Sidharth Jain
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/gemini |
| Branch: RELEASE_3_10 |
| Last Commit: 44b4098 |
| Last Changed Date: 2019-10-29 13:11:45 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:46 -0400 (Wed, 15 Apr 2020).
| Package 643/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gemini 1.0.0 Sidharth Jain
| 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 | OK | OK | OK | |
| Package: gemini |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings gemini_1.0.0.tar.gz |
| StartedAt: 2020-04-15 03:21:20 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:25:26 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 245.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gemini.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings gemini_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/gemini.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 'gemini/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gemini' 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'gemini' 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
gemini_boxplot : <anonymous>: no visible binding for global variable
'.'
gemini_boxplot: no visible binding for global variable '.'
gemini_boxplot : <anonymous>: no visible binding for global variable
'gi'
gemini_boxplot : <anonymous>: no visible binding for global variable
'hj'
gemini_boxplot: no visible binding for global variable 'label'
gemini_boxplot: no visible binding for global variable 'y'
gemini_calculate_lfc: no visible binding for global variable '.'
update_s_pb: no visible binding for global variable '.'
update_tau_pb: no visible binding for global variable '.'
Undefined global functions or variables:
. gi hj label y
* 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
gemini_inference 18.31 3.11 21.42
update_tau_pb 9.01 0.05 9.06
update_x_pb 7.04 0.03 7.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
gemini_inference 25.73 0.01 25.75
update_x_pb 11.68 0.05 11.73
update_tau_pb 11.47 0.03 11.50
gemini_initialize 6.94 0.02 6.95
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/gemini.Rcheck/00check.log'
for details.
gemini.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/gemini_1.0.0.tar.gz && rm -rf gemini.buildbin-libdir && mkdir gemini.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gemini.buildbin-libdir gemini_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL gemini_1.0.0.zip && rm gemini_1.0.0.tar.gz gemini_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
0 4076k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 4076k 100 4076k 0 0 39.9M 0 --:--:-- --:--:-- --:--:-- 41.0M
install for i386
* installing *source* package 'gemini' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gemini'
finding HTML links ... done
Input html
Model html
Sgene2Pguides_hash html
Sguide2Pguides_hash html
compound html
counts html
dot-median_normalize html
gemini_boxplot html
gemini_calculate_lfc html
gemini_create_input html
gemini_inference html
gemini_initialize html
gemini_parallelization html
gemini_plot_mae html
gemini_prepare_input html
gemini_score html
guide.annotation html
initialize_s html
initialize_tau html
initialize_x html
initialize_y html
pipe html
sample.replicate.annotation html
update_mae html
update_s_pb html
update_tau_pb html
update_x_pb html
update_y_pb 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 'gemini' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gemini' as gemini_1.0.0.zip
* DONE (gemini)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'gemini' successfully unpacked and MD5 sums checked
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gemini.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(gemini)
>
> test_check("gemini")
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
5.95 0.51 6.45
|
gemini.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(gemini)
>
> test_check("gemini")
== testthat results ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
6.48 0.50 6.95
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gemini.Rcheck/examples_i386/gemini-Ex.timings
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gemini.Rcheck/examples_x64/gemini-Ex.timings
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