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CHECK report for bgafun on malbec2

This page was generated on 2019-04-09 11:26:00 -0400 (Tue, 09 Apr 2019).

Package 124/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgafun 1.45.0
Iain Wallace
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/bgafun
Branch: master
Last Commit: c6bcffd
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: bgafun
Version: 1.45.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:bgafun.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings bgafun_1.45.0.tar.gz
StartedAt: 2019-04-08 22:57:51 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:58:33 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 42.6 seconds
RetCode: 0
Status:  OK 
CheckDir: bgafun.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:bgafun.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings bgafun_1.45.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/bgafun.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bgafun/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bgafun’ version ‘1.45.0’
* 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 ‘bgafun’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘ade4’ ‘made4’ ‘seqinr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
run_between_pca: no visible global function definition for ‘dudi.pca’
run_between_pca: no visible global function definition for ‘bca’
Undefined global functions or variables:
  bca dudi.pca
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
add_pseudo_counts 9.077  0.008   9.086
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/bgafun.Rcheck/00check.log’
for details.



Installation output

bgafun.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL bgafun
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘bgafun’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bgafun)

Tests output


Example timings

bgafun.Rcheck/bgafun-Ex.timings

nameusersystemelapsed
Calculate_Row_Weights0.1160.0120.127
add_pseudo_counts9.0770.0089.086
average_cols_aap0.5450.0040.548
bgafun1.9030.0081.911
convert_aln_AAP0.3320.0000.331
convert_aln_amino0.2150.0000.215
create_profile_strings1.6520.0001.652
remove_gaps_groups0.2410.0000.241
run_between_pca0.3240.0040.328
top_residues_2_groups1.4280.0081.437