Stephen Nyangoma
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/clippda |
| Branch: RELEASE_3_9 |
| Last Commit: 4e88b59 |
| Last Changed Date: 2019-05-02 11:53:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:22:56 -0400 (Wed, 16 Oct 2019).
| Package 283/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clippda 1.34.0 Stephen Nyangoma
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clippda.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings clippda_1.34.0.tar.gz |
| StartedAt: 2019-10-16 02:41:50 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:48:58 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 428.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clippda.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clippda.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings clippda_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/clippda.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.34.0'
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clippda-package 99.95 0.48 100.45
sampleSize 53.40 0.07 53.48
sampleSizeParameters 32.98 0.07 33.04
sample_technicalVariance 6.65 0.04 6.70
replicateCorrelations 5.90 0.04 5.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clippda-package 69.46 0.51 69.99
sampleSize 38.69 0.44 39.13
sampleSizeParameters 20.42 0.30 20.71
sample_technicalVariance 5.67 0.06 5.74
* 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:/Users/biocbuild/bbs-3.9-bioc/meat/clippda.Rcheck/00check.log'
for details.
clippda.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/clippda_1.34.0.tar.gz && rm -rf clippda.buildbin-libdir && mkdir clippda.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clippda.buildbin-libdir clippda_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL clippda_1.34.0.zip && rm clippda_1.34.0.tar.gz clippda_1.34.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 420k 100 420k 0 0 5646k 0 --:--:-- --:--:-- --:--:-- 6177k
install for i386
* installing *source* package 'clippda' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'clippda'
finding HTML links ... done
ZvaluescasesVcontrolsPlots html
ZvaluesfrommultinomPlots html
aclinicalProteomicsData-class html
aclinicalProteomicsData-methods html
betweensampleVariance-methods html
betweensampleVariance html
checkNo.replicates html
clippda-package html
f html
fisherInformation-methods html
fisherInformation html
liverRawData html
liver_pheno html
liverdata html
mostSimilarTwo html
negativeIntensitiesCorrection html
phenoDataFrame html
pheno_urine html
preProcRepeatedPeakData html
proteomicsExprsData-methods html
proteomicsExprsData html
proteomicspData-methods html
proteomicspData html
replicateCorrelations-methods html
replicateCorrelations html
sampleClusteredData html
sampleSize-methods html
sampleSize html
sampleSize3DscatterPlots html
sampleSizeContourPlots html
sampleSizeParameters-methods html
sampleSizeParameters html
sample_technicalVariance-methods html
sample_technicalVariance html
show-methods html
spectrumFilter html
ztwo html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'clippda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clippda' as clippda_1.34.0.zip
* DONE (clippda)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'clippda' successfully unpacked and MD5 sums checked
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clippda.Rcheck/examples_i386/clippda-Ex.timings
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clippda.Rcheck/examples_x64/clippda-Ex.timings
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