Sarah Voisin
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MEAT |
| git_branch: RELEASE_3_13 |
| git_last_commit: 57d07d3 |
| git_last_commit_date: 2021-05-19 12:49:22 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the MEAT package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEAT.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 1062/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MEAT 1.4.0 (landing page) Sarah Voisin
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MEAT |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MEAT_1.4.0.tar.gz |
| StartedAt: 2021-10-15 01:29:24 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:38:44 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 559.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MEAT.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MEAT_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MEAT.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEAT/DESCRIPTION' ... OK
* this is package 'MEAT' version '1.4.0'
* 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 'MEAT' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 5.7Mb
* 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data codoc mismatches from documentation object 'CpGs_in_MEAT':
Variables in data frame 'CpGs_in_MEAT'
Code: Chromatin_state_male_SM Chromosome Coefficient CpG Gene
Position
Docs: Chromatin_state_male_SM Chromosome Coefficient CpGs Gene
Position
Data codoc mismatches from documentation object 'CpGs_in_MEAT2.0':
Variables in data frame 'CpGs_in_MEAT2.0'
Code: Chromatin_state_female_SM Chromatin_state_male_SM Chromosome
Coefficient CpG Gene Position
Docs: Chromatin_state_male_SM Chromosome Coefficient CpGs Gene
Position
* 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 LazyData ... WARNING
LazyData DB of 5.7 MB without LazyDataCompression set
See ยง1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... 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
BMIQcalibration 29.29 0.99 30.28
epiage_estimation 28.51 0.05 28.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BMIQcalibration 24.67 0.17 24.85
epiage_estimation 24.39 0.12 24.52
* 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: 2 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/MEAT.Rcheck/00check.log'
for details.
MEAT.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MEAT_1.4.0.tar.gz && rm -rf MEAT.buildbin-libdir && mkdir MEAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEAT.buildbin-libdir MEAT_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MEAT_1.4.0.zip && rm MEAT_1.4.0.tar.gz MEAT_1.4.0.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
31 5045k 31 1600k 0 0 2400k 0 0:00:02 --:--:-- 0:00:02 2399k
100 5045k 100 5045k 0 0 3313k 0 0:00:01 0:00:01 --:--:-- 3314k
install for i386
* installing *source* package 'MEAT' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** help
*** installing help indices
converting help for package 'MEAT'
finding HTML links ... done
BMIQcalibration html
CpGs_in_MEAT html
CpGs_in_MEAT2.0 html
GSE121961 html
GSE121961_pheno html
MEAT-package html
clean_beta html
elasticnet_model_MEAT html
elasticnet_model_MEAT2.0 html
epiage_estimation html
gold.mean.MEAT html
gold.mean.MEAT2.0 html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'MEAT' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'MEAT' as MEAT_1.4.0.zip
* DONE (MEAT)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MEAT' successfully unpacked and MD5 sums checked
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MEAT.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(MEAT)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
>
> test_check("MEAT")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
14.34 1.25 15.59
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MEAT.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(MEAT)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
>
> test_check("MEAT")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
15.92 0.56 16.50
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MEAT.Rcheck/examples_i386/MEAT-Ex.timings
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MEAT.Rcheck/examples_x64/MEAT-Ex.timings
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