Belinda Phipson
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/missMethyl |
| Branch: RELEASE_3_10 |
| Last Commit: 6865392 |
| Last Changed Date: 2020-01-27 23:26:28 -0400 (Mon, 27 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:23:21 -0400 (Wed, 15 Apr 2020).
| Package 1063/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| missMethyl 1.20.4 Belinda Phipson
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: missMethyl |
| Version: 1.20.4 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings missMethyl_1.20.4.tar.gz |
| StartedAt: 2020-04-15 04:49:52 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:03:12 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 800.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: missMethyl.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings missMethyl_1.20.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/missMethyl.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'missMethyl/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'missMethyl' version '1.20.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'missMethyl' 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 ... OK
* 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 ... WARNING
'library' or 'require' calls not declared from:
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'
'library' or 'require' calls in package code:
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
'limma:::alias2SymbolTable' 'limma:::tricubeMovingAverage'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
SWAN.MethyLumiSet SWAN.RGChannelSet SWAN.default varFit.DGEList
varFit.MethylSet varFit.default
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.aveQuantile: no visible global function definition for 'approx'
.getFlatAnnotation: no visible binding for global variable
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
.getFlatAnnotation: no visible binding for global variable
'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'
.plotBias: no visible global function definition for 'par'
.plotBias: no visible global function definition for 'plot'
.plotBias: no visible global function definition for 'lines'
.plotBias: no visible global function definition for 'lowess'
.subsetQuantileNorm: no visible global function definition for 'approx'
SWAN.MethyLumiSet: no visible global function definition for
'DataFrame'
SWAN.MethyLumiSet: no visible global function definition for
'phenoData'
SWAN.MethyLumiSet: no visible global function definition for
'packageVersion'
SWAN.default: no visible binding for global variable
'IlluminaHumanMethylation450kmanifest'
SWAN.default: no visible binding for global variable
'IlluminaHumanMethylationEPICmanifest'
SWAN.default: no visible global function definition for 'colData'
SWAN.default: no visible global function definition for
'packageVersion'
densityByProbeType: no visible binding for global variable
'IlluminaHumanMethylation450kmanifest'
densityByProbeType: no visible binding for global variable
'IlluminaHumanMethylationEPICmanifest'
densityByProbeType : <anonymous>: no visible global function definition
for 'density'
densityByProbeType: no visible global function definition for 'plot'
densityByProbeType: no visible global function definition for 'density'
densityByProbeType: no visible global function definition for 'lines'
densityByProbeType: no visible global function definition for 'legend'
goregion: no visible binding for global variable
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
goregion: no visible binding for global variable
'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'
goregion: no visible global function definition for 'GRanges'
goregion: no visible global function definition for 'IRanges'
goregion: no visible global function definition for 'findOverlaps'
goregion: no visible global function definition for 'from'
gsaregion: no visible binding for global variable
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
gsaregion: no visible binding for global variable
'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'
gsaregion: no visible global function definition for 'GRanges'
gsaregion: no visible global function definition for 'IRanges'
gsaregion: no visible global function definition for 'findOverlaps'
gsaregion: no visible global function definition for 'from'
topVar: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
DataFrame GRanges IRanges
IlluminaHumanMethylation450kanno.ilmn12.hg19
IlluminaHumanMethylation450kmanifest
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
IlluminaHumanMethylationEPICmanifest approx colData density
findOverlaps from legend lines lowess p.adjust packageVersion par
phenoData plot
Consider adding
importFrom("graphics", "legend", "lines", "par", "plot")
importFrom("stats", "approx", "density", "lowess", "p.adjust")
importFrom("utils", "packageVersion")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGSA 36.20 3.37 39.66
topRUV 29.81 3.66 33.49
getAdj 28.95 2.05 31.00
RUVadj 28.14 2.08 30.21
SWAN 25.78 2.18 27.95
RUVfit 20.31 1.42 21.73
densityByProbeType 11.02 1.07 12.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RUVadj 36.79 1.82 38.64
topGSA 36.80 1.39 38.21
SWAN 35.20 2.98 38.27
topRUV 33.53 1.62 35.16
getAdj 32.97 1.52 34.50
RUVfit 31.81 1.43 33.25
densityByProbeType 15.70 1.34 17.06
* 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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/missMethyl.Rcheck/00check.log'
for details.
missMethyl.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/missMethyl_1.20.4.tar.gz && rm -rf missMethyl.buildbin-libdir && mkdir missMethyl.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=missMethyl.buildbin-libdir missMethyl_1.20.4.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL missMethyl_1.20.4.zip && rm missMethyl_1.20.4.tar.gz missMethyl_1.20.4.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 45541 100 45541 0 0 907k 0 --:--:-- --:--:-- --:--:-- 988k
install for i386
* installing *source* package 'missMethyl' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'missMethyl'
finding HTML links ... done
RUVadj html
finding level-2 HTML links ... done
RUVfit html
SWAN html
contrasts.varFit html
densityByProbeType html
getAdj html
getINCs html
getLeveneResiduals html
getMappedEntrezIDs html
gometh html
goregion html
gsameth html
gsaregion html
missMethyl-package html
topGSA html
topRUV html
topVar html
varFit 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 'missMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'missMethyl' as missMethyl_1.20.4.zip
* DONE (missMethyl)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'missMethyl' successfully unpacked and MD5 sums checked
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missMethyl.Rcheck/examples_i386/missMethyl-Ex.timings
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missMethyl.Rcheck/examples_x64/missMethyl-Ex.timings
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