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CHECK report for yamss on malbec1

This page was generated on 2020-04-15 12:12:03 -0400 (Wed, 15 Apr 2020).

Package 1817/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
yamss 1.12.1
Leslie Myint
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/yamss
Branch: RELEASE_3_10
Last Commit: 9709243
Last Changed Date: 2020-03-01 12:02:46 -0400 (Sun, 01 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: yamss
Version: 1.12.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:yamss.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings yamss_1.12.1.tar.gz
StartedAt: 2020-04-15 04:20:18 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:37:18 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 1019.5 seconds
RetCode: 0
Status:  OK 
CheckDir: yamss.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:yamss.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings yamss_1.12.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/yamss.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yamss/DESCRIPTION’ ... OK
* this is package ‘yamss’ version ‘1.12.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘yamss’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
slicepi      854.972  4.432 274.148
bakedpi      769.748  4.492 158.034
CMSraw-class   7.332  0.240   7.973
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/yamss.Rcheck/00check.log’
for details.



Installation output

yamss.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL yamss
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘yamss’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘ifelse’ when loading ‘yamss’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘IRanges’ for request: ‘ifelse’ when loading ‘yamss’
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘ifelse’ when loading ‘yamss’
** testing if installed package keeps a record of temporary installation path
* DONE (yamss)

Tests output

yamss.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> library(testthat)
> library(yamss)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

No methods found in package 'IRanges' for request: 'ifelse' when loading 'yamss'
> 
> test_check("yamss")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
    user   system  elapsed 
1131.100    6.820  383.511 

Example timings

yamss.Rcheck/yamss-Ex.timings

nameusersystemelapsed
CMSproc-class0.0040.0000.004
CMSraw-class7.3320.2407.973
CMSslice-class0.0880.0000.088
bakedpi769.748 4.492158.034
diffrep0.7160.0000.731
getEICS1.560.020.39
getTIC0.3520.0000.102
plotDensityRegion0.0120.0000.015
readMSdata2.6120.0362.657
slicepi854.972 4.432274.148