Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:53 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SGSeq on nebbiolo1


To the developers/maintainers of the SGSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SGSeq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1827/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SGSeq 1.30.0  (landing page)
Leonard Goldstein
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/SGSeq
git_branch: RELEASE_3_15
git_last_commit: a19e395
git_last_commit_date: 2022-04-26 11:22:24 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SGSeq
Version: 1.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SGSeq_1.30.0.tar.gz
StartedAt: 2022-10-18 21:48:50 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:57:43 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 532.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SGSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SGSeq_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SGSeq.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.30.0’
* 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 ‘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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
predictVariantEffects 38.758  0.556  40.531
analyzeFeatures       19.944  0.919  20.870
predictTxFeatures     10.737  0.256  10.996
getSGVariantCounts     6.312  0.192   6.505
getSGFeatureCounts     5.483  0.288   5.771
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/SGSeq.Rcheck/00check.log’
for details.



Installation output

SGSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SGSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.

> BiocGenerics:::testPackage("SGSeq")

Attaching package: 'BiocGenerics'

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.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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...
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
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.
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
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
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
Predicting effect of 2 variants on 3 coding transcripts...
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
Predicting effect of 3 variants on 3 coding transcripts...


RUNIT TEST PROTOCOL -- Tue Oct 18 21:57:39 2022 
*********************************************** 
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 
Warning message:
In (function (seqlevels, genome, new_style)  :
  cannot switch some of hg19's seqlevels from UCSC to NCBI style
> 
> proc.time()
   user  system elapsed 
177.406   3.449 182.076 

Example timings

SGSeq.Rcheck/SGSeq-Ex.timings

nameusersystemelapsed
SGFeatureCounts0.2050.0200.225
SGFeatures0.0470.0000.047
SGVariantCounts0.1930.0000.193
SGVariants0.1240.0160.139
TxFeatures0.0570.0000.057
analyzeFeatures19.944 0.91920.870
analyzeVariants1.8190.0201.839
annotate1.8680.0241.891
assays0.0260.0000.025
convertToSGFeatures1.3000.0241.323
convertToTxFeatures0.4170.0040.421
exportFeatures000
findSGVariants1.2930.0041.298
getBamInfo1.7640.4322.196
getSGFeatureCounts5.4830.2885.771
getSGVariantCounts6.3120.1926.505
importTranscripts000
makeSGFeatureCounts0.0540.0000.054
makeVariantNames0.0190.0000.020
mergeTxFeatures0.2130.0000.213
plotCoverage000
plotFeatures000
plotSpliceGraph0.0000.0000.001
plotVariants0.0010.0000.001
predictTxFeatures10.737 0.25610.996
predictVariantEffects38.758 0.55640.531
processTerminalExons0.2760.0000.275
slots0.0040.0000.004