Siyuan MA
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MMUPHin |
| Branch: RELEASE_3_10 |
| Last Commit: 2a6c283 |
| Last Changed Date: 2019-10-29 13:12:14 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:33:30 -0400 (Wed, 15 Apr 2020).
| Package 1074/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MMUPHin 1.0.0 Siyuan MA
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: MMUPHin |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MMUPHin.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MMUPHin_1.0.0.tar.gz |
| StartedAt: 2020-04-15 04:52:07 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:55:33 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 205.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MMUPHin.Rcheck |
| Warnings: 0 |
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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:MMUPHin.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MMUPHin_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MMUPHin.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 'MMUPHin/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MMUPHin' version '1.0.0'
* 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 '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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
continuous_discover 30.17 2.47 32.70
lm_meta 14.87 0.55 16.35
discrete_discover 13.64 0.37 14.30
adjust_batch 5.44 0.19 5.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
continuous_discover 33.25 2.37 36.61
lm_meta 17.64 0.44 20.28
discrete_discover 11.80 0.31 12.20
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/MMUPHin.Rcheck/00check.log'
for details.
MMUPHin.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/MMUPHin_1.0.0.tar.gz && rm -rf MMUPHin.buildbin-libdir && mkdir MMUPHin.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MMUPHin.buildbin-libdir MMUPHin_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MMUPHin_1.0.0.zip && rm MMUPHin_1.0.0.tar.gz MMUPHin_1.0.0.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 639k 100 639k 0 0 4434k 0 --:--:-- --:--:-- --:--:-- 4565k
install for i386
* 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
** 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 'MMUPHin' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MMUPHin' as MMUPHin_1.0.0.zip
* DONE (MMUPHin)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MMUPHin' successfully unpacked and MD5 sums checked
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MMUPHin.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(MMUPHin)
>
> test_check("MMUPHin")
== testthat results ===========================================================
[ OK: 41 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
2.56 0.17 2.71
|
MMUPHin.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(MMUPHin)
>
> test_check("MMUPHin")
== testthat results ===========================================================
[ OK: 41 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
2.82 0.06 2.87
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MMUPHin.Rcheck/examples_i386/MMUPHin-Ex.timings
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MMUPHin.Rcheck/examples_x64/MMUPHin-Ex.timings
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