Cesar Prada
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MetaVolcanoR |
| Branch: RELEASE_3_10 |
| Last Commit: c0f64a4 |
| Last Changed Date: 2019-11-04 04:38:37 -0400 (Mon, 04 Nov 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:49:39 -0400 (Wed, 15 Apr 2020).
| Package 1010/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MetaVolcanoR 1.0.1 Cesar Prada
| 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: MetaVolcanoR |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetaVolcanoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaVolcanoR_1.0.1.tar.gz |
| StartedAt: 2020-04-15 03:43:09 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:47:30 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 260.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MetaVolcanoR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetaVolcanoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaVolcanoR_1.0.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/MetaVolcanoR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaVolcanoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaVolcanoR’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MetaVolcanoR’ 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
combining_mv: no visible binding for global variable ‘study’
combining_mv: no visible binding for global variable ‘value’
combining_mv: no visible binding for global variable ‘metap’
combining_mv: no visible binding for global variable ‘idx’
draw_cum_freq: no visible binding for global variable ‘ndatasets’
draw_cum_freq: no visible binding for global variable ‘DEGs’
draw_degbar: no visible binding for global variable ‘dataset’
draw_degbar: no visible binding for global variable ‘Regulation’
draw_forest: no visible binding for global variable ‘group’
plot_mv: no visible binding for global variable ‘metap’
plot_mv: no visible binding for global variable ‘degcomb’
plot_mv: no visible binding for global variable ‘ddeg’
plot_mv: no visible binding for global variable ‘ndeg’
plot_mv: no visible binding for global variable ‘degvcount’
plot_rem: no visible binding for global variable ‘signcon’
plot_rem: no visible binding for global variable ‘randomCi.ub’
plot_rem: no visible binding for global variable ‘randomCi.lb’
plot_rem: no visible binding for global variable ‘randomSummary’
plot_rem: no visible binding for global variable ‘randomP’
plot_rem: no visible binding for global variable ‘signcon2’
plot_rem: no visible binding for global variable ‘Ci.ub’
plot_rem: no visible binding for global variable ‘Ci.lb’
rem_mv: no visible binding for global variable ‘error’
rem_mv: no visible binding for global variable ‘randomCi.ub’
rem_mv: no visible binding for global variable ‘randomCi.lb’
rem_mv: no visible binding for global variable ‘index’
rem_mv: no visible global function definition for ‘head’
votecount_mv: no visible binding for global variable ‘ddeg’
votecount_mv: no visible binding for global variable ‘ndeg’
votecount_mv: no visible binding for global variable ‘idx’
Undefined global functions or variables:
Ci.lb Ci.ub DEGs Regulation dataset ddeg degcomb degvcount error
group head idx index metap ndatasets ndeg randomCi.lb randomCi.ub
randomP randomSummary signcon signcon2 study value
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
* 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 or elapsed time > 5s
user system elapsed
combining_mv 7.740 0.746 8.619
plot_mv 6.124 1.198 5.912
votecount_mv 5.792 1.378 6.117
draw_forest 5.768 0.165 6.013
plot_rem 5.517 0.166 5.752
rem_mv 5.274 0.156 5.494
* 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
‘/Users/biocbuild/bbs-3.10-bioc/meat/MetaVolcanoR.Rcheck/00check.log’
for details.
