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This page was generated on 2021-06-19 12:06:13 -0400 (Sat, 19 Jun 2021).

CHECK results for trackViewer on riesling1

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 1896/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.29.1  (landing page)
Jianhong Ou
Snapshot Date: 2021-06-18 14:50:08 -0400 (Fri, 18 Jun 2021)
URL: https://git.bioconductor.org/packages/trackViewer
Branch: master
Last Commit: cdb4578
Last Changed Date: 2021-05-24 16:32:55 -0400 (Mon, 24 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'Rgraphviz' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: trackViewer
Version: 1.29.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trackViewer.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings trackViewer_1.29.1.tar.gz
StartedAt: 2021-06-19 02:29:02 -0400 (Sat, 19 Jun 2021)
EndedAt: 2021-06-19 02:39:44 -0400 (Sat, 19 Jun 2021)
EllapsedTime: 641.7 seconds
RetCode: 0
Status:   OK  
CheckDir: trackViewer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trackViewer.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings trackViewer_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/trackViewer.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'trackViewer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'trackViewer' version '1.29.1'
* 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 whether package 'trackViewer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.2Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/trackViewer/libs/i386/trackViewer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/trackViewer/libs/x64/trackViewer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
trackViewer-package 18.41   0.00   18.40
browseTracks        16.14   0.02   18.36
parseWIG            13.93   0.00   13.92
viewTracks          13.88   0.00   13.88
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
trackViewer-package 20.60   0.05   20.64
viewTracks          16.38   0.01   16.40
parseWIG            15.96   0.05   16.00
browseTracks        14.26   0.08   14.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/trackViewer.Rcheck/00check.log'
for details.



Installation output

trackViewer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/trackViewer_1.29.1.tar.gz && rm -rf trackViewer.buildbin-libdir && mkdir trackViewer.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=trackViewer.buildbin-libdir trackViewer_1.29.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL trackViewer_1.29.1.zip && rm trackViewer_1.29.1.tar.gz trackViewer_1.29.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 68 1785k   68 1229k    0     0  4728k      0 --:--:-- --:--:-- --:--:-- 4710k
100 1785k  100 1785k    0     0  5778k      0 --:--:-- --:--:-- --:--:-- 5778k

install for i386

* installing *source* package 'trackViewer' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
           long nviPosition = readLong(ifile);
                ^~~~~~~~~~~
hic.cpp:248:16: warning: unused variable 'nviLength' [-Wunused-variable]
           long nviLength = readLong(ifile);
                ^~~~~~~~~
hic.cpp: In function 'std::vector<cellData> getByCoor(std::__cxx11::string, int, int, std::__cxx11::string, int, int, int, std::__cxx11::string, std::__cxx11::string, HicFileHead&, HicFileFoot&, std::ifstream&)':
hic.cpp:751:19: warning: '*((void*)& bd +8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     for(int i=0; i<data.nResolutions; i++){
                  ~^~~~~~~~~~~~~~~~~~
hic.cpp:797:10: note: '*((void*)& bd +8)' was declared here
     body bd;
          ^~
hic.cpp:797:10: warning: '*((void*)& bd +12)' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o trackViewer.dll tmp.def RcppExports.o hic.o -lz -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/trackViewer.buildbin-libdir/00LOCK-trackViewer/00new/trackViewer/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'trackViewer'
    finding HTML links ... done
    GRoperator                              html  
    addArrowMark                            html  
    addGuideLine                            html  
    browseTracks-shiny                      html  
    browseTracks                            html  
    coverageGR                              html  
    dandelion.plot                          html  
    geneModelFromTxdb                       html  
    geneTrack                               html  
    getCurTrackViewport                     html  
    getGeneIDsFromTxDb                      html  
    getLocation                             html  
    gi2track                                html  
    gieStain                                html  
    gridPlot                                html  
    ideogramPlot                            html  
    importBam                               html  
    importData                              html  
    importGInteractions                     html  
    importScSeqScore                        html  
    importScore                             html  
    listChromosomes                         html  
    listResolutions                         html  
    loadIdeogram                            html  
    lolliplot                               html  
    optimizeStyle                           html  
    parse2GRanges                           html  
    parseWIG                                html  
    plotGInteractions                       html  
    plotGRanges                             html  
    plotIdeo                                html  
    plotOneIdeo                             html  
    pos-class                               html  
    trackList-class                         html  
REDIRECT:topic	 seqlevelsStyle<-,trackList-method -> trackList-class.html [ FAIL ]
    trackStyle-class                        html  
REDIRECT:topic	 seqlevelsStyle<-,track-method -> trackStyle-class.html [ FAIL ]
REDIRECT:topic	 $<-,track-method -> trackStyle-class.html [ FAIL ]
    trackViewer-package                     html  
    trackViewerStyle-class                  html  
    viewGene                                html  
    viewTracks                              html  
    xscale-class                            html  
    yaxisStyle-class                        html  
** 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

