Matthias Lienhard
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/qsea |
| Branch: RELEASE_3_9 |
| Last Commit: eeb4ef6 |
| Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:09:12 -0400 (Wed, 16 Oct 2019).
| Package 1289/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qsea 1.10.0 Matthias Lienhard
| 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: qsea |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qsea_1.10.0.tar.gz |
| StartedAt: 2019-10-16 04:12:46 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:17:25 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 279.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qsea.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qsea_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/qsea.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 ... NOTE
findCNV: no visible global function definition for ‘bpnworkers’
Undefined global functions or variables:
bpnworkers
* 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 21.933 0.599 23.141
addPatternDensity 7.106 0.156 7.267
addCNV 6.875 0.245 7.410
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/qsea.Rcheck/00check.log’
for details.
qsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL qsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘qsea’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c lm.c -o lm.o gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o qsea.so lm.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-qsea/00new/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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (qsea)
qsea.Rcheck/tests/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-pc-linux-gnu (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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
13.216 0.463 13.835
qsea.Rcheck/qsea-Ex.timings
| name | user | system | elapsed | |
| addCNV | 6.875 | 0.245 | 7.410 | |
| addContrast | 2.210 | 0.008 | 2.219 | |
| addCoverage | 3.720 | 0.052 | 3.772 | |
| addEnrichmentParameters | 0.302 | 0.020 | 0.321 | |
| addLibraryFactors | 1.143 | 0.016 | 1.161 | |
| addNewSamples | 21.933 | 0.599 | 23.141 | |
| addOffset | 0.308 | 0.004 | 0.312 | |
| addPatternDensity | 7.106 | 0.156 | 7.267 | |
| createQseaSet | 0.254 | 0.000 | 0.254 | |
| example | 0.256 | 0.000 | 0.258 | |
| fitNBglm | 1.195 | 0.008 | 1.215 | |
| getPCA | 0.715 | 0.008 | 0.723 | |
| isSignificant | 1.220 | 0.000 | 1.222 | |
| makeTable | 1.711 | 0.008 | 1.730 | |
| normMethod | 0.001 | 0.000 | 0.001 | |
| plotCNV | 0.236 | 0.000 | 0.236 | |
| plotCoverage | 0.689 | 0.000 | 0.689 | |
| plotEnrichmentProfile | 0.341 | 0.000 | 0.341 | |
| plotPCA | 0.711 | 0.000 | 0.717 | |
| qseaGLM-class | 0.001 | 0.000 | 0.002 | |
| qseaPCA-class | 0.001 | 0.000 | 0.000 | |
| qseaSet-class | 0.000 | 0.000 | 0.001 | |
| regionStats | 0.646 | 0.000 | 0.656 | |