Siyuan MA
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MMUPHin |
| git_branch: master |
| git_last_commit: ddd5156 |
| git_last_commit_date: 2022-02-06 16:43:46 -0400 (Sun, 06 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:03 -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 MMUPHin package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MMUPHin.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 1189/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MMUPHin 1.9.1 (landing page) Siyuan MA
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: MMUPHin |
| Version: 1.9.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MMUPHin.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MMUPHin_1.9.1.tar.gz |
| StartedAt: 2022-03-17 19:37:42 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:39:29 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 107.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MMUPHin.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MMUPHin.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MMUPHin_1.9.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MMUPHin.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 'MMUPHin/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MMUPHin' version '1.9.1'
* 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 'MMUPHin' 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
* 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 ... NOTE
Maaslin2_wrapper: no visible binding for global variable
'feature_rename'
Maaslin2_wrapper: no visible binding for global variable 'name'
check_exposure: no visible binding for global variable 'lvl_batch'
diagnostic_adjust_batch: no visible binding for global variable
'Adjustment'
diagnostic_adjust_batch: no visible binding for global variable 'batch'
diagnostic_adjust_batch: no visible binding for global variable
'mean_overall'
diagnostic_adjust_batch: no visible binding for global variable
'mean_batch'
diagnostic_adjust_batch: no visible binding for global variable
'Feature'
diagnostic_continuous_discover: no visible binding for global variable
'community'
diagnostic_continuous_discover: no visible binding for global variable
'correlation'
diagnostic_continuous_discover: no visible binding for global variable
'batch'
diagnostic_discrete_discover: no visible binding for global variable
'k'
Undefined global functions or variables:
Adjustment Feature batch community correlation feature_rename k
lvl_batch mean_batch mean_overall name
* 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
continuous_discover 21.41 5.65 27.06
lm_meta 11.02 0.63 11.64
discrete_discover 8.86 1.52 10.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/MMUPHin.Rcheck/00check.log'
for details.
MMUPHin.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MMUPHin
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MMUPHin' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MMUPHin'
finding HTML links ... done
AST html
CRC_abd html
CRC_meta html
LOG html
Maaslin2_wrapper html
add_back_covariates html
adjust_EB html
adjust_batch html
aprior html
back_transform_abd html
bprior html
catchToList html
check_D html
check_batch html
check_covariates html
check_covariates_random html
check_exposure html
check_feature_abd html
check_metadata html
check_options html
check_options_continuous html
check_pseudo_count html
check_rank html
check_samples html
check_samples_D html
construct_design html
construct_ind html
continuous_discover html
create_table_maaslin html
diagnostic_adjust_batch html
diagnostic_continuous_discover html
diagnostic_discrete_discover html
discrete_discover html
fill_dimnames html
fit_EB html
fit_shrink html
fit_stand_feature html
it_sol html
lm_meta html
match_control html
normalize_features html
relocate_scale html
rename_maaslin html
rma_wrapper html
set_pseudo html
shorten_name html
standardize_feature html
transform_features html
tss html
vaginal_abd html
vaginal_meta html
visualize_continuous_discover html
*** copying figures
** 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 (MMUPHin)
Making 'packages.html' ... done
MMUPHin.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(MMUPHin)
>
> test_check("MMUPHin")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 41 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 41 ]
>
> proc.time()
user system elapsed
1.29 0.29 1.57
MMUPHin.Rcheck/MMUPHin-Ex.timings
| name | user | system | elapsed | |
| CRC_abd | 0.02 | 0.04 | 0.05 | |
| CRC_meta | 0.01 | 0.00 | 0.02 | |
| adjust_batch | 2.00 | 0.31 | 2.31 | |
| continuous_discover | 21.41 | 5.65 | 27.06 | |
| discrete_discover | 8.86 | 1.52 | 10.38 | |
| lm_meta | 11.02 | 0.63 | 11.64 | |
| vaginal_abd | 0.01 | 0.00 | 0.02 | |
| vaginal_meta | 0 | 0 | 0 | |