BioC 3.3: CHECK report for QDNAseq on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:33 -0400 (Tue, 27 Oct 2015).
QDNAseq 1.7.0 Daoud Sie
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QDNAseq | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
Summary
Package: QDNAseq |
Version: 1.7.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings QDNAseq_1.7.0.tar.gz |
StartedAt: 2015-10-27 07:03:13 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 07:06:12 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 178.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: QDNAseq.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings QDNAseq_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/QDNAseq.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 ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.7.0’
* 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 ‘QDNAseq’ can be installed ... [10s/10s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘log2adhoc’ ‘sqrtadhoc’
* 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 ... [59s/59s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
frequencyPlot 15.929 0.016 15.957
callBins 15.337 0.012 15.355
segmentBins 6.832 0.004 6.841
normalizeSegmentedBins 6.345 0.004 6.362
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘QDNAseq,reproducibility.R’ [7s/7s]
Running ‘QDNAseq.R’ [11s/11s]
[19s/19s] 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/QDNAseq.Rcheck/00check.log’
for details.
QDNAseq.Rcheck/00install.out:
* installing *source* package ‘QDNAseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (QDNAseq)
QDNAseq.Rcheck/QDNAseq-Ex.timings:
name | user | system | elapsed
|
addPhenodata | 0.189 | 0.000 | 0.189 |
|
applyFilters | 0.554 | 0.004 | 0.558 |
|
binReadCounts | 0.001 | 0.000 | 0.001 |
|
callBins | 15.337 | 0.012 | 15.355 |
|
compareToReference | 1.403 | 0.000 | 1.403 |
|
correctBins | 1.083 | 0.000 | 1.083 |
|
createBins | 0.001 | 0.000 | 0.001 |
|
estimateCorrection | 1.007 | 0.004 | 1.011 |
|
exportBins | 0.001 | 0.000 | 0.001 |
|
frequencyPlot | 15.929 | 0.016 | 15.957 |
|
getBinAnnotations | 0.001 | 0.000 | 0.000 |
|
highlightFilters | 0.520 | 0.008 | 0.529 |
|
isobarPlot | 0.458 | 0.008 | 0.467 |
|
makeCgh | 0.812 | 0.008 | 0.821 |
|
noisePlot | 0.631 | 0.004 | 0.637 |
|
normalizeBins | 1.125 | 0.004 | 1.131 |
|
normalizeSegmentedBins | 6.345 | 0.004 | 6.362 |
|
plot | 1.246 | 0.004 | 1.255 |
|
poolRuns | 0.221 | 0.000 | 0.221 |
|
segmentBins | 6.832 | 0.004 | 6.841 |
|
smoothOutlierBins | 1.051 | 0.000 | 1.052 |
|