Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P [Q] R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for qsea on veracruz2

This page was generated on 2017-08-16 13:34:47 -0400 (Wed, 16 Aug 2017).

Package 1041/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsea 1.2.0
Matthias Lienhard
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/qsea
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: qsea
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qsea_1.2.0.tar.gz
StartedAt: 2017-08-16 06:55:16 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:59:40 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 263.9 seconds
RetCode: 0
Status:  OK 
CheckDir: qsea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qsea_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/qsea.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.2.0’
* 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 loading without being on the library search path ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
addNewSamples     20.241  0.708  21.575
addCNV             8.248  0.342   8.846
addPatternDensity  5.632  0.510   6.322
* 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: OK

qsea.Rcheck/00install.out:

* 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 /Users/biocbuild/bbs-3.5-bioc/meat/qsea.Rcheck/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/qsea-Ex.timings:

nameusersystemelapsed
addCNV8.2480.3428.846
addContrast1.9680.0752.113
addCoverage2.3180.1532.549
addEnrichmentParameters0.4050.0080.425
addLibraryFactors1.0350.0921.173
addNewSamples20.241 0.70821.575
addOffset0.3940.0390.438
addPatternDensity5.6320.5106.322
createQseaSet0.1990.0100.209
example0.2200.0090.234
fitNBglm1.0150.0541.088
getPCA0.7000.0460.768
isSignificant1.3130.0551.392
makeTable1.4950.0561.599
normMethod0.0020.0000.002
plotCNV0.2870.0070.315
plotCoverage0.8190.0380.888
plotEnrichmentProfile0.3530.0120.367
plotPCA0.6610.0360.719
qseaGLM-class0.0010.0000.001
qseaPCA-class0.0010.0000.001
qseaSet-class0.0010.0000.001
regionStats0.6430.0090.661