Matthias Döring
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/openPrimeR |
| Branch: RELEASE_3_9 |
| Last Commit: ca0de6f |
| Last Changed Date: 2019-05-02 11:54:08 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:39:21 -0400 (Wed, 16 Oct 2019).
| Package 1144/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| openPrimeR 1.6.0 Matthias Döring
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: openPrimeR |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings openPrimeR_1.6.0.tar.gz |
| StartedAt: 2019-10-16 05:44:18 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:51:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 448.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: openPrimeR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openPrimeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings openPrimeR_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/openPrimeR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.6.0'
* 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 ... 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 12.3Mb
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 ... NOTE
Namespace in Imports field not imported from: 'tinytex'
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 ... 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 or elapsed time > 5s
user system elapsed
Output 13.13 1.56 22.39
PrimerDesign 12.25 0.16 12.67
Plots 9.11 0.52 9.65
PrimerEval 4.82 0.26 5.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Output 15.08 1.40 24.25
PrimerDesign 14.31 0.39 14.76
Plots 7.50 0.57 8.07
PrimerEval 4.70 0.26 5.08
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-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/3.9/bioc/src/contrib/openPrimeR_1.6.0.tar.gz && rm -rf openPrimeR.buildbin-libdir && mkdir openPrimeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openPrimeR.buildbin-libdir openPrimeR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL openPrimeR_1.6.0.zip && rm openPrimeR_1.6.0.tar.gz openPrimeR_1.6.0.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
100 1770k 100 1770k 0 0 20.4M 0 --:--:-- --:--:-- --:--:-- 22.4M
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
** 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 'openPrimeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openPrimeR' as openPrimeR_1.6.0.zip
* DONE (openPrimeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'openPrimeR' successfully unpacked and MD5 sums checked
|
openPrimeR.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
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
44.62 2.34 53.51
|
openPrimeR.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
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
44.00 1.60 60.28
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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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