Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:42 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 openPrimeR package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1388/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
openPrimeR 1.21.0 (landing page) Matthias Döring
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: openPrimeR |
Version: 1.21.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openPrimeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings openPrimeR_1.21.0.tar.gz |
StartedAt: 2022-12-29 02:02:14 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 02:05:53 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 218.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: openPrimeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openPrimeR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings openPrimeR_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/openPrimeR.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'openPrimeR/DESCRIPTION' ... OK * this is package 'openPrimeR' version '1.21.0' * 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 11.9Mb 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 * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PrimerDesign 9.41 0.49 9.95 Output 8.41 0.75 27.40 Plots 5.04 0.23 5.29 * checking for unstated dependencies in 'tests' ... OK * checking tests ... 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 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/openPrimeR.Rcheck/00check.log' for details.
openPrimeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL openPrimeR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'openPrimeR' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (openPrimeR)
openPrimeR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 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. > 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") !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. [ FAIL 0 | WARN 6 | SKIP 9 | PASS 1467 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • MAFFT not available. (1) • OligoArrayAux not available. (5) • On Bioconductor (1) • Secondary structure tests require ViennaRNA. (1) • empty test (1) [ FAIL 0 | WARN 6 | SKIP 9 | PASS 1467 ] > > proc.time() user system elapsed 28.62 2.14 38.75
openPrimeR.Rcheck/openPrimeR-Ex.timings
name | user | system | elapsed | |
AnalysisStats | 1.24 | 0.01 | 1.25 | |
Data | 0.75 | 0.03 | 0.78 | |
Input | 1.73 | 0.02 | 1.77 | |
Output | 8.41 | 0.75 | 27.40 | |
Plots | 5.04 | 0.23 | 5.29 | |
PrimerDesign | 9.41 | 0.49 | 9.95 | |
PrimerEval | 3.92 | 0.12 | 4.05 | |
Primers-method | 0.02 | 0.00 | 0.01 | |
Scoring | 0.03 | 0.00 | 0.03 | |
Settings | 0.18 | 0.30 | 0.72 | |
Templates-method | 0.01 | 0.02 | 0.03 | |
TemplatesFunctions | 0.20 | 0.01 | 0.22 | |
runTutorial | 0 | 0 | 0 | |