Package: NestLink

Version: 1.0.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings NestLink_1.0.0.tar.gz

StartedAt: 2019-10-17 13:34:57 -0400 (Thu, 17 Oct 2019)

EndedAt: 2019-10-17 13:41:20 -0400 (Thu, 17 Oct 2019)

EllapsedTime: 383.4 seconds

RetCode: 0

Status:  OK

CheckDir: NestLink.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings NestLink_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/NestLink.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NestLink/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NestLink’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'AnnotationHub', 'ExperimentHub', 'Biostrings', 'gplots', 'protViz',
  'ShortRead'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘NestLink’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with no role:
  Damien Morger 
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
runNGSAnalysis           146.122  0.172 147.750
getExperimentHubFilename  16.013  0.144  17.389
getFC                      5.148  0.024   5.302
F255744                    4.256  0.168   6.332
* 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-3.9-data-experiment/meat/NestLink.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL NestLink
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘NestLink’ ...
** using staged installation
** R
** exec
** 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 (NestLink)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> #R
> 
> library(testthat)
> 
> suppressPackageStartupMessages(library(NestLink))
> 
> test_check("NestLink")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.407   0.661  21.886 

name	user	system	elapsed
F255744	4.256	0.168	6.332
NB.unambiguous	3.419	0.056	3.618
NB.unique	3.189	0.016	3.341
PGexport	1.830	0.024	2.009
WU160118	3.727	0.052	4.950
compose_GPGx8cTerm	0.005	0.002	0.007
compose_GPx10R	0.004	0.000	0.005
compose_GSx7cTerm	0.007	0.000	0.007
dot-ssrc.mascot	2.727	0.016	2.874
getExperimentHubFilename	16.013	0.144	17.389
getFC	5.148	0.024	5.302
getNB	3.014	0.040	3.200
nanobodyFlycodeLinking.as.fasta	1.724	0.012	2.112
nanobodyFlycodeLinking.summary	1.771	0.024	1.930
plot_in_silico_LCMS_map	1.471	0.008	1.478
runNGSAnalysis	146.122	0.172	147.750
twoPatternReadFilter	0.012	0.000	0.012