Belinda Phipson
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/missMethyl |
| Branch: RELEASE_3_7 |
| Last Commit: 6b9a65d |
| Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:38:59 -0400 (Wed, 17 Oct 2018).
| Package 924/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| missMethyl 1.14.0 Belinda Phipson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: missMethyl |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings missMethyl_1.14.0.tar.gz |
| StartedAt: 2018-10-17 03:26:07 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 03:39:55 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 827.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: missMethyl.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings missMethyl_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/missMethyl.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.14.0'
* 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 ... NOTE
Namespace in Imports field not imported from: 'IlluminaHumanMethylationEPICmanifest'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.aveQuantile: no visible global function definition for 'approx'
.flattenAnn: no visible binding for global variable
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
.flattenAnn: no visible binding for global variable
'IlluminaHumanMethylationEPICanno.ilm10b2.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'
gometh: no visible global function definition for 'p.adjust'
gsameth: no visible global function definition for 'phyper'
gsameth: no visible global function definition for 'p.adjust'
topVar: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
DataFrame IlluminaHumanMethylation450kanno.ilmn12.hg19
IlluminaHumanMethylation450kmanifest
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
IlluminaHumanMethylationEPICmanifest approx colData density legend
lines lowess p.adjust packageVersion par phenoData phyper plot
Consider adding
importFrom("graphics", "legend", "lines", "par", "plot")
importFrom("stats", "approx", "density", "lowess", "p.adjust",
"phyper")
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 145.41 15.46 160.91
SWAN 26.85 2.98 29.83
RUVadj 17.66 2.07 19.75
densityByProbeType 15.05 1.60 16.64
RUVfit 13.70 1.07 14.77
topRUV 11.10 0.78 11.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGSA 145.21 1.47 146.80
SWAN 22.86 2.90 25.76
RUVadj 19.58 1.40 20.99
topRUV 13.15 0.86 14.06
densityByProbeType 11.19 1.53 12.73
RUVfit 9.49 0.95 10.44
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-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://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/missMethyl_1.14.0.tar.gz && rm -rf missMethyl.buildbin-libdir && mkdir missMethyl.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=missMethyl.buildbin-libdir missMethyl_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL missMethyl_1.14.0.zip && rm missMethyl_1.14.0.tar.gz missMethyl_1.14.0.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 37693 100 37693 0 0 642k 0 --:--:-- --:--:-- --:--:-- 694k
install for i386
* installing *source* package 'missMethyl' ...
** 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
getINCs html
getLeveneResiduals html
getMappedEntrezIDs html
gometh html
gsameth html
missMethyl-package html
topGSA html
topRUV html
topVar html
varFit html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'missMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'missMethyl' as missMethyl_1.14.0.zip
* DONE (missMethyl)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'missMethyl' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
missMethyl.Rcheck/examples_i386/missMethyl-Ex.timings
|
missMethyl.Rcheck/examples_x64/missMethyl-Ex.timings
|