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BioC 2.14: CHECK report for cobindR on moscato2

This page was generated on 2014-10-08 08:55:49 -0700 (Wed, 08 Oct 2014).

Package 176/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cobindR 1.2.0
Manuela Benary
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/cobindR
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 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 

Summary

Package: cobindR
Version: 1.2.0
Command: rm -rf cobindR.buildbin-libdir && mkdir cobindR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.2.0.tar.gz >cobindR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.2.0.tar.gz
StartedAt: 2014-10-08 00:05:30 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:15:49 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 618.9 seconds
RetCode: 0
Status:  OK  
CheckDir: cobindR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cobindR.buildbin-libdir && mkdir cobindR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cobindR.buildbin-libdir cobindR_1.2.0.tar.gz >cobindR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cobindR.buildbin-libdir --install="check:cobindR-install.out" --force-multiarch --no-vignettes --timings cobindR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/cobindR.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cobindR/DESCRIPTION' ... OK
* this is package 'cobindR' version '1.2.0'
* 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 whether package 'cobindR' can be installed ... 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
* 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
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 ...
** running examples for arch 'i386' ... [176s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
testCpG                26.89   0.00   26.91
search.pwm             25.76   0.00   25.83
rtfbs                  21.81   0.05   21.95
search.gadem           18.57   0.00   18.58
write.sequences        15.35   0.00   15.35
plot.gc                 7.52   0.02    7.57
bg_binding_sites        6.26   0.19    7.19
bg_pairs                5.88   0.01    5.90
binding_sites           5.75   0.00    5.76
configuration           5.64   0.00    5.65
sequences               5.52   0.00    5.52
bg_sequences            5.43   0.02    5.45
pfm                     5.34   0.01    5.35
experiment_description  5.32   0.00    5.43
pairs_of_interest       5.29   0.00    5.29
** running examples for arch 'x64' ... [206s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
testCpG                34.69   0.02   34.72
search.pwm             30.35   0.03   30.48
rtfbs                  25.65   0.00   25.74
search.gadem           20.07   0.00   20.08
write.sequences        18.66   0.02   18.67
plot.gc                 8.83   0.03    8.91
bg_binding_sites        7.16   0.21    7.44
pfm                     6.88   0.00    6.88
bg_pairs                6.63   0.00    6.63
experiment_description  6.52   0.02    6.54
sequences               6.36   0.00    6.36
binding_sites           6.25   0.00    6.25
pairs_of_interest       6.21   0.02    6.22
configuration           6.10   0.00    6.09
bg_sequences            6.07   0.00    6.07
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [7s]
 [8s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [8s]
 [8s] 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
  'E:/biocbld/bbs-2.14-bioc/meat/cobindR.Rcheck/00check.log'
for details.

cobindR.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'cobindR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cobindR' as cobindR_1.2.0.zip
* DONE (cobindR)

cobindR.Rcheck/examples_i386/cobindR-Ex.timings:

nameusersystemelapsed
SeqObj-class000
bg_binding_sites6.260.197.19
bg_pairs5.880.015.90
bg_sequence_origin000
bg_sequence_source0.020.000.01
bg_sequence_type000
bg_sequences5.430.025.45
binding_sites5.750.005.76
cobindRConfiguration0.020.000.01
cobindr-class000
comment0.190.000.19
configuration-class000
configuration5.640.005.65
downstream0.020.000.01
experiment_description5.320.005.43
fdrThreshold000
get.bindingsite.ranges000
id0.020.000.01
location0.120.000.13
mart000
max_distance000
name0.110.000.13
pValue0.020.000.02
pairs000
pairs_of_interest5.290.005.29
path0.010.000.01
pfm5.340.015.35
pfm_path000
plot.gc7.520.027.57
pseudocount0.010.000.01
rtfbs21.81 0.0521.95
search.gadem18.57 0.0018.58
search.pwm25.76 0.0025.83
seqObj0.120.010.14
sequence0.170.030.21
sequence_origin000
sequence_source000
sequence_type0.010.000.01
sequences5.520.005.52
species0.020.000.02
testCpG26.89 0.0026.91
threshold0.020.000.02
uid0.120.000.12
upstream000
write.sequences15.35 0.0015.35

cobindR.Rcheck/examples_x64/cobindR-Ex.timings:

nameusersystemelapsed
SeqObj-class0.020.000.02
bg_binding_sites7.160.217.44
bg_pairs6.630.006.63
bg_sequence_origin0.010.000.01
bg_sequence_source000
bg_sequence_type0.020.000.02
bg_sequences6.070.006.07
binding_sites6.250.006.25
cobindRConfiguration0.020.000.02
cobindr-class000
comment0.120.020.14
configuration-class000
configuration6.100.006.09
downstream000
experiment_description6.520.026.54
fdrThreshold0.020.000.01
get.bindingsite.ranges000
id000
location0.120.010.14
mart000
max_distance000
name0.140.020.15
pValue000
pairs000
pairs_of_interest6.210.026.22
path000
pfm6.880.006.88
pfm_path000
plot.gc8.830.038.91
pseudocount0.010.000.02
rtfbs25.65 0.0025.74
search.gadem20.07 0.0020.08
search.pwm30.35 0.0330.48
seqObj0.130.000.12
sequence0.130.000.12
sequence_origin0.010.000.02
sequence_source000
sequence_type000
sequences6.360.006.36
species0.020.000.02
testCpG34.69 0.0234.72
threshold000
uid0.110.010.12
upstream000
write.sequences18.66 0.0218.67