Nima Hejazi
| Snapshot Date: 2020-06-06 16:50:24 -0400 (Sat, 06 Jun 2020) |
| URL: https://git.bioconductor.org/packages/methyvim |
| Branch: RELEASE_3_11 |
| Last Commit: 9bcf5ef |
| Last Changed Date: 2020-04-27 15:11:00 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-06-07 15:21:14 -0400 (Sun, 07 Jun 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE methyvim PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1067/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methyvim 1.10.0 Nima Hejazi
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: methyvim |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methyvim.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methyvim_1.10.0.tar.gz |
| StartedAt: 2020-06-07 08:49:16 -0400 (Sun, 07 Jun 2020) |
| EndedAt: 2020-06-07 08:58:59 -0400 (Sun, 07 Jun 2020) |
| EllapsedTime: 583.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methyvim.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methyvim.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methyvim_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/methyvim.Rcheck'
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methyvim/DESCRIPTION' ... OK
* this is package 'methyvim' version '1.10.0'
* package encoding: UTF-8
* 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 'methyvim' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim.Rd:31: file link 'GenomicRatioSet' in package 'minfi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim.Rd:53: file link 'getBeta' in package 'minfi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim.Rd:54: file link 'getM' in package 'minfi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim_tmle.Rd:34: file link 'getBeta' in package 'minfi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim_tmle.Rd:35: file link 'getM' in package 'minfi' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/methyvim.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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'tmle.npvi'
* 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 (user + system) or elapsed time > 5s
user system elapsed
methyheat 14.21 1.05 15.36
plot.methytmle 11.79 0.03 11.83
methyvolc 10.80 0.14 10.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
methyheat 13.90 0.17 14.08
methyvolc 12.25 0.03 12.28
plot.methytmle 11.69 0.11 11.81
methyvim 1.99 0.11 25.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/methyvim.Rcheck/00check.log'
for details.
methyvim.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/methyvim_1.10.0.tar.gz && rm -rf methyvim.buildbin-libdir && mkdir methyvim.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methyvim.buildbin-libdir methyvim_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL methyvim_1.10.0.zip && rm methyvim_1.10.0.tar.gz methyvim_1.10.0.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 301k 100 301k 0 0 3038k 0 --:--:-- --:--:-- --:--:-- 3281k
install for i386
* installing *source* package 'methyvim' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'methyvim'
finding HTML links ... done
cluster_sites html
fdr_msa html
force_positivity html
limma_screen html
methyheat html
methytmle-class html
methyvim html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim.Rd:31: file link 'GenomicRatioSet' in package 'minfi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim.Rd:53: file link 'getBeta' in package 'minfi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim.Rd:54: file link 'getM' in package 'minfi' does not exist and so has been treated as a topic
methyvim_tmle html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim_tmle.Rd:34: file link 'getBeta' in package 'minfi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpcHfx4d/R.INSTALL2bbc43f814c1/methyvim/man/methyvim_tmle.Rd:35: file link 'getM' in package 'minfi' does not exist and so has been treated as a topic
methyvolc html
plot.methytmle html
set_parallel html
wrap_in_try 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 'methyvim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methyvim' as methyvim_1.10.0.zip
* DONE (methyvim)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'methyvim' successfully unpacked and MD5 sums checked
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methyvim.Rcheck/tests_i386/testthat.Rout
R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(methyvim)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
methyvim v1.10.0: Targeted, Robust, and Model-free Differential Methylation Analysis
>
> set.seed(43719)
> test_check("methyvim")
== testthat results ===========================================================
[ OK: 42 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
26.67 2.64 43.21
|
methyvim.Rcheck/tests_x64/testthat.Rout
R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(methyvim)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
methyvim v1.10.0: Targeted, Robust, and Model-free Differential Methylation Analysis
>
> set.seed(43719)
> test_check("methyvim")
== testthat results ===========================================================
[ OK: 42 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
24.68 0.92 38.43
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methyvim.Rcheck/examples_i386/methyvim-Ex.timings
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methyvim.Rcheck/examples_x64/methyvim-Ex.timings
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