Matthias Lienhard
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/qsea |
| Branch: RELEASE_3_10 |
| Last Commit: c6cbd48 |
| Last Changed Date: 2019-10-29 13:09:49 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:11:33 -0400 (Wed, 15 Apr 2020).
| Package 1344/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qsea 1.12.0 Matthias Lienhard
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: qsea |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings qsea_1.12.0.tar.gz |
| StartedAt: 2020-04-15 03:56:25 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:01:18 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 293.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qsea.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings qsea_1.12.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/qsea.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.0’
* 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 23.248 0.512 24.318
addPatternDensity 7.664 0.080 7.800
addCNV 6.860 0.208 7.610
* 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-3.10-bioc/meat/qsea.Rcheck/00check.log’
for details.
qsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL qsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘qsea’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c lm.c -o lm.o gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o qsea.so lm.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
14.660 0.508 15.731
qsea.Rcheck/qsea-Ex.timings
| name | user | system | elapsed | |
| addCNV | 6.860 | 0.208 | 7.610 | |
| addContrast | 2.652 | 0.008 | 2.665 | |
| addCoverage | 3.444 | 0.052 | 3.506 | |
| addEnrichmentParameters | 0.532 | 0.004 | 0.542 | |
| addLibraryFactors | 1.132 | 0.004 | 1.137 | |
| addNewSamples | 23.248 | 0.512 | 24.318 | |
| addOffset | 0.468 | 0.000 | 0.467 | |
| addPatternDensity | 7.664 | 0.080 | 7.800 | |
| createQseaSet | 0.264 | 0.004 | 0.276 | |
| example | 0.312 | 0.000 | 0.313 | |
| fitNBglm | 1.040 | 0.004 | 1.046 | |
| getPCA | 0.736 | 0.004 | 0.740 | |
| isSignificant | 1.604 | 0.000 | 1.620 | |
| makeTable | 2.028 | 0.004 | 2.033 | |
| normMethod | 0.004 | 0.000 | 0.002 | |
| plotCNV | 0.352 | 0.004 | 0.375 | |
| plotCoverage | 1.008 | 0.000 | 1.012 | |
| plotEnrichmentProfile | 0.460 | 0.000 | 0.461 | |
| plotPCA | 0.764 | 0.000 | 0.768 | |
| qseaGLM-class | 0.000 | 0.000 | 0.002 | |
| qseaPCA-class | 0.004 | 0.000 | 0.001 | |
| qseaSet-class | 0.000 | 0.000 | 0.001 | |
| regionStats | 0.828 | 0.000 | 0.835 | |