VJ Carey
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ontoProc |
| Branch: RELEASE_3_10 |
| Last Commit: 5447ef6 |
| Last Changed Date: 2020-03-08 08:07:59 -0400 (Sun, 08 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:29:23 -0400 (Wed, 15 Apr 2020).
| Package 1191/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ontoProc 1.8.1 VJ Carey
| 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: ontoProc |
| Version: 1.8.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ontoProc_1.8.1.tar.gz |
| StartedAt: 2020-04-15 05:14:49 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:19:44 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 294.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ontoProc.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ontoProc_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ontoProc.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ontoProc/DESCRIPTION' ... OK
* this is package 'ontoProc' version '1.8.1'
* 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 'ontoProc' can be installed ... OK
* checking installed package size ... NOTE
installed size is 37.8Mb
sub-directories of 1Mb or more:
app 1.9Mb
data 2.0Mb
ontoRda 33.5Mb
* 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
CLfeat : prupdate: no visible binding for global variable 'PROSYM'
CLfeat : prupdate: no visible binding for global variable 'PRID'
CLfeat : prupdate: no visible binding for global variable 'SYMBOL'
ctmarks: no visible binding for '<<-' assignment to 'pr'
ctmarks: no visible binding for '<<-' assignment to 'go'
ctmarks : server: no visible binding for global variable 'text'
cyclicSigset: no visible binding for global variable 'sigels'
ldfToTerm: no visible binding for global variable 'PROSYM'
make_graphNEL_from_ontology_plot: no visible global function definition
for 'as'
seur3kTab: no visible global function definition for 'read.delim'
sym2CellOnto: no visible binding for global variable 'PROSYM'
sym2CellOnto: no visible binding for global variable 'SYMBOL'
Undefined global functions or variables:
PRID PROSYM SYMBOL as read.delim sigels text
Consider adding
importFrom("graphics", "text")
importFrom("methods", "as")
importFrom("utils", "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 ... NOTE
Note: found 162 marked UTF-8 strings
* 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
CLfeats 14.56 0.86 16.22
getLeavesFromTerm 13.69 0.11 13.80
fastGrep 12.75 0.47 13.42
sym2CellOnto 6.75 0.15 6.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CLfeats 17.52 0.25 17.78
fastGrep 14.11 0.14 14.25
getLeavesFromTerm 13.16 0.03 13.21
sym2CellOnto 6.16 0.01 6.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test.R'
OK
** running tests for arch 'x64' ...
Running 'test.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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/ontoProc.Rcheck/00check.log'
for details.
ontoProc.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ontoProc_1.8.1.tar.gz && rm -rf ontoProc.buildbin-libdir && mkdir ontoProc.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoProc.buildbin-libdir ontoProc_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ontoProc_1.8.1.zip && rm ontoProc_1.8.1.tar.gz ontoProc_1.8.1.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
2 37.0M 2 768k 0 0 2742k 0 0:00:13 --:--:-- 0:00:13 2772k
100 37.0M 100 37.0M 0 0 46.6M 0 --:--:-- --:--:-- --:--:-- 46.8M
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'ontoProc/vignettes/ontoProc.Rmd' to 'ontoProc/README.md'
* installing *source* package 'ontoProc' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ontoProc'
finding HTML links ... done
CLfeats html
PROSYM html
TermSet-class html
allGOterms html
c-TermSet-method html
cellTypeToGO html
cleanCLOnames html
ctmarks html
cyclicSigset html
demoApp html
dropStop html
fastGrep html
getCellOnto html
getLeavesFromTerm html
humrna html
improveNodes html
ldfToTerms html
liberalMap html
makeSelectInput html
make_graphNEL_from_ontology_plot html
mapOneNaive html
minicorpus html
nomenCheckup html
onto_plot2 html
onto_roots html
packDesc2019 html
recognizedPredicates html
secLevGen html
selectFromMap html
seur3kTab html
siblings_TAG html
stopWords html
sym2CellOnto 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
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'ontoProc/vignettes/ontoProc.Rmd' to 'ontoProc/README.md'
* installing *source* package 'ontoProc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ontoProc' as ontoProc_1.8.1.zip
* DONE (ontoProc)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ontoProc' successfully unpacked and MD5 sums checked
|
ontoProc.Rcheck/tests_i386/test.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
>
> test_check("ontoProc")
== testthat results ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
15.54 0.79 16.34
|
ontoProc.Rcheck/tests_x64/test.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
>
> test_check("ontoProc")
== testthat results ===========================================================
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
12.00 0.31 12.37
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ontoProc.Rcheck/examples_i386/ontoProc-Ex.timings
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ontoProc.Rcheck/examples_x64/ontoProc-Ex.timings
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