Alba Gutierrez-Sacristan
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/psygenet2r |
| Branch: RELEASE_3_7 |
| Last Commit: 70c1065 |
| Last Changed Date: 2018-04-30 10:35:40 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:39 -0400 (Wed, 17 Oct 2018).
| Package 1147/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psygenet2r 1.12.0 Alba Gutierrez-Sacristan
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: psygenet2r |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings psygenet2r_1.12.0.tar.gz |
| StartedAt: 2018-10-16 02:53:59 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 02:57:31 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 212.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: psygenet2r.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings psygenet2r_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/psygenet2r.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psygenet2r/DESCRIPTION’ ... OK
* this is package ‘psygenet2r’ version ‘1.12.0’
* 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 ‘psygenet2r’ can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL")
Note: possible error in 'psygenetGene(x, databse = "ALL", ': unused argument (databse = "ALL")
See ‘/home/biocbuild/bbs-3.7-bioc/meat/psygenet2r.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘GO.db’
All declared Imports should be used.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.category_plot: possible error in psygenetGene(x, databse = "ALL"):
unused argument (databse = "ALL")
.category_plot: no visible binding for global variable ‘category’
.category_plot: no visible binding for global variable ‘value’
.category_plot: no visible binding for global variable ‘variable’
.gene_plot: possible error in psygenetGene(x, databse = "ALL"): unused
argument (databse = "ALL")
.gene_plot: no visible binding for global variable ‘gene’
.gene_plot: no visible binding for global variable ‘value’
.gene_plot: no visible binding for global variable ‘variable’
.index_plot: possible error in psygenetGene(x, databse = "ALL"): unused
argument (databse = "ALL")
.index_plot: no visible binding for global variable ‘Category’
.index_plot: no visible binding for global variable ‘value’
.index_plot: no visible binding for global variable ‘variable’
.pie_plot: possible error in psygenetGene(x, databse = "ALL", verbose =
verbose): unused argument (databse = "ALL")
.pie_plot: no visible global function definition for ‘pie’
ListPsyGeNETIds: no visible global function definition for ‘read.csv’
disGenetCurated: no visible global function definition for ‘read.csv’
enrichedPD : <anonymous>: no visible global function definition for
‘phyper’
getUMLs: no visible global function definition for ‘read.csv’
jaccardEstimation: no visible binding for global variable ‘universe’
multipleInput: no visible global function definition for ‘new’
pantherGraphic: no visible binding for global variable ‘Var1’
pantherGraphic: no visible binding for global variable ‘perc’
pantherGraphic: no visible binding for global variable ‘diseases’
plot_pmids_barplot: no visible binding for global variable
‘c2.DiseaseName’
plot_pmids_barplot: no visible binding for global variable
‘c0.Number_of_Abstracts’
plot_pmids_barplot: no visible binding for global variable
‘c1.Gene_Symbol’
plot_psy_heatmap: no visible binding for global variable
‘c2.PsychiatricDisorder’
plot_psy_heatmap: no visible binding for global variable
‘c1.Gene_Symbol’
plot_psy_heatmap: no visible binding for global variable ‘value’
plot_psy_heatmapDisease: no visible binding for global variable
‘c2.DiseaseName’
plot_psy_heatmapDisease: no visible binding for global variable
‘c1.Gene_Symbol’
plot_psy_heatmapDisease: no visible binding for global variable
‘c0.Score’
plot_psy_heatmapGenes: no visible binding for global variable
‘c1.Gene_Symbol’
plot_psy_heatmapGenes: no visible binding for global variable
‘c2.DiseaseName’
plot_psy_heatmapGenes: no visible binding for global variable
‘c0.Score’
psyGenDisId: no visible global function definition for ‘read.csv’
psyPanther: no visible global function definition for ‘read.csv’
psygenetAll: no visible global function definition for ‘read.csv’
psygenetDisease: no visible global function definition for ‘read.csv’
psygenetDisease: no visible global function definition for ‘new’
psygenetDiseaseSentences: no visible global function definition for
‘read.csv’
psygenetDiseaseSentences: no visible global function definition for
‘new’
psygenetGene: no visible global function definition for ‘read.csv’
psygenetGene: no visible global function definition for ‘new’
psygenetGeneSentences: no visible global function definition for
‘read.csv’
psygenetGeneSentences: no visible global function definition for ‘new’
singleInput: no visible global function definition for ‘combn’
singleInput: no visible global function definition for ‘new’
singleInput.genes: no visible global function definition for ‘new’
topAnatEnrichment: no visible binding for global variable ‘database’
topAnatEnrichment: no visible global function definition for
‘read.delim’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
‘Disease1’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
‘Disease2’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
‘JaccardIndex’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
‘value’
plot,JaccardIndexPsy-ANY: no visible binding for global variable
‘variable’
Undefined global functions or variables:
Category Disease1 Disease2 JaccardIndex Var1 c0.Number_of_Abstracts
c0.Score c1.Gene_Symbol c2.DiseaseName c2.PsychiatricDisorder
category combn database diseases gene new perc phyper pie read.csv
read.delim universe value variable
Consider adding
importFrom("graphics", "pie")
importFrom("methods", "new")
importFrom("stats", "phyper")
importFrom("utils", "combn", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
pantherGraphic-methods 0.432 0.008 5.569
psygenetGeneSentences 0.364 0.012 27.716
JaccardIndexPsy-class 0.092 0.020 7.814
psygenetDiseaseSentences 0.036 0.004 9.583
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/psygenet2r.Rcheck/00check.log’
for details.
psygenet2r.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL psygenet2r ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘psygenet2r’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") Note: possible error in 'psygenetGene(x, databse = "ALL")': unused argument (databse = "ALL") Note: possible error in 'psygenetGene(x, databse = "ALL", ': unused argument (databse = "ALL") ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (psygenet2r)
psygenet2r.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(psygenet2r)
>
> test_check("psygenet2r")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 18 SKIPPED: 4 FAILED: 0
>
> proc.time()
user system elapsed
4.000 0.144 63.011
psygenet2r.Rcheck/psygenet2r-Ex.timings
| name | user | system | elapsed | |
| JaccardIndexPsy-class | 0.092 | 0.020 | 7.814 | |
| enrichedPD-methods | 0.128 | 0.000 | 3.340 | |
| extract | 0.004 | 0.000 | 0.006 | |
| extractSentences | 0.004 | 0.000 | 0.003 | |
| getUMLs-methods | 0.040 | 0.004 | 1.827 | |
| jaccardEstimation-methods | 0.092 | 0.000 | 1.746 | |
| ndisease | 0.004 | 0.000 | 0.001 | |
| ngene | 0.000 | 0.000 | 0.002 | |
| pantherGraphic-methods | 0.432 | 0.008 | 5.569 | |
| plot-DataGeNET.Psy-ANY-method | 0.072 | 0.004 | 0.076 | |
| plot-JaccardIndexPsy-ANY-method | 0.000 | 0.000 | 0.001 | |
| psygenetDisease-methods | 0.060 | 0.000 | 2.844 | |
| psygenetDiseaseSentences | 0.036 | 0.004 | 9.583 | |
| psygenetGene-methods | 0.040 | 0.004 | 2.662 | |
| psygenetGeneSentences | 0.364 | 0.012 | 27.716 | |
| qr | 0 | 0 | 0 | |
| topAnatEnrichment-methods | 0.000 | 0.000 | 0.001 | |
| universe | 0.004 | 0.000 | 0.004 | |