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CHECK report for exomeCopy on tokay1

This page was generated on 2021-05-06 12:31:04 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the exomeCopy package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 576/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomeCopy 1.36.0  (landing page)
Michael Love
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/exomeCopy
Branch: RELEASE_3_12
Last Commit: cbe3134
Last Changed Date: 2020-10-27 10:43:40 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: exomeCopy
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomeCopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings exomeCopy_1.36.0.tar.gz
StartedAt: 2021-05-06 02:41:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:44:26 -0400 (Thu, 06 May 2021)
EllapsedTime: 203.4 seconds
RetCode: 0
Status:   OK   
CheckDir: exomeCopy.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomeCopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings exomeCopy_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/exomeCopy.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'exomeCopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'exomeCopy' version '1.36.0'
* 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 whether package 'exomeCopy' 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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.ExomeCopy
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
emFn : <anonymous>: no visible global function definition for 'dnbinom'
exomeCopy: no visible global function definition for 'lm'
exomeCopy: no visible global function definition for 'optim'
exomeCopy: no visible global function definition for 'new'
exomeCopy: no visible global function definition for 'Rle'
getGCcontent: no visible global function definition for
  'letterFrequency'
plot.ExomeCopy: no visible global function definition for 'segments'
plot.ExomeCopy: no visible global function definition for 'legend'
plotCompiledCNV: no visible global function definition for 'axis'
plotCompiledCNV: no visible global function definition for 'segments'
plot,ExomeCopy-missing: no visible global function definition for
  'segments'
plot,ExomeCopy-missing: no visible global function definition for
  'legend'
Undefined global functions or variables:
  Rle axis dnbinom legend letterFrequency lm new optim segments
Consider adding
  importFrom("graphics", "axis", "legend", "segments")
  importFrom("methods", "new")
  importFrom("stats", "dnbinom", "lm", "optim")
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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/exomeCopy/libs/i386/exomeCopy.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/exomeCopy/libs/x64/exomeCopy.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plotCompiledCNV          6.54   0.00    6.58
plot.exomeCopyObject     6.26   0.01    6.28
compileCopyCountSegments 5.22   0.08    5.29
exomeCopy                5.12   0.00    5.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
compileCopyCountSegments 6.50   0.03    6.53
copyCountSegments        5.58   0.01    5.59
plotCompiledCNV          4.72   0.00    5.89
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/exomeCopy.Rcheck/00check.log'
for details.



Installation output

exomeCopy.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/exomeCopy_1.36.0.tar.gz && rm -rf exomeCopy.buildbin-libdir && mkdir exomeCopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=exomeCopy.buildbin-libdir exomeCopy_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL exomeCopy_1.36.0.zip && rm exomeCopy_1.36.0.tar.gz exomeCopy_1.36.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 80051  100 80051    0     0  3364k      0 --:--:-- --:--:-- --:--:-- 3553k

install for i386

* installing *source* package 'exomeCopy' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exomeCopy.c -o exomeCopy.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o exomeCopy.dll tmp.def exomeCopy.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/exomeCopy.buildbin-libdir/00LOCK-exomeCopy/00new/exomeCopy/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'exomeCopy'
    finding HTML links ... done
    ExomeCopy-class                         html  
    compileCopyCountSegments                html  
    copyCountSegments                       html  
    countBamInGRanges                       html  
    finding level-2 HTML links ... done

    exomeCopy-package                       html  
    exomeCopy                               html  
    exomecounts                             html  
    generateBackground                      html  
    getGCcontent                            html  
    negLogLike                              html  
    plot.exomeCopyObject                    html  
    plotCompiledCNV                         html  
    subdivideGRanges                        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 'exomeCopy' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exomeCopy.c -o exomeCopy.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o exomeCopy.dll tmp.def exomeCopy.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/exomeCopy.buildbin-libdir/exomeCopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'exomeCopy' as exomeCopy_1.36.0.zip
* DONE (exomeCopy)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'exomeCopy' successfully unpacked and MD5 sums checked

Tests output


Example timings

exomeCopy.Rcheck/examples_i386/exomeCopy-Ex.timings

nameusersystemelapsed
ExomeCopy-class000
compileCopyCountSegments5.220.085.29
copyCountSegments4.840.024.86
countBamInGRanges0.390.000.39
exomeCopy5.120.005.13
generateBackground0.160.010.17
getGCcontent0.010.000.02
negLogLike0.020.020.03
plot.exomeCopyObject6.260.016.28
plotCompiledCNV6.540.006.58
subdivideGRanges0.170.000.17

exomeCopy.Rcheck/examples_x64/exomeCopy-Ex.timings

nameusersystemelapsed
ExomeCopy-class000
compileCopyCountSegments6.500.036.53
copyCountSegments5.580.015.59
countBamInGRanges0.420.020.44
exomeCopy4.830.004.83
generateBackground0.150.000.16
getGCcontent0.020.000.01
negLogLike0.010.000.02
plot.exomeCopyObject4.690.004.68
plotCompiledCNV4.720.005.89
subdivideGRanges0.110.000.11