Tiago Lubiana
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/PubScore |
| git_branch: RELEASE_3_14 |
| git_last_commit: 9794604 |
| git_last_commit_date: 2021-10-26 12:56:26 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:08 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the PubScore package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PubScore.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1484/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PubScore 1.6.0 (landing page) Tiago Lubiana
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: PubScore |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PubScore.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PubScore_1.6.0.tar.gz |
| StartedAt: 2022-04-13 00:58:31 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:06:13 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 463.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PubScore.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PubScore.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PubScore_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PubScore.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PubScore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PubScore' version '1.6.0'
* 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 'PubScore' 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
get_literature_score: no visible binding for global variable
'gene2pubmed_db'
get_literature_score: no visible binding for global variable
'hgcn_entrez_reference'
get_sum_of_weights: no visible binding for global variable 'Genes'
get_sum_of_weights: no visible binding for global variable 'Topic'
plot_literature_score: no visible binding for global variable 'Genes'
plot_literature_score: no visible binding for global variable 'Topic'
plot_literature_score: no visible binding for global variable
'number_of_articles'
show,PubScore: no visible binding for global variable 'pub'
Undefined global functions or variables:
Genes Topic gene2pubmed_db hgcn_entrez_reference number_of_articles
pub
* 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 LazyData ... 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 (user + system) or elapsed time > 5s
user system elapsed
test_score 27.72 8.84 43.30
plot_literature_score 0.66 0.01 24.66
plot_literature_graph 0.61 0.00 6.97
get_literature_score 0.11 0.02 9.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
test_score 29.64 0.05 36.42
plot_literature_score 0.70 0.00 25.09
plot_literature_graph 0.63 0.00 6.98
get_literature_score 0.19 0.00 9.48
* 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-3.14-bioc/meat/PubScore.Rcheck/00check.log'
for details.
PubScore.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PubScore_1.6.0.tar.gz && rm -rf PubScore.buildbin-libdir && mkdir PubScore.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PubScore.buildbin-libdir PubScore_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PubScore_1.6.0.zip && rm PubScore_1.6.0.tar.gz PubScore_1.6.0.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
12 3061k 12 392k 0 0 806k 0 0:00:03 --:--:-- 0:00:03 806k
66 3061k 66 2030k 0 0 1369k 0 0:00:02 0:00:01 0:00:01 1368k
100 3061k 100 3061k 0 0 1571k 0 0:00:01 0:00:01 --:--:-- 1570k
install for i386
* installing *source* package 'PubScore' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PubScore'
finding HTML links ... done
PubScore-class html
all_counts html
dot-getSimulation_test html
dot-query_pubmed html
gene2pubmed_db html
getScore html
get_all_counts html
get_literature_score html
heatmapViz html
hgcn_entrez_reference html
initialize-PubScore-method html
networkViz html
plot_literature_graph html
plot_literature_score html
pubscore html
set_all_counts html
test_score 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 'PubScore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PubScore' as PubScore_1.6.0.zip
* DONE (PubScore)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PubScore' successfully unpacked and MD5 sums checked
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PubScore.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(PubScore)
>
> test_check("PubScore")
~~~ Initializing PubScore Object ~~~
[1] 1197.889
~~~ Initializing PubScore Object ~~~
~~~ Initializing PubScore Object ~~~
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
>
> proc.time()
user system elapsed
34.07 0.37 112.18
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PubScore.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(PubScore)
>
> test_check("PubScore")
~~~ Initializing PubScore Object ~~~
[1] 1197.889
~~~ Initializing PubScore Object ~~~
~~~ Initializing PubScore Object ~~~
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
>
> proc.time()
user system elapsed
34.75 0.26 90.85
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PubScore.Rcheck/examples_i386/PubScore-Ex.timings
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PubScore.Rcheck/examples_x64/PubScore-Ex.timings
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