MetaVolcanoR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetaVolcanoR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘MetaVolcanoR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (MetaVolcanoR)
MetaVolcanoR.Rcheck/tests/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-apple-darwin15.6.0 (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(MetaVolcanoR)
>
> test_check('MetaVolcanoR')
index Symbol Log2FC_1 CI.L_1 CI.R_1 vi_1 Log2FC_2
1 4795 MXRA5 0.8150851 0.3109324 1.3192377 0.06616251 1.3001104
2 2166 COL6A6 -1.7480348 -2.5780749 -0.9179947 0.17934364 -0.8388366
3 2053 CIDEA NA NA NA NA NA
4 7115 SULT1A4 0.9689025 0.5103475 1.4274575 0.05473571 0.7513323
5 130 ACACB -0.8431142 -1.4708480 -0.2153804 0.10257437 -1.1119841
6 6528 SLC27A2 -0.6782948 -0.9931027 -0.3634869 0.02579759 -1.8916655
CI.L_2 CI.R_2 vi_2 Log2FC_3 CI.L_3 CI.R_3 vi_3
1 0.6603306 1.9398901 0.10654886 1.1895480 0.8401301 1.5389659 0.031781777
2 -1.3578456 -0.3198277 0.07011930 -1.0300519 -1.4730328 -0.5870710 0.051080819
3 NA NA NA -1.0111528 -1.3226326 -0.6996729 0.025255027
4 0.4707021 1.0319624 0.02050012 NA NA NA NA
5 -1.7417389 -0.4822293 0.10323592 -0.5305046 -0.6957455 -0.3652637 0.007107599
6 -2.6822584 -1.1010726 0.16270229 -1.2126830 -1.6702908 -0.7550753 0.054509799
Log2FC_4 CI.L_4 CI.R_4 vi_4 Log2FC_5 CI.L_5 CI.R_5
1 0.2188594 -1.052230 1.4899492 0.4205720 0.8051543 0.1367255 1.4735830
2 -1.3755263 -2.162453 -0.5885999 0.1611967 -0.7213490 -1.5714484 0.1287505
3 -1.7991026 -2.918939 -0.6792665 0.3264351 -0.8738120 -1.6373061 -0.1103179
4 NA NA NA NA NA NA NA
5 -0.7991042 -1.457868 -0.1403403 0.1129659 -0.5155929 -0.8606782 -0.1705076
6 -1.3554403 -2.288444 -0.4224370 0.2265970 -1.4905464 -2.5565023 -0.4245905
vi_5 signcon ntimes randomSummary randomCi.lb randomCi.ub randomP
1 0.11630493 5 5 1.0333001 0.7882044 1.2783958 1.420312e-16
2 0.18811668 -5 5 -1.0649749 -1.3396138 -0.7903361 2.956522e-14
3 0.15173972 -3 3 -1.0417876 -1.3210774 -0.7624977 2.653168e-13
4 NA 2 2 0.8106154 0.5712566 1.0499741 3.187477e-11
5 0.03099851 -5 5 -0.5830624 -0.7212245 -0.4449003 1.324963e-16
6 0.29577833 -5 5 -1.2207058 -1.6760435 -0.7653680 1.484852e-07
het_QE het_QEp het_QM het_QMp error se rank
1 4.179945 0.38220032 68.27752 1.420312e-16 FALSE 0.12504883 1
2 4.580708 0.33308457 57.76318 2.956522e-14 FALSE 0.14012185 2
3 1.980047 0.37156797 53.44957 2.653168e-13 FALSE 0.14249482 3
4 0.629179 0.42765661 44.05825 3.187477e-11 FALSE 0.12212181 4
5 4.317851 0.36469506 68.41455 1.324963e-16 FALSE 0.07049086 5
6 11.099093 0.02547263 27.60901 1.484852e-07 FALSE 0.23231516 6
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6 | SKIPPED: 0 | WARNINGS: 522 | FAILED: 0 ]
>
> proc.time()
user system elapsed
162.239 4.288 166.577
MetaVolcanoR.Rcheck/MetaVolcanoR-Ex.timings
| name | user | system | elapsed | |
| calc_vi | 0.034 | 0.005 | 0.040 | |
| collapse_deg | 0.029 | 0.005 | 0.033 | |
| combining_mv | 7.740 | 0.746 | 8.619 | |
| cum_freq_data | 0.225 | 0.017 | 0.248 | |
| deg_def | 0.093 | 0.009 | 0.103 | |
| draw_cum_freq | 0.607 | 0.015 | 0.627 | |
| draw_degbar | 0.558 | 0.027 | 0.595 | |
| draw_forest | 5.768 | 0.165 | 6.013 | |
| plot_mv | 6.124 | 1.198 | 5.912 | |
| plot_rem | 5.517 | 0.166 | 5.752 | |
| rem_mv | 5.274 | 0.156 | 5.494 | |
| remodel | 0.021 | 0.000 | 0.022 | |
| rename_col | 0.026 | 0.001 | 0.027 | |
| set_degbar_data | 0.067 | 0.008 | 0.076 | |
| votecount_mv | 5.792 | 1.378 | 6.117 | |