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CHECK report for TransView on malbec2

This page was generated on 2018-10-17 08:24:41 -0400 (Wed, 17 Oct 2018).

Package 1500/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.24.0
Julius Muller
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/TransView
Branch: RELEASE_3_7
Last Commit: 3f81a94
Last Changed Date: 2018-04-30 10:35:27 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TransView
Version: 1.24.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:TransView.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings TransView_1.24.0.tar.gz
StartedAt: 2018-10-16 04:15:48 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 04:17:17 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 89.2 seconds
RetCode: 0
Status:  OK 
CheckDir: TransView.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:TransView.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings TransView_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/TransView.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TransView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TransView’ version ‘1.24.0’
* 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 ‘TransView’ 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
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.gene2window : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
.gene2window: no visible binding for global variable ‘approx’
.onAttach: no visible global function definition for
  ‘packageDescription’
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
annotatePeaks : <anonymous>: no visible global function definition for
  ‘median’
gtf2gr: no visible global function definition for ‘read.table’
gtf2gr: no visible global function definition for ‘ave’
macs2gr: no visible global function definition for ‘read.delim’
meltPeak: no visible global function definition for ‘approx’
meltPeak: no visible global function definition for ‘lowess’
plotTV: no visible global function definition for ‘quantile’
plotTV: no visible global function definition for ‘kmeans’
plotTV: no visible global function definition for ‘as.dendrogram’
plotTV: no visible global function definition for ‘hclust’
plotTV: no visible global function definition for ‘as.dist’
plotTV: no visible global function definition for ‘dist’
plotTV: no visible global function definition for ‘order.dendrogram’
plotTV: no visible global function definition for ‘par’
plotTV: no visible global function definition for ‘layout’
plotTV: no visible global function definition for ‘image’
plotTV: no visible global function definition for ‘hist’
plotTV: no visible global function definition for ‘title’
plotTV: no visible global function definition for ‘mtext’
plotTV: no visible global function definition for ‘lines’
plotTV: no visible global function definition for ‘axis’
plotTV: no visible global function definition for ‘rainbow’
plotTV: no visible global function definition for ‘plot’
plotTV: no visible global function definition for ‘text’
plotTV: no visible global function definition for ‘rgb’
plotTV: no visible global function definition for ‘plot.new’
setTV: no visible global function definition for ‘object.size’
.setTV,DensityContainer-character-character-numeric-numeric-numeric-logical-character-character-logical:
  no visible global function definition for ‘object.size’
Undefined global functions or variables:
  approx as.dendrogram as.dist ave axis defineTestSuite dist hclust
  hist image kmeans layout lines lowess median mtext object.size
  order.dendrogram packageDescription par plot plot.new
  printTextProtocol quantile rainbow read.delim read.table rgb
  runTestSuite text title
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "axis", "hist", "image", "layout", "lines",
             "mtext", "par", "plot", "plot.new", "text", "title")
  importFrom("stats", "approx", "as.dendrogram", "as.dist", "ave",
             "dist", "hclust", "kmeans", "lowess", "median",
             "order.dendrogram", "quantile")
  importFrom("utils", "object.size", "packageDescription", "read.delim",
             "read.table")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/TransView/libs/TransView.so’:
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘TransView_unit_tests.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/TransView.Rcheck/00check.log’
for details.



Installation output

TransView.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL TransView
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘TransView’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_TransView.c -o R_init_TransView.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c bin_density.c -o bin_density.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c construct_dc.c -o construct_dc.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c parse_sam.c -o parse_sam.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c slice_dc.c -o slice_dc.o
slice_dc.c: In function ‘slice_dc’:
slice_dc.c:179:5: warning: ‘slicep’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
     ^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c visuals.c -o visuals.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o TransView.so R_init_TransView.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/TransView/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
* DONE (TransView)

Tests output

TransView.Rcheck/tests/TransView_unit_tests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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("TransView") || stop("unable to load TransView package")
Loading required package: TransView
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Welcome to TransView version 1.24.0

Attaching package: 'TransView'

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

    pos

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

    pos

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

    pos

[1] TRUE
> TransView:::.test()
Version 2.09+ detected
21 peaks matching
172 rows matching
2862 rows matching
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit
Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit


RUNIT TEST PROTOCOL -- Tue Oct 16 04:17:13 2018 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TransView RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.616   0.224   8.225 

Example timings

TransView.Rcheck/TransView-Ex.timings

nameusersystemelapsed
DensityContainer-class0.0000.0040.002
TVResults-class0.0000.0000.001
TransView-package000
annotatePeaks1.4760.0001.488
gtf2gr0.040.000.04
macs2gr0.0160.0000.017
meltPeak0.7640.0280.807
parseReads0.0560.0200.078
peak2tss0.7320.0001.150
plotTV0.2000.0440.353
plotTVData0.1920.0320.299
rmTV0.3920.0280.592
slice10.1920.0200.282
slice1T0.8680.0081.160