cobindR 1.6.0
Manuela Benary
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cobindR | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | 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 cobindR_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/cobindR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘genoPlotR’
* 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 ‘cobindR’ can be installed ... [27s/28s] 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
'library' or 'require' calls in package code:
‘MotifDb’ ‘parallel’ ‘snowfall’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
parallelize: no visible global function definition for ‘mclapply’
parallelize: no visible global function definition for ‘sfCpus’
parallelize: no visible global function definition for ‘sfInit’
parallelize: no visible global function definition for ‘sfLapply’
parallelize: no visible global function definition for ‘sfStop’
query.motifDb: no visible binding for global variable ‘MotifDb’
get.bindingsite.ranges,cobindr : .local: no visible global function
definition for ‘GRanges’
get.bindingsite.ranges,cobindr : .local: no visible binding for global
variable ‘sequence_names’
get.bindingsite.ranges,cobindr : .local: no visible binding for global
variable ‘pwm’
plot.positions,cobindr : .local: no visible binding for global variable
‘n.cpu’
plot.positions,cobindr : .local: no visible global function definition
for ‘grid.newpage’
plot.positions,cobindr : .local: no visible global function definition
for ‘pushViewport’
plot.positions,cobindr : .local: no visible global function definition
for ‘viewport’
plot.positions,cobindr : .local: no visible global function definition
for ‘plot_gene_map’
plot.positions,cobindr : .local: no visible global function definition
for ‘popViewport’
plot.positions,cobindr : .local: no visible global function definition
for ‘gpar’
plot.positions,cobindr : .local: no visible global function definition
for ‘grid_legend’
plot.tfbs.venndiagram,cobindr : .local: no visible global function
definition for ‘venn.diagram’
plot.tfbs.venndiagram,cobindr : .local: no visible global function
definition for ‘grid.draw’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
function definition for ‘makePWM’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
function definition for ‘seqLogo’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
function definition for ‘grid.text’
plot.tfbslogo,cobindr : .local : <anonymous>: no visible global
function definition for ‘gpar’
search.gadem,cobindr : .local : <anonymous>: no visible global function
definition for ‘GADEM’
search.gadem,cobindr : .local: no visible global function definition
for ‘GADEM’
search.gadem,cobindr : .local: no visible global function definition
for ‘nMotifs’
search.pwm,cobindr : .local: no visible global function definition for
‘error’
write.bindingsites.table,cobindr : .local: no visible global function
definition for ‘mcols’
* 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 ... [410s/179s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot.gc 21.607 37.638 13.671
rtfbs 35.893 14.306 15.798
testCpG 34.897 11.868 23.984
search.pwm 31.638 11.108 19.728
search.gadem 27.231 8.146 17.304
write.sequences 25.856 8.219 17.647
sequences 13.259 3.257 6.247
pairs_of_interest 9.996 5.598 5.697
configuration 9.996 5.319 6.525
bg_binding_sites 9.584 4.351 7.378
bg_sequences 9.106 4.415 6.840
bg_pairs 8.934 4.549 6.024
binding_sites 8.547 4.894 5.944
pfm 7.415 2.667 5.587
experiment_description 6.271 2.049 5.484
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [14s/14s]
[14s/14s] 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/cobindR.Rcheck/00check.log’
for details.
* installing *source* package ‘cobindR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘sequence’ in package ‘cobindR’
Creating a generic function for ‘write’ from package ‘base’ in package ‘cobindR’
Creating a generic function for ‘write.fasta’ from package ‘seqinr’ in package ‘cobindR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cobindR)