.70
plot_gene_coverage 6.63 0.04 6.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [49s]
[49s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [57s]
[57s] 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 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/chipenrich.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'chipenrich' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'chipenrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipenrich' as chipenrich_1.8.0.zip
* DONE (chipenrich)