Jianhong Ou
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/trackViewer |
| git_branch: RELEASE_3_16 |
| git_last_commit: 9daa482 |
| git_last_commit_date: 2022-11-01 11:09:09 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:56 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 2072/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| trackViewer 1.34.0 (landing page) Jianhong Ou
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: trackViewer |
| Version: 1.34.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:trackViewer.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings trackViewer_1.34.0.tar.gz |
| StartedAt: 2023-04-11 06:51:20 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 06:59:32 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 492.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: trackViewer.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:trackViewer.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings trackViewer_1.34.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/trackViewer.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.34.0'
* 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 whether package 'trackViewer' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
extdata 2.9Mb
libs 1.1Mb
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/trackViewer/libs/x64/trackViewer.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
trackViewer-package 21.81 0.16 21.97
parseWIG 15.83 0.13 15.95
viewTracks 15.78 0.16 15.94
browseTracks 15.52 0.11 15.84
geneModelFromTxdb 5.37 0.35 5.77
* 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/trackViewer.Rcheck/00check.log'
for details.
trackViewer.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL trackViewer
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'trackViewer' ...
** using staged installation
** libs
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
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 -s -static-libgcc -o trackViewer.dll tmp.def RcppExports.o hic.o -lz -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-trackViewer/00new/trackViewer/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (trackViewer)
trackViewer.Rcheck/tests/runTests.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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, aperm, 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 -- Tue Apr 11 06:59:21 2023
***********************************************
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
15.42 1.03 16.40
trackViewer.Rcheck/trackViewer-Ex.timings
| name | user | system | elapsed | |
| GRoperator | 3.50 | 0.12 | 3.62 | |
| addArrowMark | 0.02 | 0.00 | 0.02 | |
| addGuideLine | 0 | 0 | 0 | |
| browseTracks | 15.52 | 0.11 | 15.84 | |
| coverageGR | 0.19 | 0.02 | 0.20 | |
| dandelion.plot | 2.45 | 0.01 | 2.47 | |
| geneModelFromTxdb | 5.37 | 0.35 | 5.77 | |
| geneTrack | 2.00 | 0.03 | 2.03 | |
| getCurTrackViewport | 0.02 | 0.00 | 0.01 | |
| getGeneIDsFromTxDb | 0.89 | 0.00 | 0.89 | |
| getLocation | 2.81 | 0.11 | 3.80 | |
| gi2track | 0.05 | 0.00 | 0.04 | |
| gieStain | 0.01 | 0.00 | 0.02 | |
| ideogramPlot | 0 | 0 | 0 | |
| importBam | 0.30 | 0.00 | 0.31 | |
| importData | 2.79 | 0.01 | 2.83 | |
| importGInteractions | 0.49 | 0.02 | 0.50 | |
| importScSeqScore | 0 | 0 | 0 | |
| importScore | 0.52 | 0.00 | 0.53 | |
| listChromosomes | 0.45 | 0.01 | 0.47 | |
| listResolutions | 0 | 0 | 0 | |
| loadIdeogram | 0 | 0 | 0 | |
| lolliplot | 0.74 | 0.02 | 0.75 | |
| optimizeStyle | 0.73 | 0.01 | 0.76 | |
| parse2GRanges | 0.02 | 0.00 | 0.02 | |
| parseWIG | 15.83 | 0.13 | 15.95 | |
| plotGInteractions | 1.29 | 0.01 | 1.33 | |
| plotGRanges | 1.58 | 0.04 | 1.61 | |
| plotIdeo | 0.00 | 0.01 | 0.01 | |
| plotOneIdeo | 0 | 0 | 0 | |
| trackStyle-class | 0.05 | 0.00 | 0.05 | |
| trackViewer-package | 21.81 | 0.16 | 21.97 | |
| trackViewerStyle-class | 0 | 0 | 0 | |
| viewGene | 4.63 | 0.12 | 4.75 | |
| viewTracks | 15.78 | 0.16 | 15.94 | |