VJ Carey
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ontoProc |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2ba1033 |
| git_last_commit_date: 2021-05-19 12:31:28 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:14 -0400 (Fri, 15 Oct 2021).
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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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1311/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ontoProc 1.14.0 (landing page) VJ Carey
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ontoProc_1.14.0.tar.gz |
| StartedAt: 2021-10-15 02:56:08 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 03:03:06 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 417.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ontoProc.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoProc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ontoProc_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ontoProc.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.14.0'
* 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 41.7Mb
sub-directories of 1Mb or more:
app 1.9Mb
data 2.0Mb
ontoRda 37.2Mb
* 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
common_classes 26.25 1.79 33.50
CLfeats 14.76 0.94 15.79
fastGrep 12.96 0.56 14.00
getLeavesFromTerm 8.58 0.11 8.69
sym2CellOnto 7.35 0.61 7.96
getCellOnto 5.39 0.08 5.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
common_classes 23.80 2.03 27.75
CLfeats 16.31 0.29 16.81
fastGrep 11.28 0.10 11.37
getLeavesFromTerm 10.30 0.03 10.32
sym2CellOnto 7.07 0.06 7.12
* 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-3.13-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://155.52.207.165/BBS/3.13/bioc/src/contrib/ontoProc_1.14.0.tar.gz && rm -rf ontoProc.buildbin-libdir && mkdir ontoProc.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoProc.buildbin-libdir ontoProc_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ontoProc_1.14.0.zip && rm ontoProc_1.14.0.tar.gz ontoProc_1.14.0.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
3 40.7M 3 1658k 0 0 1842k 0 0:00:22 --:--:-- 0:00:22 1842k
10 40.7M 10 4544k 0 0 2448k 0 0:00:17 0:00:01 0:00:16 2448k
20 40.7M 20 8512k 0 0 2982k 0 0:00:13 0:00:02 0:00:11 2982k
28 40.7M 28 11.5M 0 0 3059k 0 0:00:13 0:00:03 0:00:10 3059k
28 40.7M 28 11.5M 0 0 2430k 0 0:00:17 0:00:04 0:00:13 2430k
28 40.7M 28 11.6M 0 0 2029k 0 0:00:20 0:00:05 0:00:15 2062k
33 40.7M 33 13.6M 0 0 2044k 0 0:00:20 0:00:06 0:00:14 1894k
42 40.7M 42 17.1M 0 0 2241k 0 0:00:18 0:00:07 0:00:11 1818k
52 40.7M 52 21.4M 0 0 2478k 0 0:00:16 0:00:08 0:00:08 2027k
65 40.7M 65 26.6M 0 0 2768k 0 0:00:15 0:00:09 0:00:06 3100k
80 40.7M 80 32.7M 0 0 3089k 0 0:00:13 0:00:10 0:00:03 4335k
97 40.7M 97 39.7M 0 0 3429k 0 0:00:12 0:00:11 0:00:01 5326k
100 40.7M 100 40.7M 0 0 3461k 0 0:00:12 0:00:12 --:--:-- 5743k
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* 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) :
restoring symbolic link as a file copy
* installing *source* package 'ontoProc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ontoProc' as ontoProc_1.14.0.zip
* DONE (ontoProc)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ontoProc' successfully unpacked and MD5 sums checked
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ontoProc.Rcheck/tests_i386/test.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
>
> test_check("ontoProc")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 8 ]
>
>
> proc.time()
user system elapsed
22.40 1.07 23.45
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ontoProc.Rcheck/tests_x64/test.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
>
> test_check("ontoProc")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 8 ]
>
>
> proc.time()
user system elapsed
20.21 0.65 20.84
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ontoProc.Rcheck/examples_i386/ontoProc-Ex.timings
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ontoProc.Rcheck/examples_x64/ontoProc-Ex.timings
|