install for x64

* installing *source* package 'trackViewer' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
           long nviPosition = readLong(ifile);
                ^~~~~~~~~~~
hic.cpp:248:16: warning: unused variable 'nviLength' [-Wunused-variable]
           long nviLength = readLong(ifile);
                ^~~~~~~~~
hic.cpp: In function 'std::vector<cellData> getByCoor(std::__cxx11::string, int, int, std::__cxx11::string, int, int, int, std::__cxx11::string, std::__cxx11::string, HicFileHead&, HicFileFoot&, std::ifstream&)':
hic.cpp:807:17: warning: 'cd.cellDatas::cells' may be used uninitialized in this function [-Wmaybe-uninitialized]
       cellDatas cd;
                 ^~
hic.cpp:807:17: warning: 'cd.cellDatas::cellCount' may be used uninitialized in this function [-Wmaybe-uninitialized]
hic.cpp:751:19: warning: '*((void*)& bd +8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     for(int i=0; i<data.nResolutions; i++){
                  ~^~~~~~~~~~~~~~~~~~
hic.cpp:797:10: note: '*((void*)& bd +8)' was declared here
     body bd;
          ^~
hic.cpp:797:10: warning: '*((void*)& bd +16)' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o trackViewer.dll tmp.def RcppExports.o hic.o -lz -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/trackViewer.buildbin-libdir/trackViewer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trackViewer' as trackViewer_1.29.1.zip
* DONE (trackViewer)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'trackViewer' successfully unpacked and MD5 sums checked

Tests output

trackViewer.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

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 -- Sat Jun 19 02:37:49 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 
  10.21    0.73   10.90 

trackViewer.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 -- Sat Jun 19 02:38:03 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 
  12.31    0.85   13.15 

Example timings

trackViewer.Rcheck/examples_i386/trackViewer-Ex.timings

nameusersystemelapsed
GRoperator2.700.132.83
addArrowMark000
addGuideLine000
browseTracks16.14 0.0218.36
coverageGR0.180.000.18
dandelion.plot2.290.013.47
geneModelFromTxdb4.760.245.00
geneTrack1.740.011.75
getCurTrackViewport000
getGeneIDsFromTxDb0.680.000.69
getLocation1.670.061.73
gi2track0.050.000.05
gieStain000
ideogramPlot000
importBam0.250.020.27
importData1.810.001.81
importGInteractions1.070.081.15
importScSeqScore000
importScore0.390.000.41
listChromosomes0.280.000.28
listResolutions0.000.000.02
loadIdeogram000
lolliplot0.810.000.81
optimizeStyle0.440.000.45
parse2GRanges0.010.000.02
parseWIG13.93 0.0013.92
plotGInteractions0.960.000.97
plotGRanges1.290.001.28
plotIdeo000
plotOneIdeo000
trackStyle-class0.040.000.05
trackViewer-package18.41 0.0018.40
trackViewerStyle-class000
viewGene4.030.044.08
viewTracks13.88 0.0013.88

trackViewer.Rcheck/examples_x64/trackViewer-Ex.timings

nameusersystemelapsed
GRoperator3.440.073.52
addArrowMark0.020.000.01
addGuideLine000
browseTracks14.26 0.0814.35
coverageGR0.240.000.23
dandelion.plot2.540.002.55
geneModelFromTxdb4.140.214.34
geneTrack1.860.031.89
getCurTrackViewport000
getGeneIDsFromTxDb0.690.040.74
getLocation1.120.021.14
gi2track0.050.000.04
gieStain0.020.000.02
ideogramPlot000
importBam0.280.000.28
importData2.220.032.25
importGInteractions1.170.021.20
importScSeqScore000
importScore0.440.000.44
listChromosomes0.290.000.30
listResolutions0.000.000.01
loadIdeogram000
lolliplot0.940.010.96
optimizeStyle0.580.030.61
parse2GRanges0.010.000.01
parseWIG15.96 0.0516.00
plotGInteractions1.110.031.14
plotGRanges1.490.001.48
plotIdeo000
plotOneIdeo000
trackStyle-class0.040.000.05
trackViewer-package20.60 0.0520.64
trackViewerStyle-class000
viewGene4.040.084.12
viewTracks16.38 0.0116.40