Stephen Nyangoma
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/clippda |
| Branch: master |
| Last Commit: 0a72ad7 |
| Last Changed Date: 2019-10-29 13:35:06 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:32:09 -0500 (Thu, 16 Jan 2020).
| Package 298/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clippda 1.37.0 Stephen Nyangoma
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: clippda |
| Version: 1.37.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clippda.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clippda_1.37.0.tar.gz |
| StartedAt: 2020-01-16 02:56:21 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:02:46 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 385.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clippda.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clippda.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clippda_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/clippda.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.37.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘clippda’ can be installed ... WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/clippda.Rcheck/00install.out’ for details.
* 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 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
ZvaluescasesVcontrolsPlots: no visible global function definition for
‘plot’
ZvaluescasesVcontrolsPlots: no visible global function definition for
‘lines’
ZvaluescasesVcontrolsPlots: no visible global function definition for
‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
‘rmultinom’
ZvaluesfrommultinomPlots: no visible global function definition for
‘density’
ZvaluesfrommultinomPlots: no visible global function definition for
‘plot’
ZvaluesfrommultinomPlots: no visible global function definition for
‘lines’
ZvaluesfrommultinomPlots: no visible global function definition for
‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
‘cloud’
ZvaluesfrommultinomPlots: no visible global function definition for
‘var’
Undefined global functions or variables:
cloud density legend lines plot rmultinom var
Consider adding
importFrom("graphics", "legend", "lines", "plot")
importFrom("stats", "density", "rmultinom", "var")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clippda-package 119.283 12.380 133.204
sampleSize 69.593 7.555 77.274
sampleSizeParameters 36.630 3.779 41.282
sample_technicalVariance 9.661 1.052 10.742
replicateCorrelations 5.844 0.693 6.538
* 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: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/clippda.Rcheck/00check.log’
for details.
clippda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clippda ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘clippda’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server 2: 'rgl_init' failed, running with rgl.useNULL = TRUE ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** testing if installed package can be loaded from final location Warning in rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE ** testing if installed package keeps a record of temporary installation path * DONE (clippda)
clippda.Rcheck/clippda-Ex.timings
| name | user | system | elapsed | |
| ZvaluescasesVcontrolsPlots | 0.023 | 0.007 | 0.037 | |
| ZvaluesfrommultinomPlots | 0.747 | 0.099 | 0.901 | |
| aclinicalProteomicsData-class | 0.074 | 0.010 | 0.084 | |
| aclinicalProteomicsData-methods | 1.197 | 0.893 | 2.132 | |
| betweensampleVariance | 3.085 | 0.344 | 3.452 | |
| checkNo.replicates | 0.142 | 0.021 | 0.164 | |
| clippda-package | 119.283 | 12.380 | 133.204 | |
| f | 0.001 | 0.000 | 0.001 | |
| fisherInformation | 0.102 | 0.012 | 0.115 | |
| liverRawData | 0.007 | 0.004 | 0.011 | |
| liver_pheno | 0.003 | 0.003 | 0.006 | |
| liverdata | 2.010 | 0.288 | 2.299 | |
| mostSimilarTwo | 0.003 | 0.000 | 0.004 | |
| negativeIntensitiesCorrection | 0.438 | 0.071 | 0.509 | |
| phenoDataFrame | 0.066 | 0.007 | 0.073 | |
| pheno_urine | 0.003 | 0.003 | 0.006 | |
| preProcRepeatedPeakData | 1.816 | 0.264 | 2.080 | |
| proteomicsExprsData | 0.310 | 0.013 | 0.322 | |
| proteomicspData | 0.063 | 0.009 | 0.072 | |
| replicateCorrelations | 5.844 | 0.693 | 6.538 | |
| sampleClusteredData | 0.466 | 0.081 | 0.547 | |
| sampleSize | 69.593 | 7.555 | 77.274 | |
| sampleSize3DscatterPlots | 0.045 | 0.010 | 0.072 | |
| sampleSizeContourPlots | 0.039 | 0.002 | 0.078 | |
| sampleSizeParameters | 36.630 | 3.779 | 41.282 | |
| sample_technicalVariance | 9.661 | 1.052 | 10.742 | |
| spectrumFilter | 1.730 | 0.233 | 1.981 | |
| ztwo | 0.000 | 0.001 | 0.000 | |