Matthias Döring
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/openPrimeR |
| Branch: RELEASE_3_11 |
| Last Commit: b79ca1e |
| Last Changed Date: 2020-08-14 03:49:12 -0400 (Fri, 14 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:19 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE openPrimeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1237/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| openPrimeR 1.10.4 Matthias Döring
| malbec2 | Linux (Ubuntu 18.04.4 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: openPrimeR |
| Version: 1.10.4 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings openPrimeR_1.10.4.tar.gz |
| StartedAt: 2020-10-17 06:38:15 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:47:50 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 575.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: openPrimeR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings openPrimeR_1.10.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/openPrimeR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'openPrimeR/DESCRIPTION' ... OK
* this is package 'openPrimeR' version '1.10.4'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'openPrimeR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.2Mb
sub-directories of 1Mb or more:
R 1.3Mb
extdata 10.0Mb
* 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 ... OK
* 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 R/sysdata.rda ... 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
Output 12.57 1.78 55.01
PrimerDesign 13.44 0.38 14.54
PrimerEval 6.97 0.20 7.18
Plots 6.63 0.47 7.10
Input 2.32 0.12 6.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PrimerDesign 17.48 0.25 17.82
Output 15.10 1.42 44.89
Plots 7.72 0.44 8.16
PrimerEval 7.87 0.26 8.10
* 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-3.11-bioc/meat/openPrimeR.Rcheck/00check.log'
for details.
openPrimeR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/openPrimeR_1.10.4.tar.gz && rm -rf openPrimeR.buildbin-libdir && mkdir openPrimeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openPrimeR.buildbin-libdir openPrimeR_1.10.4.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL openPrimeR_1.10.4.zip && rm openPrimeR_1.10.4.tar.gz openPrimeR_1.10.4.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 1772k 100 1772k 0 0 24.3M 0 --:--:-- --:--:-- --:--:-- 26.6M
install for i386
* installing *source* package 'openPrimeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'openPrimeR'
finding HTML links ... done
AnalysisStats html
Data html
Input html
Output html
Plots html
PrimerDesign html
PrimerEval html
Primers-method html
Scoring html
Settings html
Templates-method html
TemplatesFunctions html
check_cvg_constraints html
create_report-Primers-Templates-method
html
create_report-list-list-method html
filterLimits-methods html
filters-methods html
get_cvg_stats-Primers-method html
get_cvg_stats-list-method html
openPrimeR-package html
plot_constraint-Primers-method html
plot_constraint-list-method html
plot_constraint_deviation-Primers-method
html
plot_constraint_deviation-list-method html
plot_constraint_fulfillment-Primers-method
html
plot_constraint_fulfillment-list-method
html
plot_cvg_constraints-Primers-method html
plot_cvg_constraints-list-method html
plot_primer_binding_regions-Primers-Templates-method
html
plot_primer_binding_regions-list-list-method
html
plot_primer_cvg-Primers-Templates-method
html
plot_primer_cvg-list-list-method html
plot_template_cvg-Primers-Templates-method
html
plot_template_cvg-list-list-method html
runTutorial html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Melting not available
ViennaRNA not available
OligoArrayAux not available
** testing if installed package can be loaded from final location
Melting not available
ViennaRNA not available
OligoArrayAux not available
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'openPrimeR' ...
** testing if installed package can be loaded
Melting not available
ViennaRNA not available
OligoArrayAux not available
* MD5 sums
packaged installation of 'openPrimeR' as openPrimeR_1.10.4.zip
* DONE (openPrimeR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'openPrimeR' successfully unpacked and MD5 sums checked
|
openPrimeR.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.
> require(testthat)
Loading required package: testthat
> require(openPrimeR)
Loading required package: openPrimeR
Melting not available
ViennaRNA not available
OligoArrayAux not available
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are
installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
o ViennaRNA (http://www.tbi.univie.ac.at/RNA/)
o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php)
o MAFFT (http://mafft.cbrc.jp/alignment/software/)
> #test_package("openPrimeR")
> test_check("openPrimeR")
== testthat results ===========================================================
[ OK: 1467 | SKIPPED: 8 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
50.01 2.60 74.90
|
openPrimeR.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.
> require(testthat)
Loading required package: testthat
> require(openPrimeR)
Loading required package: openPrimeR
Melting not available
ViennaRNA not available
OligoArrayAux not available
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are
installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
o ViennaRNA (http://www.tbi.univie.ac.at/RNA/)
o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php)
o MAFFT (http://mafft.cbrc.jp/alignment/software/)
> #test_package("openPrimeR")
> test_check("openPrimeR")
== testthat results ===========================================================
[ OK: 1467 | SKIPPED: 8 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
54.29 1.96 78.12
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openPrimeR.Rcheck/examples_i386/openPrimeR-Ex.timings
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openPrimeR.Rcheck/examples_x64/openPrimeR-Ex.timings
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