BioC 3.2: CHECK report for clippda on windows1.bioconductor.org
This page was generated on 2015-10-27 17:28:58 -0400 (Tue, 27 Oct 2015).
clippda 1.20.0
Stephen Nyangoma
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/clippda | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
Summary
| Package: clippda
|
| Version: 1.20.0
|
| Command: rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.20.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.20.0.tar.gz
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| StartedAt: 2015-10-27 00:36:48 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 00:43:51 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 422.6 seconds
|
| RetCode: 0
|
| Status: WARNINGS
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| CheckDir: clippda.Rcheck
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| Warnings: 1
|
Command output
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### Running command:
###
### rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.20.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.20.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/clippda.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.20.0'
* 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' ... [183s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
clippda-package 82.05 0.25 82.30
sampleSize 46.22 0.09 46.31
sampleSizeParameters 23.15 0.03 23.19
sample_technicalVariance 6.19 0.02 6.20
** running examples for arch 'x64' ... [183s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
clippda-package 80.94 0.21 81.14
sampleSize 48.46 0.02 48.50
sampleSizeParameters 23.23 0.03 23.26
sample_technicalVariance 5.99 0.00 5.99
* 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
'C:/biocbld/bbs-3.2-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_1.20.0.zip
* DONE (clippda)
clippda.Rcheck/examples_i386/clippda-Ex.timings:
| name | user | system | elapsed
|
| ZvaluescasesVcontrolsPlots | 0.06 | 0.00 | 0.06 |
|
| ZvaluesfrommultinomPlots | 0.64 | 0.03 | 0.67 |
|
| aclinicalProteomicsData-class | 0.1 | 0.0 | 0.1 |
|
| aclinicalProteomicsData-methods | 0.29 | 0.11 | 0.40 |
|
| betweensampleVariance | 1.83 | 0.00 | 1.83 |
|
| checkNo.replicates | 0.17 | 0.00 | 0.17 |
|
| clippda-package | 82.05 | 0.25 | 82.30 |
|
| f | 0 | 0 | 0 |
|
| fisherInformation | 0.07 | 0.02 | 0.07 |
|
| liverRawData | 0.01 | 0.00 | 0.02 |
|
| liver_pheno | 0 | 0 | 0 |
|
| liverdata | 4.82 | 0.00 | 4.81 |
|
| mostSimilarTwo | 0 | 0 | 0 |
|
| negativeIntensitiesCorrection | 1.93 | 0.00 | 1.94 |
|
| phenoDataFrame | 0.07 | 0.01 | 0.08 |
|
| pheno_urine | 0 | 0 | 0 |
|
| preProcRepeatedPeakData | 3.59 | 0.00 | 3.59 |
|
| proteomicsExprsData | 0.19 | 0.02 | 0.21 |
|
| proteomicspData | 0.11 | 0.00 | 0.10 |
|
| replicateCorrelations | 4.01 | 0.00 | 4.02 |
|
| sampleClusteredData | 1.61 | 0.00 | 1.61 |
|
| sampleSize | 46.22 | 0.09 | 46.31 |
|
| sampleSize3DscatterPlots | 0.02 | 0.00 | 0.02 |
|
| sampleSizeContourPlots | 0.03 | 0.00 | 0.03 |
|
| sampleSizeParameters | 23.15 | 0.03 | 23.19 |
|
| sample_technicalVariance | 6.19 | 0.02 | 6.20 |
|
| spectrumFilter | 3.89 | 0.02 | 3.91 |
|
| ztwo | 0 | 0 | 0 |
|
clippda.Rcheck/examples_x64/clippda-Ex.timings:
| name | user | system | elapsed
|
| ZvaluescasesVcontrolsPlots | 0.08 | 0.00 | 0.08 |
|
| ZvaluesfrommultinomPlots | 0.64 | 0.00 | 0.64 |
|
| aclinicalProteomicsData-class | 0.08 | 0.00 | 0.08 |
|
| aclinicalProteomicsData-methods | 0.18 | 0.11 | 0.30 |
|
| betweensampleVariance | 2.11 | 0.00 | 2.11 |
|
| checkNo.replicates | 0.19 | 0.00 | 0.18 |
|
| clippda-package | 80.94 | 0.21 | 81.14 |
|
| f | 0 | 0 | 0 |
|
| fisherInformation | 0.09 | 0.00 | 0.10 |
|
| liverRawData | 0 | 0 | 0 |
|
| liver_pheno | 0.02 | 0.00 | 0.01 |
|
| liverdata | 4.79 | 0.01 | 4.82 |
|
| mostSimilarTwo | 0 | 0 | 0 |
|
| negativeIntensitiesCorrection | 1.35 | 0.00 | 1.34 |
|
| phenoDataFrame | 0.06 | 0.00 | 0.06 |
|
| pheno_urine | 0 | 0 | 0 |
|
| preProcRepeatedPeakData | 3.25 | 0.00 | 3.25 |
|
| proteomicsExprsData | 0.25 | 0.00 | 0.25 |
|
| proteomicspData | 0.13 | 0.00 | 0.12 |
|
| replicateCorrelations | 4.09 | 0.01 | 4.11 |
|
| sampleClusteredData | 1.48 | 0.00 | 1.49 |
|
| sampleSize | 48.46 | 0.02 | 48.50 |
|
| sampleSize3DscatterPlots | 0.03 | 0.00 | 0.03 |
|
| sampleSizeContourPlots | 0.03 | 0.00 | 0.03 |
|
| sampleSizeParameters | 23.23 | 0.03 | 23.26 |
|
| sample_technicalVariance | 5.99 | 0.00 | 5.99 |
|
| spectrumFilter | 3.40 | 0.00 | 3.41 |
|
| ztwo | 0 | 0 | 0 |
|