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CHECK report for SGSeq on celaya2

This page was generated on 2019-04-09 13:12:55 -0400 (Tue, 09 Apr 2019).

Package 1476/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SGSeq 1.17.2
Leonard Goldstein
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SGSeq
Branch: master
Last Commit: 4d31337
Last Changed Date: 2018-12-18 20:26:44 -0400 (Tue, 18 Dec 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: SGSeq
Version: 1.17.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SGSeq_1.17.2.tar.gz
StartedAt: 2019-04-09 05:27:04 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:40:14 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 789.5 seconds
RetCode: 0
Status:  OK 
CheckDir: SGSeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SGSeq_1.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SGSeq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGSeq’ version ‘1.17.2’
* 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 ‘SGSeq’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlotsAsDF’
  See the note in ?`:::` about the use of this operator.
* 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
predictVariantEffects 55.848  0.273  56.484
analyzeFeatures       33.632  0.573  35.350
predictTxFeatures     19.725  0.276  20.785
getSGVariantCounts     9.532  0.023   9.573
getSGFeatureCounts     9.494  0.030   9.736
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/SGSeq.Rcheck/00check.log’
for details.



Installation output

SGSeq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SGSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SGSeq’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SGSeq)

Tests output

SGSeq.Rcheck/tests/runTests.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> BiocGenerics:::testPackage("SGSeq")

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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

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


Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    type

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

    aperm, apply, rowsum

Predict features...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Process features...
Obtain counts...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer
Predicting effect of 2 variants on 3 coding transcripts...
Predicting effect of 3 variants on 3 coding transcripts...


RUNIT TEST PROTOCOL -- Tue Apr  9 05:40:05 2019 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SGSeq RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
254.144   3.345 257.506 

Example timings

SGSeq.Rcheck/SGSeq-Ex.timings

nameusersystemelapsed
SGFeatureCounts0.3220.0210.343
SGFeatures0.1160.0190.137
SGVariantCounts0.5340.0980.633
SGVariants0.4080.0720.480
TxFeatures0.1110.0180.128
analyzeFeatures33.632 0.57335.350
analyzeVariants2.9900.0603.151
annotate2.9160.0083.057
assays0.0350.0010.045
convertToSGFeatures2.0570.0052.122
convertToTxFeatures0.7290.0010.768
exportFeatures0.0010.0000.001
findSGVariants2.3650.0072.474
getBamInfo1.7290.3042.082
getSGFeatureCounts9.4940.0309.736
getSGVariantCounts9.5320.0239.573
importTranscripts0.0000.0000.001
makeSGFeatureCounts0.0530.0000.053
makeVariantNames0.0200.0000.021
mergeTxFeatures0.3730.0010.375
plotCoverage0.0000.0000.001
plotFeatures0.0010.0010.000
plotSpliceGraph0.0010.0010.001
plotVariants000
predictTxFeatures19.725 0.27620.785
predictVariantEffects55.848 0.27356.484
processTerminalExons0.4310.0010.432
slots0.0030.0010.003