Stephen Nyangoma
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/clippda |
| git_branch: master |
| git_last_commit: 2acb6b4 |
| git_last_commit_date: 2021-10-26 11:54:30 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:12 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the clippda package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clippda.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 325/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clippda 1.45.0 (landing page) Stephen Nyangoma
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: clippda |
| Version: 1.45.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clippda.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings clippda_1.45.0.tar.gz |
| StartedAt: 2022-03-17 18:44:01 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:47:00 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 178.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clippda.Rcheck |
| Warnings: 1 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clippda.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings clippda_1.45.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/clippda.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.45.0'
* 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
* 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
'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
'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 rmultinom var
Consider adding
importFrom("graphics", "legend", "lines")
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clippda-package 56.29 1.50 57.80
sampleSize 42.50 0.50 43.00
sampleSizeParameters 15.97 0.22 16.19
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/clippda.Rcheck/00check.log'
for details.
clippda.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL clippda
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (clippda)
Making 'packages.html' ... done
clippda.Rcheck/clippda-Ex.timings
| name | user | system | elapsed | |
| ZvaluescasesVcontrolsPlots | 0.04 | 0.00 | 0.04 | |
| ZvaluesfrommultinomPlots | 1.05 | 0.07 | 1.13 | |
| aclinicalProteomicsData-class | 0.05 | 0.00 | 0.06 | |
| aclinicalProteomicsData-methods | 0.17 | 0.19 | 0.36 | |
| betweensampleVariance | 0.94 | 0.08 | 1.02 | |
| checkNo.replicates | 0.03 | 0.05 | 0.07 | |
| clippda-package | 56.29 | 1.50 | 57.80 | |
| f | 0 | 0 | 0 | |
| fisherInformation | 0.05 | 0.00 | 0.04 | |
| liverRawData | 0.01 | 0.00 | 0.02 | |
| liver_pheno | 0 | 0 | 0 | |
| liverdata | 0.91 | 0.07 | 0.98 | |
| mostSimilarTwo | 0 | 0 | 0 | |
| negativeIntensitiesCorrection | 0.14 | 0.07 | 0.21 | |
| phenoDataFrame | 0.05 | 0.00 | 0.04 | |
| pheno_urine | 0 | 0 | 0 | |
| preProcRepeatedPeakData | 0.57 | 0.04 | 0.63 | |
| proteomicsExprsData | 0.11 | 0.00 | 0.11 | |
| proteomicspData | 0.04 | 0.02 | 0.05 | |
| replicateCorrelations | 2.95 | 0.05 | 3.00 | |
| sampleClusteredData | 0.17 | 0.00 | 0.17 | |
| sampleSize | 42.5 | 0.5 | 43.0 | |
| sampleSize3DscatterPlots | 0.02 | 0.00 | 0.01 | |
| sampleSizeContourPlots | 0.01 | 0.00 | 0.02 | |
| sampleSizeParameters | 15.97 | 0.22 | 16.19 | |
| sample_technicalVariance | 4.39 | 0.01 | 4.40 | |
| spectrumFilter | 0.75 | 0.05 | 0.80 | |
| ztwo | 0 | 0 | 0 | |