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CHECK report for seqCNA on merida1

This page was generated on 2019-04-16 11:57:00 -0400 (Tue, 16 Apr 2019).

Package 1419/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqCNA 1.28.0
David Mosen-Ansorena
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/seqCNA
Branch: RELEASE_3_8
Last Commit: c0ef4aa
Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: seqCNA
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqCNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqCNA_1.28.0.tar.gz
StartedAt: 2019-04-16 02:43:08 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:44:11 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 62.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: seqCNA.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqCNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqCNA_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/seqCNA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqCNA’ version ‘1.28.0’
* 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 ‘seqCNA’ can be installed ... WARNING
Found the following significant warnings:
  seqCNA.cpp:107:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/seqCNA.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  ‘GLAD’ ‘adehabitatLT’ ‘doSNOW’ ‘methods’ ‘seqCNA.annot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.autoTrim: no visible global function definition for ‘makeCluster’
.autoTrim: no visible global function definition for ‘registerDoSNOW’
.autoTrim: no visible global function definition for ‘%dopar%’
.autoTrim: no visible global function definition for ‘foreach’
.autoTrim: no visible global function definition for ‘wawotest’
.autoTrim: no visible global function definition for ‘quantile’
.autoTrim: no visible global function definition for ‘stopCluster’
.autoTrim: no visible global function definition for ‘loess’
.autoTrim: no visible global function definition for ‘tail’
.buildGenomeInfo: no visible global function definition for
  ‘makeCluster’
.buildGenomeInfo: no visible global function definition for
  ‘registerDoSNOW’
.buildGenomeInfo: no visible global function definition for ‘%dopar%’
.buildGenomeInfo: no visible global function definition for ‘foreach’
.buildGenomeInfo: no visible global function definition for
  ‘stopCluster’
.makeFormula: no visible global function definition for ‘as.formula’
.olBarplot: no visible global function definition for ‘par’
.olBarplot: no visible global function definition for ‘barplot’
.overLapper : <anonymous>: no visible global function definition for
  ‘combn’
.resample: no visible global function definition for ‘makeCluster’
.resample: no visible global function definition for ‘registerDoSNOW’
.resample: no visible global function definition for ‘%dopar%’
.resample: no visible global function definition for ‘foreach’
.resample: no visible global function definition for ‘stopCluster’
.seqnorm: no visible binding for global variable ‘head’
.seqnorm: no visible global function definition for ‘tail’
.seqnorm: no visible global function definition for ‘flush.console’
.seqnorm: no visible binding for global variable ‘tail’
.seqnorm: no visible global function definition for ‘makeCluster’
.seqnorm: no visible global function definition for ‘registerDoSNOW’
.seqnorm: no visible global function definition for ‘%dopar%’
.seqnorm: no visible global function definition for ‘foreach’
.seqnorm: no visible global function definition for ‘as.profileCGH’
.seqnorm: no visible global function definition for ‘glad’
.seqnorm : <anonymous>: no visible global function definition for
  ‘quantile’
.seqnorm : .getSegmLm: no visible global function definition for
  ‘quantile’
.seqnorm: no visible global function definition for ‘predict’
.seqnorm: no visible global function definition for ‘median’
.seqnorm : <anonymous>: no visible global function definition for
  ‘median’
.seqnorm: no visible global function definition for ‘stopCluster’
.seqnorm: no visible global function definition for ‘jpeg’
.seqnorm: no visible global function definition for ‘quantile’
.seqnorm: no visible global function definition for ‘layout’
.seqnorm: no visible global function definition for ‘par’
.seqnorm: no visible global function definition for ‘density’
.seqnorm: no visible global function definition for ‘plot’
.seqnorm: no visible global function definition for ‘points’
.seqnorm: no visible global function definition for ‘plot.new’
.seqnorm: no visible global function definition for ‘legend’
.seqnorm: no visible global function definition for ‘abline’
.seqnorm: no visible global function definition for ‘dev.off’
.seqnorm: no visible global function definition for ‘lines’
.seqnorm: no visible global function definition for ‘smoothScatter’
.seqnorm: no visible global function definition for ‘colorRampPalette’
.summary.SeqCNAInfo: no visible global function definition for ‘head’
.summary.SeqCNAInfo: no visible global function definition for ‘tail’
.vennPlot: no visible global function definition for ‘symbols’
.vennPlot: no visible global function definition for ‘text’
.vennPlot : plotellipse: no visible global function definition for
  ‘par’
.vennPlot : plotellipse: no visible global function definition for
  ‘plot’
.vennPlot : ellipseVenn: no visible global function definition for
