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CHECK report for dexus on merida1

This page was generated on 2021-05-06 12:34:47 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the dexus package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 471/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dexus 1.30.0  (landing page)
Guenter Klambauer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/dexus
Branch: RELEASE_3_12
Last Commit: 6735357
Last Changed Date: 2020-10-27 10:49:40 -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: dexus
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dexus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dexus_1.30.0.tar.gz
StartedAt: 2021-05-06 01:06:33 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:07:30 -0400 (Thu, 06 May 2021)
EllapsedTime: 56.3 seconds
RetCode: 0
Status:   OK  
CheckDir: dexus.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dexus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dexus_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/dexus.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dexus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dexus’ version ‘1.30.0’
* 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 ‘dexus’ 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 ... 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/dexus.Rcheck/00check.log’
for details.



Installation output

dexus.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dexus
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘dexus’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dexus.cpp -o dexus.o
dexus.cpp:136:15: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if ((innerCyc==maxInnerCyc))
             ~~~~~~~~^~~~~~~~~~~~~
dexus.cpp:136:15: note: remove extraneous parentheses around the comparison to silence this warning
        if ((innerCyc==maxInnerCyc))
            ~        ^            ~
dexus.cpp:136:15: note: use '=' to turn this equality comparison into an assignment
        if ((innerCyc==maxInnerCyc))
                     ^~
                     =
dexus.cpp:193:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
dexus.cpp:575:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 dexus.so dexus.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-dexus/00new/dexus/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 (dexus)

Tests output


Example timings

dexus.Rcheck/dexus-Ex.timings

nameusersystemelapsed
DEXUSResult-class0.0010.0010.003
DEXUSResult-subset1.3110.0561.369
INI1.4360.0251.464
INIThreshold-set0.7230.0170.741
accessors0.7600.0320.792
dexss1.2980.0341.333
dexus0.8310.0210.853
dexus.parallel0.7470.0140.762
getSizeNB0.0000.0010.001
normalizeData0.8860.0470.933
plot1.2140.0261.240
sort1.1070.0161.124