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CHECK report for qsea on merida2

This page was generated on 2018-10-17 08:56:46 -0400 (Wed, 17 Oct 2018).

Package 1160/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsea 1.6.0
Matthias Lienhard
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/qsea
Branch: RELEASE_3_7
Last Commit: 6a95c78
Last Changed Date: 2018-04-30 10:35:42 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: qsea
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2018-10-16 23:26:54 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:33:27 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 392.9 seconds
RetCode: 0
Status:  OK 
CheckDir: qsea.Rcheck
Warnings: 0

Command output

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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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/qsea.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.0’
* 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     113.290  1.470 115.369
addCNV             20.134  0.674  20.932
addCoverage        14.986  0.298  15.390
addPatternDensity   7.301  0.849   8.196
* 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-3.7-bioc/meat/qsea.Rcheck/00check.log’
for details.



Installation output

qsea.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qsea
###
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##############################################################################


* 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)

Tests output

qsea.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 
 11.561   0.563  12.188 

Example timings

qsea.Rcheck/qsea-Ex.timings

nameusersystemelapsed
addCNV20.134 0.67420.932
addContrast2.1980.1292.344
addCoverage14.986 0.29815.390
addEnrichmentParameters0.5440.0190.566
addLibraryFactors1.4830.1161.603
addNewSamples113.290 1.470115.369
addOffset1.0010.0291.032
addPatternDensity7.3010.8498.196
createQseaSet0.2310.0150.247
example0.2750.0380.318
fitNBglm1.1670.0621.232
getPCA0.7330.0550.792
isSignificant1.6620.0701.744
makeTable1.9290.0612.003
normMethod0.0030.0000.004
plotCNV0.3250.0120.339
plotCoverage0.8310.0330.876
plotEnrichmentProfile0.4270.0180.450
plotPCA0.7380.0450.788
qseaGLM-class0.0020.0000.002
qseaPCA-class0.0010.0000.001
qseaSet-class0.0030.0000.004
regionStats0.6710.0090.689