BioC 3.3: CHECK report for TarSeqQC on linux2.bioconductor.org

Package: TarSeqQC

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.1.0.tar.gz

StartedAt: 2015-10-27 08:32:58 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:35:37 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 159.2 seconds

RetCode: 0

Status:  OK

CheckDir: TarSeqQC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TarSeqQC.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TarSeqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TarSeqQC’ version ‘1.1.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TarSeqQC’ can be installed ... [8s/8s] 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘TarSeqQC’ for: ‘plot’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [96s/32s] OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
TargetExperiment-setters           23.371  2.524   7.534
pileupCounts                       20.974  1.727   5.504
TargetExperiment-initialize        15.912  2.531   7.131
TargetExperiment-buildFeaturePanel 14.136  1.083   6.070
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [84s/33s]
 [84s/33s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.

* installing *source* package ‘TarSeqQC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘TarSeqQC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TarSeqQC)

name	user	system	elapsed
TargetExperiment-buildFeaturePanel	14.136	1.083	6.070
TargetExperiment-buildReport	3.081	0.660	0.748
TargetExperiment-constructor	0.002	0.000	0.002
TargetExperiment-getters	0.186	0.024	0.210
TargetExperiment-initialize	15.912	2.531	7.131
TargetExperiment-plot	0.001	0.000	0.001
TargetExperiment-plotAttrExpl	0.001	0.000	0.001
TargetExperiment-plotFeatPerform	1.073	0.359	0.002
TargetExperiment-plotFeature	0.540	0.165	0.001
TargetExperiment-plotGeneAttrPerFeat	0.000	0.000	0.001
TargetExperiment-plotNtdPercentage	0.001	0.000	0.000
TargetExperiment-plotRegion	0.001	0.000	0.002
TargetExperiment-print	0.026	0.004	0.030
TargetExperiment-setters	23.371	2.524	7.534
TargetExperiment-show	0.577	0.157	0.031
TargetExperiment-statistics	0.018	0.000	0.018
TargetExperiment-summarizePanel	0.565	0.234	0.945
pileupCounts	20.974	1.727	5.504