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BioC 2.13: CHECK report for cobindR on zin1

This page was generated on 2014-04-05 09:48:42 -0700 (Sat, 05 Apr 2014).

Package 162/750HostnameOS / ArchBUILDCHECKBUILD BIN
cobindR 1.0.0
Manuela Benary
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/cobindR
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: cobindR
Version: 1.0.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings cobindR_1.0.0.tar.gz
StartedAt: 2014-04-05 00:29:04 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:33:24 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 259.6 seconds
RetCode: 0
Status:  OK 
CheckDir: cobindR.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/cobindR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.0.0’
* 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 ... [13s/13s] OK
* 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 ... OK
* 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 ‘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’
* 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 ... [191s/132s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
testCpG                26.010  0.852  20.083
search.pwm             22.998  1.236  15.329
rtfbs                  21.885  1.152  13.198
search.gadem           16.713  0.476  13.107
write.sequences        15.841  0.416  12.571
plot.gc                 9.196  5.876   7.768
sequences               9.508  0.412   4.653
bg_pairs                6.788  0.584   5.167
bg_binding_sites        6.176  0.340   5.264
experiment_description  5.868  0.368   4.719
bg_sequences            5.785  0.384   4.419
binding_sites           5.796  0.344   4.734
configuration           5.756  0.368   4.700
pairs_of_interest       5.641  0.448   4.492
pfm                     5.669  0.388   4.454
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [6s/6s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/cobindR.Rcheck/00check.log’
for details.

cobindR.Rcheck/00install.out:

* installing *source* package ‘cobindR’ ...
** R
** inst
** preparing package for lazy loading
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
* DONE (cobindR)

cobindR.Rcheck/cobindR-Ex.timings:

nameusersystemelapsed
SeqObj-class0.0040.0000.004
bg_binding_sites6.1760.3405.264
bg_pairs6.7880.5845.167
bg_sequence_origin0.0080.0000.011
bg_sequence_source0.0040.0080.013
bg_sequence_type0.0120.0000.012
bg_sequences5.7850.3844.419
binding_sites5.7960.3444.734
cobindRConfiguration0.0080.0000.011
cobindr-class0.0040.0000.004
comment0.1040.0160.119
configuration-class0.0000.0040.004
configuration5.7560.3684.700
downstream0.0080.0040.012
experiment_description5.8680.3684.719
fdrThreshold0.0160.0000.015
get.bindingsite.ranges0.0040.0000.003
id0.0080.0000.012
location0.2760.0400.314
mart0.0080.0000.009
max_distance0.0080.0000.009
name0.1040.0120.119
pValue0.0120.0000.010
pairs0.0040.0040.011
pairs_of_interest5.6410.4484.492
path0.0120.0000.010
pfm5.6690.3884.454
pfm_path0.0080.0000.010
plot.gc9.1965.8767.768
pseudocount0.0120.0000.012
rtfbs21.885 1.15213.198
search.gadem16.713 0.47613.107
search.pwm22.998 1.23615.329
seqObj0.1240.0160.141
sequence0.1320.0000.136
sequence_origin0.0120.0000.011
sequence_source0.0120.0000.011
sequence_type0.0080.0040.010
sequences9.5080.4124.653
species0.0080.0000.011
testCpG26.010 0.85220.083
threshold0.0120.0000.013
uid0.1320.0040.135
upstream0.0120.0000.011
write.sequences15.841 0.41612.571