Matthias Lienhard
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/qsea |
| Branch: RELEASE_3_8 |
| Last Commit: 7e31008 |
| Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:44 -0400 (Tue, 16 Apr 2019).
| Package 1227/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qsea 1.8.0 Matthias Lienhard
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: qsea |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qsea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qsea_1.8.0.tar.gz |
| StartedAt: 2019-04-16 02:07:09 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:14:03 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 413.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qsea.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qsea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qsea_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/qsea.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qsea’ version ‘1.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘qsea’ can be installed ... OK
* checking installed package size ... OK
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
addNewSamples 123.759 1.656 127.662
addCNV 20.221 0.566 21.100
addCoverage 16.890 0.282 17.615
addPatternDensity 6.444 0.764 7.268
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/qsea.Rcheck/00check.log’
for details.
qsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qsea ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘qsea’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c lm.c -o lm.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o qsea.so lm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/qsea/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (qsea)
qsea.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(testthat)
> library(qsea)
>
> test_check("qsea")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 3 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.505 0.601 13.186
qsea.Rcheck/qsea-Ex.timings
| name | user | system | elapsed | |
| addCNV | 20.221 | 0.566 | 21.100 | |
| addContrast | 3.948 | 0.158 | 4.210 | |
| addCoverage | 16.890 | 0.282 | 17.615 | |
| addEnrichmentParameters | 0.484 | 0.031 | 0.516 | |
| addLibraryFactors | 1.091 | 0.112 | 1.207 | |
| addNewSamples | 123.759 | 1.656 | 127.662 | |
| addOffset | 0.482 | 0.045 | 0.529 | |
| addPatternDensity | 6.444 | 0.764 | 7.268 | |
| createQseaSet | 0.248 | 0.013 | 0.264 | |
| example | 0.296 | 0.011 | 0.308 | |
| fitNBglm | 1.645 | 0.149 | 1.817 | |
| getPCA | 0.673 | 0.041 | 0.717 | |
| isSignificant | 1.499 | 0.098 | 1.614 | |
| makeTable | 1.651 | 0.073 | 1.735 | |
| normMethod | 0.002 | 0.000 | 0.002 | |
| plotCNV | 0.257 | 0.009 | 0.267 | |
| plotCoverage | 0.854 | 0.034 | 0.893 | |
| plotEnrichmentProfile | 0.418 | 0.053 | 0.474 | |
| plotPCA | 0.571 | 0.027 | 0.599 | |
| qseaGLM-class | 0.001 | 0.000 | 0.001 | |
| qseaPCA-class | 0.001 | 0.000 | 0.001 | |
| qseaSet-class | 0.001 | 0.001 | 0.001 | |
| regionStats | 0.755 | 0.011 | 0.773 | |