BioC 2.14: CHECK report for clippda on morelia
This page was generated on 2014-10-08 09:04:03 -0700 (Wed, 08 Oct 2014).
clippda 1.14.0
Stephen Nyangoma
| 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/clippda | | 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 | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |
Summary
| Package: clippda |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.14.0.tar.gz |
| StartedAt: 2014-10-07 22:00:04 -0700 (Tue, 07 Oct 2014) |
| EndedAt: 2014-10-07 22:06:31 -0700 (Tue, 07 Oct 2014) |
| EllapsedTime: 387.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clippda.Rcheck |
| Warnings: 1 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/clippda.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘limma’ ‘statmod’ ‘rgl’ ‘lattice’ ‘scatterplot3d’ ‘Biobase’ ‘tools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘clippda’ can be installed ... [5s/5s] 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in bibentry(bibtype = entry, textVersion = textVersion, header = header, footer = footer, ...): argument "textVersion" is missing, with no default
* 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 to packages already attached by Depends:
‘lattice’ ‘limma’ ‘rgl’ ‘scatterplot3d’ ‘statmod’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘lattice’ ‘rgl’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [318s/319s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
clippda-package 136.245 4.255 140.699
sampleSize 84.809 2.463 87.456
sampleSizeParameters 42.638 1.219 43.908
sample_technicalVariance 9.663 0.372 10.045
replicateCorrelations 6.867 0.215 7.098
liverdata 5.944 0.072 6.021
spectrumFilter 5.098 0.078 5.180
preProcRepeatedPeakData 5.021 0.082 5.113
* 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
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/clippda.Rcheck/00check.log’
for details.
clippda.Rcheck/00install.out:
* installing *source* package ‘clippda’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (clippda)
clippda.Rcheck/clippda-Ex.timings:
| name | user | system | elapsed
|
| ZvaluescasesVcontrolsPlots | 0.060 | 0.001 | 0.062 |
|
| ZvaluesfrommultinomPlots | 0.834 | 0.030 | 0.870 |
|
| aclinicalProteomicsData-class | 0.063 | 0.003 | 0.067 |
|
| aclinicalProteomicsData-methods | 0.564 | 0.216 | 0.781 |
|
| betweensampleVariance | 4.230 | 0.063 | 4.294 |
|
| checkNo.replicates | 0.511 | 0.021 | 0.533 |
|
| clippda-package | 136.245 | 4.255 | 140.699 |
|
| f | 0.002 | 0.000 | 0.002 |
|
| fisherInformation | 0.090 | 0.002 | 0.092 |
|
| liverRawData | 0.005 | 0.000 | 0.005 |
|
| liver_pheno | 0.001 | 0.000 | 0.002 |
|
| liverdata | 5.944 | 0.072 | 6.021 |
|
| mostSimilarTwo | 0.003 | 0.000 | 0.003 |
|
| negativeIntensitiesCorrection | 2.048 | 0.014 | 2.077 |
|
| phenoDataFrame | 0.065 | 0.002 | 0.066 |
|
| pheno_urine | 0.002 | 0.000 | 0.003 |
|
| preProcRepeatedPeakData | 5.021 | 0.082 | 5.113 |
|
| proteomicsExprsData | 0.258 | 0.006 | 0.264 |
|
| proteomicspData | 0.063 | 0.005 | 0.069 |
|
| replicateCorrelations | 6.867 | 0.215 | 7.098 |
|
| sampleClusteredData | 1.948 | 0.021 | 1.976 |
|
| sampleSize | 84.809 | 2.463 | 87.456 |
|
| sampleSize3DscatterPlots | 0.019 | 0.001 | 0.021 |
|
| sampleSizeContourPlots | 0.036 | 0.002 | 0.038 |
|
| sampleSizeParameters | 42.638 | 1.219 | 43.908 |
|
| sample_technicalVariance | 9.663 | 0.372 | 10.045 |
|
| spectrumFilter | 5.098 | 0.078 | 5.180 |
|
| ztwo | 0.001 | 0.000 | 0.001 |
|