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CHECK report for fastseg on malbec2

This page was generated on 2020-10-17 11:54:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE fastseg PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 585/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fastseg 1.34.0
Guenter Klambauer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/fastseg
Branch: RELEASE_3_11
Last Commit: 55c0344
Last Changed Date: 2020-04-27 14:27:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: fastseg
Version: 1.34.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:fastseg.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings fastseg_1.34.0.tar.gz
StartedAt: 2020-10-17 01:17:03 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:18:33 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 89.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: fastseg.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:fastseg.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings fastseg_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/fastseg.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fastseg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastseg’ version ‘1.34.0’
* 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 ‘fastseg’ 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
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
segPlot: no visible global function definition for ‘dev.cur’
segPlot: no visible global function definition for ‘dev.new’
segPlot: no visible global function definition for ‘dev.interactive’
Undefined global functions or variables:
  dev.cur dev.interactive dev.new
Consider adding
  importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new")
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 ... WARNING
Documented arguments not in \usage in documentation object 'fastseg':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/fastseg.Rcheck/00check.log’
for details.



Installation output

fastseg.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL fastseg
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘fastseg’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_fastseg.c -o R_init_fastseg.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c segment.cpp -o segment.o
segment.cpp: In function ‘SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
segment.cpp:60:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
  double globalMean,globalSd,diff,M2,globalVariance;
                    ^~~~~~~~
segment.cpp:61:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
  double oldStatistic, meanLeft,meanRight,varLeft,varRight;
         ^~~~~~~~~~~~
segment.cpp:62:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                               ^~~~~~~~~~~~
segment.cpp:63:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable]
  double newPValue, maxPValue,oldPValue,maxIdx;
                                        ^~~~~~
In file included from segment.cpp:10:0:
/home/biocbuild/bbs-3.11-bioc/R/include/Rmath.h:212:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
 #define beta  Rf_beta
               ^
segment.cpp:65:9: note: in expansion of macro ‘beta’
  double beta,nn;
         ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c segmentCyberT.cpp -o segmentCyberT.o
segmentCyberT.cpp: In function ‘SEXPREC* segmentCyberT(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
segmentCyberT.cpp:59:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
  double globalMean,globalSd,diff,M2,globalVariance;
                    ^~~~~~~~
segmentCyberT.cpp:60:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
  double oldStatistic,meanLeft,meanRight,varLeft,varRight;
         ^~~~~~~~~~~~
segmentCyberT.cpp:61:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
  double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
                               ^~~~~~~~~~~~
In file included from segmentCyberT.cpp:10:0:
/home/biocbuild/bbs-3.11-bioc/R/include/Rmath.h:212:15: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
 #define beta  Rf_beta
               ^
segmentCyberT.cpp:63:50: note: in expansion of macro ‘beta’
  double newStatisticBptLeft,newStatisticBptRight,beta,nn;
                                                  ^~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o fastseg.so R_init_fastseg.o segment.o segmentCyberT.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-fastseg/00new/fastseg/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 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 (fastseg)

Tests output


Example timings

fastseg.Rcheck/fastseg-Ex.timings

nameusersystemelapsed
fastseg3.1980.0563.256
segPlot1.4050.0041.409
toDNAcopyObj2.4620.0082.488