Alba Gutierrez-Sacristan
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/psygenet2r |
| Branch: RELEASE_3_9 |
| Last Commit: f558bdc |
| Last Changed Date: 2019-05-02 11:54:00 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:35:13 -0400 (Wed, 16 Oct 2019).
| Package 1274/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psygenet2r 1.16.0 Alba Gutierrez-Sacristan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: psygenet2r |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psygenet2r.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings psygenet2r_1.16.0.tar.gz |
| StartedAt: 2019-10-16 06:12:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:17:37 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 284.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: psygenet2r.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:psygenet2r.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings psygenet2r_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/psygenet2r.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'psygenet2r/DESCRIPTION' ... OK * this is package 'psygenet2r' version '1.16.0' * 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 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") Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSA3QI1/R.INSTALL198462fd6a74/psygenet2r/man/topAnatEnrichment-methods.Rd:21: file link 'runTest' in package 'topGO' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-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 * 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 ... 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 :: 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 ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed pantherGraphic-methods 0.66 0.00 5.05 psygenetGeneSentences 0.48 0.02 14.14 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed pantherGraphic-methods 0.71 0.02 5.02 psygenetGeneSentences 0.50 0.02 14.18 * 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 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/psygenet2r.Rcheck/00check.log' for details.
psygenet2r.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/psygenet2r_1.16.0.tar.gz && rm -rf psygenet2r.buildbin-libdir && mkdir psygenet2r.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psygenet2r.buildbin-libdir psygenet2r_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL psygenet2r_1.16.0.zip && rm psygenet2r_1.16.0.tar.gz psygenet2r_1.16.0.zip
###
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install for i386
* installing *source* package 'psygenet2r' ...
** using staged installation
** 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
converting help for package 'psygenet2r'
finding HTML links ... done
DataGeNET.Psy-class html
JaccardIndexPsy-class html
enrichedPD-methods html
extract html
extractSentences html
geneAttrPlot-methods html
getUMLs-methods html
jaccardEstimation-methods html
ndisease html
ngene html
pantherGraphic-methods html
plot-DataGeNET.Psy-ANY-method html
plot-JaccardIndexPsy-ANY-method html
psygenet2r html
psygenetDisease-methods html
psygenetDiseaseSentences html
psygenetGene-methods html
psygenetGeneSentences html
qr html
topAnatEnrichment-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpSA3QI1/R.INSTALL198462fd6a74/psygenet2r/man/topAnatEnrichment-methods.Rd:21: file link 'runTest' in package 'topGO' does not exist and so has been treated as a topic
universe 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 'psygenet2r' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psygenet2r' as psygenet2r_1.16.0.zip
* DONE (psygenet2r)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'psygenet2r' successfully unpacked and MD5 sums checked
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psygenet2r.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(psygenet2r)
>
> test_check("psygenet2r")
== testthat results ===========================================================
[ OK: 18 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
4.84 0.37 41.96
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psygenet2r.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(psygenet2r)
>
> test_check("psygenet2r")
== testthat results ===========================================================
[ OK: 18 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
6.07 0.28 43.21
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psygenet2r.Rcheck/examples_i386/psygenet2r-Ex.timings
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psygenet2r.Rcheck/examples_x64/psygenet2r-Ex.timings
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