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CHECK report for hummingbird on malbec1

This page was generated on 2021-05-06 12:27:54 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the hummingbird package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 853/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hummingbird 1.0.3  (landing page)
Eleni Adam
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/hummingbird
Branch: RELEASE_3_12
Last Commit: 457ac10
Last Changed Date: 2021-04-17 13:34:10 -0400 (Sat, 17 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: hummingbird
Version: 1.0.3
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hummingbird.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hummingbird_1.0.3.tar.gz
StartedAt: 2021-05-06 02:31:04 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:33:47 -0400 (Thu, 06 May 2021)
EllapsedTime: 163.2 seconds
RetCode: 0
Status:   OK  
CheckDir: hummingbird.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hummingbird.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hummingbird_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/hummingbird.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hummingbird/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hummingbird’ version ‘1.0.3’
* package encoding: UTF-8
* 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 ‘hummingbird’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/hummingbird.Rcheck/00check.log’
for details.



Installation output

hummingbird.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL hummingbird
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘hummingbird’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c em.cpp -o em.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c postAdjustment.cpp -o postAdjustment.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o hummingbird.so RcppExports.o em.o init.o postAdjustment.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-hummingbird/00new/hummingbird/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 (hummingbird)

Tests output


Example timings

hummingbird.Rcheck/hummingbird-Ex.timings

nameusersystemelapsed
abnormM0.0360.0320.066
abnormUM0.0240.0400.063
exampleHummingbird0.1960.0200.215
exampleSECase0.2720.0040.276
exampleSEControl0.2200.0000.219
hummingbirdEM2.1280.0482.176
hummingbirdEMinternal1.8280.0041.836
hummingbirdGraph1.8440.0041.851
hummingbirdPostAdjustment2.0520.0122.069
hummingbirdPostAdjustmentInternal1.5240.0001.528
normM0.0200.0240.043
normUM0.0040.0360.042
pos0.0040.0160.018