BioC 3.1: CHECK report for clippda on moscato2
This page was generated on 2015-10-09 09:28:37 -0700 (Fri, 09 Oct 2015).
clippda 1.18.0 Stephen Nyangoma
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/clippda | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 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
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Version: 1.18.0
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Command: rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.18.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.18.0.tar.gz
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StartedAt: 2015-10-09 00:23:35 -0700 (Fri, 09 Oct 2015)
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EndedAt: 2015-10-09 00:33:13 -0700 (Fri, 09 Oct 2015)
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EllapsedTime: 578.2 seconds
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RetCode: 0
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Status: WARNINGS
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CheckDir: clippda.Rcheck
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Warnings: 1
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Command output
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### Running command:
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### rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.18.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.18.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/clippda.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clippda/DESCRIPTION' ... OK
* this is package 'clippda' version '1.18.0'
* checking package namespace information ... NOTE
Namespaces with empty importFrom:
'Biobase' 'tools'
* 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 whether package 'clippda' 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 ... 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
* 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 ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ZvaluesfrommultinomPlots: no visible global function definition for
'cloud'
* 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 ...
** running examples for arch 'i386' ... [262s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
clippda-package 113.32 0.33 113.64
sampleSize 69.64 0.15 69.80
sampleSizeParameters 34.39 0.11 34.51
sample_technicalVariance 12.06 0.00 12.06
spectrumFilter 6.29 0.00 6.29
liverdata 5.56 0.01 5.56
replicateCorrelations 5.50 0.00 5.51
** running examples for arch 'x64' ... [242s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
clippda-package 108.94 0.28 109.22
sampleSize 62.65 0.07 62.76
sampleSizeParameters 31.07 0.00 31.07
sample_technicalVariance 7.71 0.02 7.74
replicateCorrelations 5.45 0.00 5.44
liverdata 5.40 0.00 5.40
* 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 WARNING, 4 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/clippda.Rcheck/00check.log'
for details.
clippda.Rcheck/00install.out:
install for i386
* installing *source* package 'clippda' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'clippda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clippda' as clippda_1.18.0.zip
* DONE (clippda)
clippda.Rcheck/examples_i386/clippda-Ex.timings:
name | user | system | elapsed
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ZvaluescasesVcontrolsPlots | 0.07 | 0.00 | 0.20 |
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ZvaluesfrommultinomPlots | 0.86 | 0.02 | 0.87 |
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aclinicalProteomicsData-class | 0.1 | 0.0 | 0.1 |
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aclinicalProteomicsData-methods | 0.35 | 0.03 | 0.39 |
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betweensampleVariance | 2.13 | 0.01 | 2.13 |
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checkNo.replicates | 0.17 | 0.00 | 0.18 |
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clippda-package | 113.32 | 0.33 | 113.64 |
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f | 0 | 0 | 0 |
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fisherInformation | 0.15 | 0.02 | 0.17 |
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liverRawData | 0 | 0 | 0 |
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liver_pheno | 0.01 | 0.00 | 0.02 |
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liverdata | 5.56 | 0.01 | 5.56 |
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mostSimilarTwo | 0 | 0 | 0 |
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negativeIntensitiesCorrection | 1.95 | 0.02 | 1.97 |
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phenoDataFrame | 0.09 | 0.00 | 0.09 |
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pheno_urine | 0.02 | 0.00 | 0.02 |
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preProcRepeatedPeakData | 4.49 | 0.00 | 4.49 |
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proteomicsExprsData | 0.23 | 0.00 | 0.24 |
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proteomicspData | 0.10 | 0.00 | 0.09 |
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replicateCorrelations | 5.50 | 0.00 | 5.51 |
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sampleClusteredData | 2.53 | 0.00 | 2.52 |
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sampleSize | 69.64 | 0.15 | 69.80 |
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sampleSize3DscatterPlots | 0.02 | 0.02 | 0.03 |
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sampleSizeContourPlots | 0.03 | 0.00 | 0.03 |
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sampleSizeParameters | 34.39 | 0.11 | 34.51 |
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sample_technicalVariance | 12.06 | 0.00 | 12.06 |
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spectrumFilter | 6.29 | 0.00 | 6.29 |
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ztwo | 0 | 0 | 0 |
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clippda.Rcheck/examples_x64/clippda-Ex.timings:
name | user | system | elapsed
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ZvaluescasesVcontrolsPlots | 0.09 | 0.00 | 0.10 |
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ZvaluesfrommultinomPlots | 0.98 | 0.00 | 0.99 |
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aclinicalProteomicsData-class | 0.08 | 0.01 | 0.09 |
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aclinicalProteomicsData-methods | 0.31 | 0.08 | 0.39 |
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betweensampleVariance | 2.69 | 0.00 | 2.68 |
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checkNo.replicates | 0.23 | 0.02 | 0.25 |
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clippda-package | 108.94 | 0.28 | 109.22 |
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f | 0 | 0 | 0 |
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fisherInformation | 0.12 | 0.00 | 0.12 |
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liverRawData | 0 | 0 | 0 |
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liver_pheno | 0 | 0 | 0 |
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liverdata | 5.4 | 0.0 | 5.4 |
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mostSimilarTwo | 0 | 0 | 0 |
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negativeIntensitiesCorrection | 1.90 | 0.00 | 1.91 |
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phenoDataFrame | 0.08 | 0.01 | 0.09 |
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pheno_urine | 0 | 0 | 0 |
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preProcRepeatedPeakData | 4.76 | 0.02 | 4.77 |
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proteomicsExprsData | 0.23 | 0.00 | 0.24 |
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proteomicspData | 0.09 | 0.02 | 0.11 |
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replicateCorrelations | 5.45 | 0.00 | 5.44 |
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sampleClusteredData | 1.89 | 0.00 | 1.89 |
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sampleSize | 62.65 | 0.07 | 62.76 |
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sampleSize3DscatterPlots | 0.12 | 0.00 | 0.12 |
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sampleSizeContourPlots | 0.05 | 0.00 | 0.05 |
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sampleSizeParameters | 31.07 | 0.00 | 31.07 |
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sample_technicalVariance | 7.71 | 0.02 | 7.74 |
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spectrumFilter | 4.34 | 0.00 | 4.34 |
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ztwo | 0 | 0 | 0 |
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