  ‘plot.new’
.vennPlot : ellipseVenn: no visible global function definition for
  ‘text’
applyFilters: no visible global function definition for
  ‘supported.builds’
applyFilters: no visible global function definition for ‘data’
applyFilters: no visible global function definition for ‘quantile’
applyFilters: no visible global function definition for ‘flush.console’
applyFilters: no visible global function definition for ‘jpeg’
applyFilters: no visible global function definition for ‘layout’
applyFilters: no visible global function definition for ‘par’
applyFilters: no visible global function definition for ‘smoothScatter’
applyFilters: no visible global function definition for
  ‘colorRampPalette’
applyFilters: no visible global function definition for ‘points’
applyFilters: no visible global function definition for ‘dev.off’
applyFilters: no visible global function definition for ‘density’
applyFilters: no visible global function definition for ‘plot’
applyFilters: no visible global function definition for ‘rect’
applyFilters: no visible global function definition for ‘abline’
applyFilters: no visible global function definition for ‘lines’
applyFilters: no visible global function definition for ‘text’
plotCNProfile: no visible global function definition for ‘jpeg’
plotCNProfile: no visible global function definition for ‘par’
plotCNProfile: no visible global function definition for ‘quantile’
plotCNProfile: no visible global function definition for
  ‘smoothScatter’
plotCNProfile: no visible global function definition for
  ‘colorRampPalette’
plotCNProfile: no visible global function definition for ‘abline’
plotCNProfile: no visible global function definition for ‘tail’
plotCNProfile : <anonymous>: no visible global function definition for
  ‘lines’
plotCNProfile: no visible global function definition for ‘median’
plotCNProfile: no visible global function definition for ‘text’
plotCNProfile: no visible global function definition for ‘dev.off’
readSeqsumm: no visible global function definition for
  ‘supported.builds’
readSeqsumm: no visible global function definition for ‘flush.console’
readSeqsumm: no visible global function definition for ‘read.table’
readSeqsumm: no visible global function definition for ‘data’
readSeqsumm: no visible global function definition for ‘new’
runGLAD: no visible global function definition for ‘flush.console’
runGLAD: no visible global function definition for ‘makeCluster’
runGLAD: no visible global function definition for ‘registerDoSNOW’
runGLAD: no visible global function definition for ‘%dopar%’
runGLAD: no visible global function definition for ‘foreach’
runGLAD: no visible global function definition for ‘as.profileCGH’
runGLAD: no visible global function definition for ‘glad’
runGLAD: no visible global function definition for ‘stopCluster’
writeCNProfile: no visible global function definition for ‘write.table’
summary,SeqCNAInfo: no visible global function definition for ‘head’
summary,SeqCNAInfo: no visible global function definition for ‘tail’
Undefined global functions or variables:
  %dopar% abline as.formula as.profileCGH barplot colorRampPalette
  combn data density dev.off flush.console foreach glad head jpeg
  layout legend lines loess makeCluster median new par plot plot.new
  points predict quantile read.table rect registerDoSNOW smoothScatter
  stopCluster supported.builds symbols tail text wawotest write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "jpeg")
  importFrom("graphics", "abline", "barplot", "layout", "legend",
             "lines", "par", "plot", "plot.new", "points", "rect",
             "smoothScatter", "symbols", "text")
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "density", "loess", "median",
             "predict", "quantile")
  importFrom("utils", "combn", "data", "flush.console", "head",
             "read.table", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqCNA/libs/seqCNA.so’:
  Found ‘___stdoutp’, 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotCNProfile   0.610  0.068   5.444
writeCNProfile  0.409  0.037   5.698
applyThresholds 0.363  0.060   5.294
runGLAD         0.341  0.038   5.442
* 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 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/seqCNA.Rcheck/00check.log’
for details.



Installation output

seqCNA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqCNA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘seqCNA’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c seqCNA.cpp -o seqCNA.o
seqCNA.cpp:107:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
                                        if (index<0) goto next;
                                            ˜˜˜˜˜^˜
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o seqCNA.so seqCNA.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqCNA/libs
** R
** data
** 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 (seqCNA)

Tests output


Example timings

seqCNA.Rcheck/seqCNA-Ex.timings

nameusersystemelapsed
SeqCNAInfo-class0.0020.0000.001
applyFilters0.1280.0241.560
applyThresholds0.3630.0605.294
plotCNProfile0.6100.0685.444
readSeqsumm0.0260.0040.031
runGLAD0.3410.0385.442
runSeqnorm0.3250.0273.810
runSeqsumm0.0040.0030.012
seqsumm_HCC11430.0210.0020.022
writeCNProfile0.4090.0375.698