VJ Carey
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/ontoProc |
| git_branch: RELEASE_3_14 |
| git_last_commit: 45a31ef |
| git_last_commit_date: 2021-10-26 12:39:25 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:02 -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 ontoProc package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.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 1337/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ontoProc 1.16.0 (landing page) VJ Carey
| 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: ontoProc |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ontoProc_1.16.0.tar.gz |
| StartedAt: 2022-04-13 00:00:47 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 00:15:45 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 897.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ontoProc.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:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ontoProc_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ontoProc.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 'ontoProc/DESCRIPTION' ... OK
* this is package 'ontoProc' version '1.16.0'
* 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 'ontoProc' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
app 1.9Mb
data 2.0Mb
ontoRda 2.8Mb
* 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 'PRID'
CLfeat : prupdate: no visible binding for global variable 'SYMBOL'
bind_formal_tags: no visible global function definition for 'colData'
bind_formal_tags: no visible global function definition for 'colData<-'
common_classes: no visible global function definition for 'colData'
connect_classes: no visible global function definition for 'colData'
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'
ldfToTerm: no visible binding for global variable 'PROSYM'
subset_descendants: no visible global function definition for 'colData'
sym2CellOnto: no visible binding for global variable 'SYMBOL'
Undefined global functions or variables:
PRID PROSYM SYMBOL colData colData<- text
Consider adding
importFrom("graphics", "text")
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 ... NOTE
Note: found 162 marked UTF-8 strings
* 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
getCellOnto 34.94 1.49 38.23
common_classes 28.19 1.55 34.96
CLfeats 26.17 2.50 30.46
siblings_TAG 27.25 1.36 30.28
fastGrep 20.02 2.04 23.06
getLeavesFromTerm 19.08 0.36 20.02
sym2CellOnto 14.07 0.42 15.03
TermSet-class 10.14 0.58 11.33
secLevGen 9.14 0.44 10.11
cleanCLOnames 7.51 0.37 8.55
nomenCheckup 7.25 0.38 8.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
siblings_TAG 37.32 1.33 60.19
getCellOnto 33.03 1.42 36.06
common_classes 29.82 1.68 33.95
CLfeats 26.50 1.37 29.62
fastGrep 22.66 0.58 23.77
getLeavesFromTerm 15.52 0.55 16.72
sym2CellOnto 14.15 0.59 15.31
nomenCheckup 11.28 0.49 18.47
secLevGen 10.48 0.37 11.67
cleanCLOnames 9.35 0.49 14.82
TermSet-class 8.72 0.36 9.61
* 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-3.14-bioc/meat/ontoProc.Rcheck/00check.log'
for details.
ontoProc.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/ontoProc_1.16.0.tar.gz && rm -rf ontoProc.buildbin-libdir && mkdir ontoProc.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoProc.buildbin-libdir ontoProc_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ontoProc_1.16.0.zip && rm ontoProc_1.16.0.tar.gz ontoProc_1.16.0.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 8330k 12 1000k 0 0 1215k 0 0:00:06 --:--:-- 0:00:06 1215k
29 8330k 29 2459k 0 0 1347k 0 0:00:06 0:00:01 0:00:05 1347k
53 8330k 53 4445k 0 0 1575k 0 0:00:05 0:00:02 0:00:03 1575k
83 8330k 83 6988k 0 0 1816k 0 0:00:04 0:00:03 0:00:01 1817k
100 8330k 100 8330k 0 0 1842k 0 0:00:04 0:00:04 --:--:-- 1842k
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
bind_formal_tags html
c-TermSet-method html
cellTypeToGO html
cleanCLOnames html
common_classes html
connect_classes html
ctmarks html
cyclicSigset html
demoApp html
dropStop html
fastGrep html
findCommonAncestors html
finding level-2 HTML links ... done
getCellOnto html
getLeavesFromTerm html
humrna html
improveNodes html
ldfToTerms html
liberalMap html
makeSelectInput html
make_graphNEL_from_ontology_plot html
map2prose 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
subset_descendants 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_1.16.0.zip
* DONE (ontoProc)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ontoProc' successfully unpacked and MD5 sums checked
|
ontoProc.Rcheck/tests_i386/test.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(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
>
> test_check("ontoProc")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]
>
>
> proc.time()
user system elapsed
81.82 5.15 97.61
|
ontoProc.Rcheck/tests_x64/test.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(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
>
> test_check("ontoProc")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 8 ]
>
>
> proc.time()
user system elapsed
75.40 3.15 82.73
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ontoProc.Rcheck/examples_i386/ontoProc-Ex.timings
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ontoProc.Rcheck/examples_x64/ontoProc-Ex.timings
|