Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2021-06-18 14:06:02 -0400 (Fri, 18 Jun 2021).

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? here 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 1942/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.28.0  (landing page)
Jianhong Ou
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/trackViewer
Branch: RELEASE_3_13
Last Commit: 14d6faa
Last Changed Date: 2021-05-19 12:02:40 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: trackViewer
Version: 1.28.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings trackViewer_1.28.0.tar.gz
StartedAt: 2021-06-17 13:55:14 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 14:03:06 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 471.9 seconds
RetCode: 0
Status:   OK  
CheckDir: trackViewer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings trackViewer_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/trackViewer.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.28.0’
* 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 27.944  0.068  28.014
viewTracks          21.462  0.048  21.511
parseWIG            21.074  0.055  21.134
browseTracks        19.166  0.052  19.223
geneModelFromTxdb    5.866  0.280   6.147
viewGene             5.498  0.036   5.535
* 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-3.13-bioc/meat/trackViewer.Rcheck/00check.log’
for details.



Installation output

trackViewer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL trackViewer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘trackViewer’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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:833:59: warning: ‘values.doubleValues::values’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  833 |             double nvnv = normVector1.values[rec_norm.binX] *
      |                                                           ^
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-3.13-bioc/R/lib -L/usr/local/lib -o trackViewer.so RcppExports.o hic.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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
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.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 -- Thu Jun 17 14:03:03 2021 
*********************************************** 
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 
 16.933   1.078  18.001 

Example timings

trackViewer.Rcheck/trackViewer-Ex.timings

nameusersystemelapsed
GRoperator2.9490.2073.157
addArrowMark0.0050.0040.008
addGuideLine0.0030.0000.004
browseTracks19.166 0.05219.223
coverageGR0.280.000.28
dandelion.plot3.2850.0003.285
geneModelFromTxdb5.8660.2806.147
geneTrack3.5010.0563.556
getCurTrackViewport0.0020.0000.003
getGeneIDsFromTxDb0.8300.0070.838
getLocation1.2140.0071.222
gi2track0.0690.0000.070
gieStain0.0070.0000.006
ideogramPlot0.0010.0000.000
importBam0.3830.0010.382
importData3.3180.0083.325
importGInteractions1.6030.0071.616
importScSeqScore0.0000.0000.001
importScore0.7190.0290.749
listChromosomes0.3880.0040.393
listResolutions0.0030.0000.003
loadIdeogram0.0010.0000.000
lolliplot1.2120.0001.212
optimizeStyle0.6810.0080.689
parse2GRanges0.0190.0000.019
parseWIG21.074 0.05521.134
plotGInteractions1.3850.0121.397
plotGRanges1.9140.0081.922
plotIdeo000
plotOneIdeo000
trackStyle-class0.0650.0000.065
trackViewer-package27.944 0.06828.014
trackViewerStyle-class000
viewGene5.4980.0365.535
viewTracks21.462 0.04821.511