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CHECK report for NestLink on riesling1

This page was generated on 2021-01-14 15:59:10 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE NestLink PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 248/385HostnameOS / ArchINSTALLBUILDCHECK
NestLink 1.7.0
Lennart Opitz
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/NestLink
Branch: master
Last Commit: 3b487be
Last Changed Date: 2020-10-27 10:29:06 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: NestLink
Version: 1.7.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NestLink.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NestLink_1.7.0.tar.gz
StartedAt: 2021-01-14 11:31:53 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:40:55 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 542.3 seconds
RetCode: 0
Status:  OK  
CheckDir: NestLink.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NestLink.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NestLink_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/NestLink.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NestLink/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NestLink' version '1.7.0'
* 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 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 <damien.morger@rqmicro.com>
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
runNGSAnalysis           97.56   0.49   98.59
getExperimentHubFilename 17.56   1.21   21.58
F255744                   3.64   0.73    5.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
runNGSAnalysis           100.45   0.54  101.40
getExperimentHubFilename  18.49   0.98   21.85
F255744                    3.85   0.97    5.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/NestLink.Rcheck/00check.log'
for details.



Installation output

NestLink.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/NestLink_1.7.0.tar.gz && rm -rf NestLink.buildbin-libdir && mkdir NestLink.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NestLink.buildbin-libdir NestLink_1.7.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL NestLink_1.7.0.zip && rm NestLink_1.7.0.tar.gz NestLink_1.7.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1203k  100 1203k    0     0  4134k      0 --:--:-- --:--:-- --:--:-- 4134k

install for i386

* installing *source* package 'NestLink' ...
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NestLink'
    finding HTML links ... done
    F255744                                 html  
REDIRECT:topic	 F255744 -> F255744.html [ SUCCESS ]
    NB.unambiguous                          html  
REDIRECT:topic	 NB.unambiguous -> NB.unambiguous.html [ SUCCESS ]
    NB.unique                               html  
REDIRECT:topic	 NB.unique -> NB.unique.html [ SUCCESS ]
    PGexport                                html  
REDIRECT:topic	 PGexport -> PGexport.html [ SUCCESS ]
    WU160118                                html  
REDIRECT:topic	 WU160118 -> WU160118.html [ SUCCESS ]
    compose_GPGx8cTerm                      html  
REDIRECT:topic	 compose_GPGx8cTerm -> compose_GPGx8cTerm.html [ SUCCESS ]
    compose_GPx10R                          html  
REDIRECT:topic	 compose_GPx10R -> compose_GPx10R.html [ SUCCESS ]
    compose_GSx7cTerm                       html  
REDIRECT:topic	 compose_GSx7cTerm -> compose_GSx7cTerm.html [ SUCCESS ]
    dot-ssrc.mascot                         html  
REDIRECT:topic	 .ssrc.mascot -> dot-ssrc.mascot.html [ SUCCESS ]
REDIRECT:file	 dot-ssrc.mascot.html -> dot-ssrc.mascot.html [ SUCCESS ]
    getExperimentHubFilename                html  
REDIRECT:topic	 getExperimentHubFilename -> getExperimentHubFilename.html [ SUCCESS ]
    getFC                                   html  
REDIRECT:topic	 getFC -> getFC.html [ SUCCESS ]
    getNB                                   html  
REDIRECT:topic	 getNB -> getNB.html [ SUCCESS ]
    nanobodyFlycodeLinking.as.fasta         html  
REDIRECT:topic	 nanobodyFlycodeLinking.as.fasta -> nanobodyFlycodeLinking.as.fasta.html [ SUCCESS ]
    nanobodyFlycodeLinking.summary          html  
REDIRECT:topic	 nanobodyFlycodeLinking.summary -> nanobodyFlycodeLinking.summary.html [ SUCCESS ]
    plot_in_silico_LCMS_map                 html  
REDIRECT:topic	 plot_in_silico_LCMS_map -> plot_in_silico_LCMS_map.html [ SUCCESS ]
    runNGSAnalysis                          html  
REDIRECT:topic	 runNGSAnalysis -> runNGSAnalysis.html [ SUCCESS ]
    twoPatternReadFilter                    html  
REDIRECT:topic	 twoPatternReadFilter -> twoPatternReadFilter.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'NestLink' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NestLink' as NestLink_1.7.0.zip
* DONE (NestLink)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'NestLink' successfully unpacked and MD5 sums checked

Tests output

NestLink.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
  18.23    1.71   21.15 

NestLink.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
  19.73    1.70   22.45 

Example timings

NestLink.Rcheck/examples_i386/NestLink-Ex.timings

nameusersystemelapsed
F2557443.640.735.06
NB.unambiguous3.200.163.64
NB.unique3.360.083.69
PGexport2.370.073.06
WU1601183.900.154.34
compose_GPGx8cTerm0.020.000.02
compose_GPx10R0.000.000.01
compose_GSx7cTerm000
dot-ssrc.mascot3.280.213.76
getExperimentHubFilename17.56 1.2121.58
getFC4.330.204.80
getNB3.100.163.56
nanobodyFlycodeLinking.as.fasta2.260.112.72
nanobodyFlycodeLinking.summary2.750.123.16
plot_in_silico_LCMS_map1.240.001.24
runNGSAnalysis97.56 0.4998.59
twoPatternReadFilter0.010.000.02

NestLink.Rcheck/examples_x64/NestLink-Ex.timings

nameusersystemelapsed
F2557443.850.975.34
NB.unambiguous3.320.123.77
NB.unique3.390.143.84
PGexport2.370.132.80
WU1601183.800.184.31
compose_GPGx8cTerm0.020.000.01
compose_GPx10R0.000.000.02
compose_GSx7cTerm000
dot-ssrc.mascot3.370.153.90
getExperimentHubFilename18.49 0.9821.85
getFC4.420.114.89
getNB3.200.123.58
nanobodyFlycodeLinking.as.fasta2.330.133.01
nanobodyFlycodeLinking.summary2.300.122.69
plot_in_silico_LCMS_map1.230.001.25
runNGSAnalysis100.45 0.54101.40
twoPatternReadFilter000