Weijun Luo
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/SBGNview |
| Branch: RELEASE_3_12 |
| Last Commit: 7b38509 |
| Last Changed Date: 2021-03-03 18:46:53 -0400 (Wed, 03 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:25 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the SBGNview package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1621/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SBGNview 1.4.1 (landing page) Weijun Luo
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SBGNview |
| Version: 1.4.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SBGNview_1.4.1.tar.gz |
| StartedAt: 2021-05-06 06:35:38 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:43:00 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 442.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SBGNview.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SBGNview_1.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SBGNview.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SBGNview/DESCRIPTION' ... OK
* this is package 'SBGNview' version '1.4.1'
* 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 whether package 'SBGNview' 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 ... NOTE
Namespace in Imports field not imported from: 'bookdown'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'SBGNview/R/zzz.R':
.onLoad calls:
packageStartupMessage(disclaimer)
See section 'Good practice' in '?.onAttach'.
generate.cpd.mapping.table: no visible binding for global variable
'cpd.simtypes'
generate.ko.mapping.list: no visible binding for global variable 'korg'
loadMappingTable: no visible binding for global variable 'korg'
mapping.ko.to.arbitrary.id.type: no visible binding for global variable
'gene.idtype.list'
mapping.ko.to.arbitrary.id.type: no visible binding for global variable
'korg'
mol.sum.multiple.mapping: no visible binding for global variable 'IQR'
Undefined global functions or variables:
IQR cpd.simtypes gene.idtype.list korg
Consider adding
importFrom("stats", "IQR")
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SBGNview 17.83 1.58 19.92
sbgnNodes 10.84 0.12 11.19
print.SBGNview 7.77 0.34 8.16
downloadSbgnFile 7.42 0.28 7.71
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SBGNview 20.02 0.91 21.11
sbgnNodes 9.98 0.57 10.58
print.SBGNview 7.56 0.29 7.89
downloadSbgnFile 7.25 0.30 7.55
* 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-3.12-bioc/meat/SBGNview.Rcheck/00check.log'
for details.
SBGNview.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SBGNview_1.4.1.tar.gz && rm -rf SBGNview.buildbin-libdir && mkdir SBGNview.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SBGNview.buildbin-libdir SBGNview_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SBGNview_1.4.1.zip && rm SBGNview_1.4.1.tar.gz SBGNview_1.4.1.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
100 1659k 100 1659k 0 0 9782k 0 --:--:-- --:--:-- --:--:-- 9819k
install for i386
* installing *source* package 'SBGNview' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SBGNview'
finding HTML links ... done
SBGNhub.id.mapping.tables html
SBGNview html
arc-class html
changeDataId html
changeIds html
downloadSbgnFile html
findPathways html
glyph-class html
highlightArcs html
highlightNodes html
highlightPath html
loadMappingTable html
mapped.ids html
outputFile-set html
outputFile html
pathways.info html
pathways.stats html
plus-.SBGNview html
print.SBGNview html
renderSbgn html
sbgn.gsets html
sbgnNodes html
spline.arc-class 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 'SBGNview' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SBGNview' as SBGNview_1.4.1.zip
* DONE (SBGNview)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SBGNview' successfully unpacked and MD5 sums checked
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SBGNview.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(SBGNview)
Loading required package: pathview
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Loading required package: SBGNview.data
##############################################################################
SBGNview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html.
Users are required to formally cite the SBGNview paper and Pathview paper (not
just mention them) in publications or products. For details, do
'citation("SBGNview"); citation("Pathview")' within R.
##############################################################################
>
> test_check("SBGNview")
trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/compound.name_metacyc.SBGN.RData'
Content type 'application/octet-stream' length 1795999 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/kegg_metacyc.SBGN.RData'
Content type 'application/octet-stream' length 171925 bytes (167 KB)
==================================================
downloaded 167 KB
trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/kegg_pathway.id.RData'
Content type 'application/octet-stream' length 195623 bytes (191 KB)
==================================================
downloaded 191 KB
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 14 ]
>
> proc.time()
user system elapsed
34.68 3.67 39.53
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SBGNview.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(SBGNview)
Loading required package: pathview
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Loading required package: SBGNview.data
##############################################################################
SBGNview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html.
Users are required to formally cite the SBGNview paper and Pathview paper (not
just mention them) in publications or products. For details, do
'citation("SBGNview"); citation("Pathview")' within R.
##############################################################################
>
> test_check("SBGNview")
trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/compound.name_metacyc.SBGN.RData'
Content type 'application/octet-stream' length 1795999 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/kegg_metacyc.SBGN.RData'
Content type 'application/octet-stream' length 171925 bytes (167 KB)
==================================================
downloaded 167 KB
trying URL 'https://raw.githubusercontent.com/datapplab/SBGNhub/master/data/id.mapping.unique.pair.name/kegg_pathway.id.RData'
Content type 'application/octet-stream' length 195623 bytes (191 KB)
==================================================
downloaded 191 KB
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 14 ]
>
> proc.time()
user system elapsed
33.28 1.10 34.61
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SBGNview.Rcheck/examples_i386/SBGNview-Ex.timings
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SBGNview.Rcheck/examples_x64/SBGNview-Ex.timings
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