Back to Build/check report for BioC 3.15
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This page was generated on 2022-06-27 11:10:11 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 trackViewer on nebbiolo1


To the developers/maintainers of the trackViewer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trackViewer.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 2032/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.32.1  (landing page)
Jianhong Ou
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/trackViewer
git_branch: RELEASE_3_15
git_last_commit: 7878202
git_last_commit_date: 2022-05-04 16:37:29 -0400 (Wed, 04 May 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: trackViewer
Version: 1.32.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings trackViewer_1.32.1.tar.gz
StartedAt: 2022-06-26 22:17:47 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 22:26:00 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 493.0 seconds
RetCode: 0
Status:   OK  
CheckDir: trackViewer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings trackViewer_1.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/trackViewer.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.32.1’
* package encoding: UTF-8
* 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 ‘trackViewer’ 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
trackViewer-package 24.595  0.287  24.882
viewTracks          17.434  0.164  17.598
parseWIG            16.807  0.240  17.047
browseTracks        15.761  0.355  16.121
importGInteractions  7.627  0.124   7.754
geneModelFromTxdb    5.873  0.496   6.370
viewGene             5.948  0.072   6.021
* 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/trackViewer.Rcheck/00check.log’
for details.



Installation output

trackViewer.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘trackViewer’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c hic.cpp -o hic.o
hic.cpp: In member function ‘void HicFileHead::readHeader(std::ifstream&)’:
hic.cpp:247:16: warning: unused variable ‘nviPosition’ [-Wunused-variable]
  247 |           long nviPosition = readLong(ifile);
      |                ^~~~~~~~~~~
hic.cpp:248:16: warning: unused variable ‘nviLength’ [-Wunused-variable]
  248 |           long nviLength = readLong(ifile);
      |                ^~~~~~~~~
hic.cpp: In function ‘std::vector<cellData> getByCoor(std::string, int, int, std::string, int, int, int, std::string, std::string, HicFileHead&, HicFileFoot&, std::ifstream&)’:
hic.cpp:751:19: warning: ‘*((void*)(& bd)+8).resolutions::nResolutions’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  751 |     for(int i=0; i<data.nResolutions; i++){
      |                  ~^~~~~~~~~~~~~~~~~~
hic.cpp:797:10: note: ‘*((void*)(& bd)+8).resolutions::nResolutions’ was declared here
  797 |     body bd;
      |          ^~
hic.cpp:797:10: warning: ‘*((void*)(& bd)+8).resolutions::res’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o trackViewer.so RcppExports.o hic.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-trackViewer/00new/trackViewer/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (trackViewer)

Tests output

trackViewer.Rcheck/tests/runTests.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
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.

> require("trackViewer") || stop("unable to load Package:trackViewer")
Loading required package: trackViewer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: grid
Loading required package: Rcpp
[1] TRUE
> require("RUnit") || stop("unable to load Package:RUnit")
Loading required package: RUnit
[1] TRUE
> BiocGenerics:::testPackage("trackViewer")


RUNIT TEST PROTOCOL -- Sun Jun 26 22:25:56 2022 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
trackViewer RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 19.460   0.740  20.188 

Example timings

trackViewer.Rcheck/trackViewer-Ex.timings

nameusersystemelapsed
GRoperator3.2900.2763.566
addArrowMark0.0080.0000.008
addGuideLine0.0040.0000.004
browseTracks15.761 0.35516.121
coverageGR0.2130.0000.213
dandelion.plot2.2650.0322.296
geneModelFromTxdb5.8730.4966.370
geneTrack2.0350.0322.067
getCurTrackViewport0.0010.0020.003
getGeneIDsFromTxDb0.9420.0160.957
getLocation1.3750.0361.411
gi2track0.0460.0000.046
gieStain0.0030.0040.006
ideogramPlot0.0010.0000.000
importBam0.3450.0040.349
importData3.1850.1243.309
importGInteractions7.6270.1247.754
importScSeqScore000
importScore2.0030.0002.004
listChromosomes0.4490.0080.456
listResolutions0.0030.0000.004
loadIdeogram0.0000.0000.001
lolliplot0.8350.0020.837
optimizeStyle0.5630.0040.567
parse2GRanges0.0080.0040.011
parseWIG16.807 0.24017.047
plotGInteractions1.3580.0121.370
plotGRanges1.6680.0001.668
plotIdeo000
plotOneIdeo0.0000.0000.001
trackStyle-class0.0790.0000.079
trackViewer-package24.595 0.28724.882
trackViewerStyle-class0.0000.0000.001
viewGene5.9480.0726.021
viewTracks17.434 0.16417.598